Contacts of the helix formed by residues 62 - 91 (chain A) in PDB entry 1GIA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 62 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLY 3.7 2.2 + - - -
61A TYR* 1.3 76.7 - - - +
63A GLU* 1.3 65.4 + - - +
64A GLU* 3.5 15.9 + - - +
65A GLU* 2.9 33.9 + - - +
66A CYS* 2.9 22.7 + - - -
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A SER* 1.3 73.7 - - - +
64A GLU* 1.3 75.3 + - - +
66A CYS* 3.4 7.2 + - - +
67A LYS* 3.0 53.1 + - - +
168A ILE* 3.9 27.3 - - + +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A SER* 3.3 16.5 + - - +
63A GLU* 1.3 94.8 + - - +
65A GLU* 1.3 61.0 + - + +
67A LYS* 3.5 10.9 + - + +
68A GLN* 3.3 26.8 + - - +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS* 2.7 38.3 + - - -
60A GLY 4.1 0.5 - - - +
61A TYR* 3.9 14.1 - - + -
62A SER* 2.9 33.5 + - - +
64A GLU* 1.3 76.1 - - + +
66A CYS* 1.3 63.1 + - - +
68A GLN* 3.1 24.1 + - + +
69A TYR* 3.3 15.4 - - + -
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Residues in contact with CYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 3.8 25.1 - - - -
62A SER 2.9 21.0 + - - +
63A GLU* 3.7 5.6 - - - +
65A GLU* 1.3 76.2 - - - +
67A LYS* 1.3 58.0 + - - +
69A TYR* 2.9 18.0 + - - +
168A ILE* 3.8 10.1 - - + -
169A PRO* 3.3 47.6 - - + +
170A THR 4.8 0.4 - - - -
171A GLN* 3.8 12.3 - - - -
174A VAL* 4.2 17.0 - - - -
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 3.0 43.0 + - + +
64A GLU* 3.8 10.1 - - + +
65A GLU 3.3 0.2 - - - -
66A CYS* 1.3 75.9 - - - +
68A GLN* 1.3 65.3 + - - +
70A LYS* 3.2 28.2 - - + +
71A ALA 4.5 0.5 + - - -
167A TYR 5.4 1.8 - - - +
168A ILE* 3.5 39.5 - - + +
169A PRO* 4.4 1.8 - - + -
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 3.3 16.3 + - - +
65A GLU* 3.1 17.5 + - - +
67A LYS* 1.3 80.2 + - - +
69A TYR* 1.3 64.4 + - + +
70A LYS 3.2 1.0 + - - -
71A ALA* 3.9 10.7 + - - +
72A VAL* 4.3 7.4 - - - +
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Residues in contact with TYR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS* 3.8 18.7 + - - +
61A TYR* 4.0 21.3 + + - -
65A GLU* 3.3 24.9 + - + -
66A CYS 2.9 8.7 + - - +
68A GLN* 1.3 78.6 - - + +
70A LYS* 1.3 63.0 + - - +
71A ALA 3.2 2.9 - - - -
72A VAL* 3.0 19.6 + - + +
73A VAL* 3.0 24.1 + - + +
169A PRO* 4.1 5.2 - - + -
174A VAL* 3.9 37.0 - - + -
177A THR* 3.9 33.2 - - + -
179A VAL* 5.7 3.8 - - + -
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Residues in contact with LYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A CYS 3.3 3.4 + - - -
67A LYS* 3.2 23.4 + - + +
69A TYR* 1.3 77.0 - - - +
71A ALA* 1.3 62.2 + - - +
73A VAL* 3.4 4.4 + - - +
74A TYR* 3.2 53.7 + - + -
117A GLY* 3.3 22.8 + - - +
118A PHE* 5.1 1.2 - - - +
119A MET 5.3 0.8 - - - +
164A GLN 5.5 1.0 + - - -
166A ASN* 5.2 2.2 - - - +
167A TYR* 3.0 45.3 - - + +
169A PRO* 3.6 17.3 - - + -
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS 4.5 0.8 + - - -
68A GLN 3.9 8.9 + - - +
69A TYR 3.2 0.6 - - - -
70A LYS* 1.3 78.1 - - - +
72A VAL* 1.3 59.3 + - + +
74A TYR* 3.9 1.9 - - - +
75A SER* 2.9 30.7 + - - -
114A ALA 4.4 1.9 - - - +
115A GLU 4.3 8.5 - - - +
116A GLU 4.8 1.3 - - - -
117A GLY* 4.0 29.1 - - - +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN 4.3 5.4 - - - +
69A TYR* 3.0 28.0 + - + +
71A ALA* 1.3 72.8 - - + +
73A VAL* 1.3 58.2 + - - +
75A SER* 3.7 4.7 - - - -
76A ASN* 2.7 51.5 + - - +
177A THR* 3.7 23.3 - - + -
178A ARG 4.2 0.2 - - - +
179A VAL* 3.5 33.0 - - + -
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 3.0 17.7 + - + +
70A LYS* 3.6 8.3 - - - +
72A VAL* 1.3 77.6 - - - +
74A TYR* 1.3 63.2 + - + +
76A ASN* 3.6 5.9 - - - +
77A THR* 2.8 33.3 + - - -
155A TYR* 3.8 32.7 - - + +
162A ILE* 4.1 16.6 - - + -
167A TYR* 3.8 26.2 - - + +
169A PRO* 4.3 9.9 - - + -
173A ASP* 4.4 6.3 - - + +
177A THR* 4.0 16.4 - - + -
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Residues in contact with TYR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 3.2 47.8 + - + +
71A ALA 3.9 1.3 - - - +
73A VAL* 1.3 81.2 - - + +
75A SER* 1.3 62.6 + - - +
77A THR* 3.3 4.8 + - - -
78A ILE* 3.0 28.9 + - - +
114A ALA* 3.4 22.2 - - + +
117A GLY* 3.5 25.4 - - - -
118A PHE 3.9 6.5 - - - -
119A MET* 3.6 38.8 - - + +
162A ILE* 2.8 37.8 + - + -
163A ALA* 4.6 0.3 - - - -
164A GLN 4.5 3.6 + - - -
167A TYR* 3.5 21.4 - + - +
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA 2.9 19.8 + - - -
72A VAL* 3.7 6.5 - - - -
73A VAL 3.3 0.2 - - - -
74A TYR* 1.3 79.4 - - - +
76A ASN* 1.3 60.4 + - - +
78A ILE* 3.4 5.2 + - - +
79A GLN* 3.0 40.7 + - - +
114A ALA 4.5 2.4 + - - -
115A GLU* 5.0 16.6 - - - +
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Residues in contact with ASN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 2.7 30.9 + - - +
73A VAL 3.6 4.3 - - - +
75A SER* 1.3 76.2 + - - +
77A THR* 1.3 58.5 + - - +
79A GLN* 3.6 4.2 + - - +
80A SER* 2.8 30.8 + - - -
149A ASN* 4.2 15.8 + - - +
151A SER* 6.2 0.2 - - - -
155A TYR* 3.9 19.3 - - + -
176A ARG 4.4 0.2 - - - +
177A THR* 3.3 13.0 - - - +
178A ARG* 2.8 49.1 + - - +
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Residues in contact with THR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL 2.8 19.7 + - - -
74A TYR* 3.7 7.2 - - - -
75A SER 3.2 0.2 - - - -
76A ASN* 1.3 74.1 - - - +
78A ILE* 1.3 72.8 + - + +
80A SER* 3.2 7.5 + - - -
81A ILE* 3.2 22.2 + - - +
119A MET* 5.2 2.9 - - + -
127A ILE* 4.9 4.3 - - + -
155A TYR* 3.4 26.2 - - + +
156A LEU* 3.8 25.4 - - + +
159A LEU* 4.1 19.3 - - + -
162A ILE* 3.8 11.3 - - + +
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR 3.0 15.2 + - - +
75A SER* 4.0 4.0 - - - +
77A THR* 1.3 78.0 - - + +
79A GLN* 1.3 73.8 + - - +
81A ILE* 3.2 5.6 - - - +
82A ILE* 3.0 44.9 + - + +
107A LEU* 4.8 5.6 - - + -
111A ALA* 4.3 23.3 - - + +
114A ALA* 3.6 31.2 - - + -
115A GLU* 5.3 8.1 - - + +
119A MET* 4.1 10.5 - - + -
123A LEU* 4.4 2.9 - - + -
127A ILE* 3.6 29.8 - - + -
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Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A SER* 3.0 29.7 + - - +
76A ASN* 4.0 5.4 - - - +
78A ILE* 1.3 90.9 - - - +
80A SER* 1.3 56.2 + - - +
82A ILE* 3.8 15.4 - - - +
83A ALA* 2.9 30.1 + - - +
86A ARG* 4.7 12.3 + - - -
115A GLU* 6.1 3.4 - - - +
149A ASN* 5.1 7.2 - - - +
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASN* 2.8 22.9 + - - +
77A THR* 3.2 7.2 + - - -
79A GLN* 1.3 73.9 - - - +
81A ILE* 1.3 64.9 + - - +
83A ALA* 3.3 1.7 + - - -
84A ILE* 3.2 28.4 + - - +
148A LEU* 3.6 10.5 - - - +
149A ASN* 3.9 15.5 + - - +
151A SER 5.1 0.3 - - - -
152A ALA* 3.6 37.3 - - - +
155A TYR* 5.8 0.5 - - - -
156A LEU* 4.3 6.5 - - - -
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR 3.2 10.5 + - - +
78A ILE* 3.2 17.7 - - - +
80A SER* 1.3 77.4 - - - +
82A ILE* 1.3 60.0 + - - +
84A ILE* 3.3 10.9 + - + +
85A ILE* 3.0 42.6 + - + +
107A LEU* 4.1 21.8 - - + -
127A ILE* 4.4 24.2 - - + -
130A LEU* 4.2 24.9 - - + -
131A TRP* 4.4 13.2 - - + +
136A VAL* 4.4 15.7 - - + -
156A LEU* 4.5 15.1 - - + +
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Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 3.0 41.0 + - + +
79A GLN* 3.8 17.0 - - - +
81A ILE* 1.3 75.2 - - + +
83A ALA* 1.3 64.6 + - - +
85A ILE* 3.3 6.9 + - - +
86A ARG* 2.9 42.2 + - + +
107A LEU* 4.2 18.8 - - + -
108A PHE* 4.1 34.9 - - + -
111A ALA* 4.7 10.1 - - + -
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN 2.9 18.6 + - - +
80A SER 3.3 5.6 + - - +
82A ILE* 1.3 75.5 - - - +
84A ILE* 1.3 63.2 + - - +
86A ARG* 3.5 27.7 + - - +
87A ALA* 3.1 22.7 + - - +
146A TYR* 4.1 5.0 - - + -
147A GLN 4.0 19.1 - - - +
148A LEU* 4.0 10.5 - - + -
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER 3.2 18.1 + - - +
81A ILE* 3.6 12.8 - - + +
82A ILE 3.2 0.4 - - - -
83A ALA* 1.3 75.5 - - - +
85A ILE* 1.3 65.0 + - - +
87A ALA* 3.1 4.3 + - - +
88A MET* 3.1 22.7 + - - +
131A TRP* 4.0 29.6 - - + -
136A VAL* 3.8 35.0 - - + +
139A CYS* 3.7 14.2 - - + -
140A PHE* 4.0 15.0 - - + +
146A TYR* 3.8 19.5 - - - +
148A LEU* 4.0 13.9 - - + -
152A ALA* 5.4 0.7 - - + -
156A LEU* 4.6 4.7 - - + -
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 3.0 27.7 + - + +
82A ILE* 3.9 4.9 - - - +
84A ILE* 1.3 75.5 - - + +
86A ARG* 1.3 62.1 + - - +
88A MET* 3.5 22.4 + - - +
89A GLY* 3.7 3.8 + - - -
95A PHE* 4.8 20.4 - - + -
104A ALA* 4.8 14.4 - - + -
107A LEU* 3.4 33.0 - - + -
108A PHE* 4.6 19.7 - - + -
130A LEU* 3.7 20.9 - - + -
136A VAL* 5.3 3.4 - - + -
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN* 4.7 11.3 + - - -
82A ILE* 2.9 35.3 + - + +
83A ALA* 3.5 33.5 + - - +
85A ILE* 1.3 79.3 - - - +
87A ALA* 1.3 61.0 + - - +
89A GLY* 3.2 12.3 + - - -
90A ARG* 3.1 54.7 + - - +
146A TYR* 6.0 1.0 - - - -
147A GLN 5.1 3.2 + - - -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA 3.1 16.7 + - - +
84A ILE 3.1 5.7 + - - +
86A ARG* 1.3 71.4 - - - +
88A MET* 1.3 66.1 + - - +
89A GLY 3.1 2.0 - - - -
90A ARG* 3.1 9.9 + - - +
91A LEU* 2.9 31.3 + - + +
139A CYS* 3.7 4.7 - - - -
146A TYR* 3.6 43.1 - - + -
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Residues in contact with MET 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 3.1 19.0 + - - +
85A ILE* 3.7 16.6 - - - +
86A ARG 3.3 0.4 - - - -
87A ALA* 1.3 76.8 - - - +
89A GLY* 1.3 57.8 + - - +
92A LYS* 2.9 8.1 + - - -
93A ILE* 2.7 49.9 + - + +
94A ASP 3.6 26.0 - - - +
95A PHE* 3.6 36.3 - - + +
135A GLY 3.8 13.7 - - - +
136A VAL* 3.9 22.2 - - - -
139A CYS* 3.7 22.4 - - + -
----------------------------------------------------------
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Residues in contact with GLY 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE 3.7 4.9 + - - -
86A ARG 3.2 8.7 + - - -
87A ALA 3.1 1.0 - - - -
88A MET* 1.3 80.2 - - - +
90A ARG* 1.3 58.6 + - - +
92A LYS* 3.0 32.6 + - - +
----------------------------------------------------------
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 3.1 50.0 + - - +
87A ALA* 3.1 9.6 + - - +
89A GLY* 1.3 78.4 - - - +
91A LEU* 1.3 63.9 + - + +
92A LYS* 3.3 18.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA* 2.9 20.0 + - + +
90A ARG* 1.3 80.8 - - + +
92A LYS* 1.3 71.5 - - - +
93A ILE* 3.8 23.4 - - + +
139A CYS* 4.5 9.9 - - - -
142A ARG* 3.8 31.9 + - + +
145A GLU* 3.8 39.9 - - + +
146A TYR* 4.6 8.7 - - + -
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il