Contacts of the helix formed by residues 76 - 103 (chain A) in PDB entry 5NDD
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 VAL 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 2.7 49.0 + - + +
74A THR 3.4 0.2 - - - -
75A THR* 1.3 82.0 - - - +
77A PHE* 1.3 66.7 + - - +
78A LEU 3.4 0.7 - - - -
79A PRO* 3.4 5.2 - - - +
80A ILE* 3.1 45.5 + - + +
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS 3.0 6.7 + - - +
73A LEU* 3.2 33.0 - - + +
76A VAL* 1.3 79.2 - - - +
78A LEU* 1.3 78.9 + - + +
80A ILE* 3.3 8.2 + - + +
81A VAL* 3.1 47.9 + - + +
328A VAL* 4.9 16.4 - - + -
331A CYS* 4.2 12.8 - - - -
332A LEU* 5.1 10.5 - - + -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.3 17.0 + - + +
74A THR* 3.4 12.6 - - + +
77A PHE* 1.3 88.4 - - + +
79A PRO* 1.4 69.5 - - + +
80A ILE 3.1 0.5 + - - -
81A VAL* 3.2 2.1 + - - +
82A TYR* 2.8 37.8 + - + +
135A HIS* 3.5 31.6 - - + +
327A ILE* 3.7 30.3 - - + -
328A VAL* 5.2 0.2 - - - -
331A CYS* 3.5 36.6 - - + -
2201A 8TZ 3.8 10.1 - - + +
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Residues in contact with PRO 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR 3.3 19.3 - - - +
75A THR 3.4 17.0 - - - +
76A VAL* 3.4 17.7 - - - +
78A LEU* 1.4 89.1 - - + +
80A ILE* 1.3 52.6 + - + +
82A TYR* 4.3 7.2 - - + -
83A THR* 2.6 38.4 + - - -
132A ILE* 3.7 18.4 - - + +
135A HIS* 4.0 6.5 - - + -
136A ILE* 3.6 29.2 - - + -
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 3.1 35.6 + - + +
77A PHE* 3.3 6.9 + - + +
78A LEU 3.1 0.6 - - - -
79A PRO* 1.3 76.0 - - + +
81A VAL* 1.3 70.3 + - + +
83A THR* 3.2 7.3 + - - -
84A ILE* 3.0 37.9 + - + +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.1 46.0 + - + +
78A LEU 3.8 0.4 - - - +
80A ILE* 1.3 79.4 - - + +
82A TYR* 1.3 58.5 + - + +
84A ILE* 3.2 14.2 + - + +
85A VAL* 3.0 30.3 + - + +
331A CYS* 3.6 28.0 - - - +
332A LEU* 5.4 5.6 - - + -
335A LEU* 4.4 22.4 - - + -
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 2.8 31.1 + - + +
79A PRO* 4.0 2.2 - - + +
81A VAL* 1.3 77.5 - - - +
83A THR* 1.3 56.3 + - - +
85A VAL* 3.3 1.8 + - - -
86A PHE* 2.9 24.6 + - - +
128A PHE* 3.4 27.0 - + + -
131A LYS* 3.5 25.2 + - + -
132A ILE* 3.9 18.4 - - + -
135A HIS* 3.7 32.3 - + - -
330A LEU 4.2 1.2 + - - -
331A CYS* 3.5 24.8 + - + +
334A THR* 3.7 34.5 - - + -
2201A 8TZ 2.5 31.9 + - - -
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Residues in contact with THR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO 2.6 25.7 + - - -
80A ILE* 3.4 6.9 - - - -
82A TYR* 1.3 72.6 - - - +
84A ILE* 1.3 68.0 + - + +
86A PHE* 3.1 6.4 + - + +
87A VAL* 3.0 32.5 + - + +
132A ILE* 3.3 28.3 - - + +
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.0 32.4 + - + +
81A VAL* 3.4 15.5 - - + +
83A THR* 1.3 77.7 - - + +
85A VAL* 1.3 60.5 + - + +
87A VAL* 3.1 6.8 + - - +
88A VAL* 2.8 43.5 + - + +
335A LEU* 6.0 2.9 - - + -
338A CYS* 5.4 2.9 - - - -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 3.0 20.9 + - + +
82A TYR* 3.6 7.4 - - - +
84A ILE* 1.3 75.6 - - + +
86A PHE* 1.3 56.1 + - - +
89A ALA* 2.7 40.9 + - + +
125A VAL* 4.4 4.0 - - + -
128A PHE* 3.7 21.3 - - + -
334A THR* 3.7 20.6 - - - +
335A LEU* 3.7 28.7 - - + -
337A SER* 3.7 23.1 - - - +
338A CYS* 3.7 14.4 - - - -
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Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR 2.9 14.4 + - - +
83A THR* 3.1 12.8 + - + +
85A VAL* 1.3 78.7 - - - +
87A VAL* 1.3 73.5 + - + +
90A LEU* 3.2 55.4 + - + +
91A PRO* 3.9 0.2 - - - +
125A VAL* 3.3 37.7 - - + -
126A ILE* 4.7 3.6 - - - -
128A PHE* 4.1 7.4 - - + -
129A PRO* 3.7 30.3 - - + -
132A ILE* 4.6 5.2 - - + -
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 3.0 25.1 + - + +
84A ILE* 3.7 7.4 - - - +
86A PHE* 1.3 86.2 - - + +
88A VAL* 1.3 63.2 + - + +
91A PRO* 3.0 25.9 - - - +
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 2.8 32.2 + - + +
87A VAL* 1.3 82.2 - - + +
89A ALA* 1.3 56.3 + - - +
91A PRO* 3.6 6.9 - - - +
92A SER* 2.7 31.6 + - - +
338A CYS* 3.8 29.2 - - + +
341A PRO* 5.8 1.3 - - + -
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 2.7 27.4 + - + +
88A VAL* 1.3 75.7 - - - +
90A LEU* 1.3 63.7 + - - +
92A SER* 3.0 11.2 + - - -
93A ASN* 2.9 24.7 + - - +
122A LEU* 4.7 0.3 - - - +
125A VAL* 4.1 7.9 - - + -
337A SER* 3.4 44.6 - - - +
338A CYS* 4.1 1.8 - - - -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL 4.0 0.2 + - - -
86A PHE* 3.2 47.8 + - + +
89A ALA* 1.3 78.5 - - - +
91A PRO* 1.3 63.7 - - + +
94A GLY* 2.9 26.2 + - - -
122A LEU* 3.5 22.0 - - + +
125A VAL* 3.9 19.8 - - + +
126A ILE* 3.7 31.2 - - + +
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Residues in contact with PRO 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE 3.9 0.4 - - - +
87A VAL* 3.0 29.4 - - - +
88A VAL 3.6 3.6 - - - +
90A LEU* 1.3 95.0 - - + +
92A SER* 1.3 58.9 + - - +
94A GLY* 3.6 2.4 - - - +
95A MET* 2.8 31.4 + - - +
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 2.7 26.1 + - - +
89A ALA* 3.0 10.7 + - - -
91A PRO* 1.3 82.6 - - - +
93A ASN* 1.3 62.8 + - - +
95A MET* 3.4 6.8 + - - +
96A ALA* 3.0 26.4 + - - +
341A PRO* 3.5 30.6 - - - +
351A PHE* 4.3 8.4 - - - -
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Residues in contact with ASN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ALA* 2.9 24.5 + - - +
92A SER* 1.3 81.7 + - - +
94A GLY* 1.3 61.0 + - - +
95A MET 3.3 0.2 - - - -
96A ALA* 3.7 6.0 - - - +
97A LEU* 2.9 32.2 + - - +
118A ALA* 3.6 11.9 - - + +
121A ASP* 2.7 34.2 + - + +
122A LEU* 4.0 15.0 - - + +
337A SER 3.0 25.7 + - - -
340A ASP* 4.1 1.0 - - - +
341A PRO* 4.5 2.1 - - - +
344A TYR* 3.0 25.0 + - - -
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Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU 2.9 20.2 + - - -
91A PRO* 3.6 2.9 - - - -
92A SER 3.2 0.2 - - - -
93A ASN* 1.3 79.3 - - - +
95A MET* 1.3 60.3 + - - +
97A LEU* 3.7 3.3 + - - +
98A TRP* 3.3 20.1 + - - +
122A LEU* 3.8 14.1 - - - +
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Residues in contact with MET 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PRO 2.8 16.4 + - - +
92A SER* 3.9 5.4 - - - +
94A GLY* 1.3 74.8 - - - +
96A ALA* 1.3 60.8 + - - +
98A TRP* 3.1 22.3 + - + +
99A VAL* 2.9 35.8 + - + +
351A PHE* 3.7 29.6 - - + -
354A HIS* 3.8 37.9 - - + +
355A ALA* 4.2 5.4 - - + +
358A ALA* 4.8 10.1 - - + -
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A SER 3.0 18.4 + - - +
93A ASN* 3.7 4.5 - - - +
94A GLY 3.4 0.2 - - - -
95A MET* 1.3 77.4 - - - +
97A LEU* 1.3 57.0 + - - +
99A VAL* 3.2 2.4 + - - +
100A PHE* 3.0 42.9 + - + -
118A ALA* 4.6 0.7 - - + -
344A TYR* 3.6 36.3 - - + -
351A PHE* 3.6 19.2 - - + -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASN 2.9 17.9 + - - +
94A GLY 3.9 4.7 - - - +
96A ALA* 1.3 77.4 - - - +
98A TRP* 1.3 64.1 + - - +
100A PHE* 3.6 3.9 + - - +
101A LEU* 3.2 57.0 + - + +
115A ALA* 3.3 31.9 - - + +
118A ALA* 4.2 5.7 - - + +
119A LEU* 4.7 12.1 - - + +
122A LEU* 4.1 18.4 - - + -
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Residues in contact with TRP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY 3.3 12.4 + - - +
95A MET* 3.1 20.5 + - + +
97A LEU* 1.3 80.4 - - - +
99A VAL* 1.3 73.2 + - + +
101A LEU* 4.8 2.0 - - - -
102A PHE* 2.8 68.0 + + + +
103A ARG* 3.3 47.6 - - + -
354A HIS* 3.4 26.9 - + - -
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A MET* 2.9 22.6 + - + +
96A ALA* 3.2 8.5 + - - +
98A TRP* 1.3 86.0 - - + +
100A PHE* 1.3 61.2 + - + +
103A ARG* 2.9 19.5 + - + -
104A THR* 2.6 44.8 + - - +
350A ASP* 4.1 26.5 - - + +
351A PHE* 4.1 13.2 - - + +
354A HIS* 3.7 31.6 - - + +
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Residues in contact with PHE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 3.0 37.7 + - + +
97A LEU* 4.0 5.2 - - - +
99A VAL* 1.3 78.1 - - + +
101A LEU* 1.3 62.1 + - + +
104A THR* 3.7 12.1 - - - -
107A LYS* 3.7 18.4 - - - +
111A VAL* 3.7 30.1 - - + +
114A MET* 3.6 35.4 - - + -
115A ALA* 3.7 31.6 - - + -
118A ALA* 4.8 0.7 - - + -
344A TYR* 3.9 26.5 - + + -
348A SER* 3.6 26.5 - - - -
351A PHE* 4.4 7.4 - - + -
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 3.2 53.4 + - + +
98A TRP 4.0 1.3 - - - +
99A VAL 3.2 0.2 - - - -
100A PHE* 1.3 85.7 - - - +
102A PHE* 1.3 95.0 + - + +
103A ARG 3.7 0.4 - - - -
104A THR 4.8 1.3 - - - +
107A LYS* 4.1 18.2 + - - +
115A ALA* 4.3 12.6 - - + -
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Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TRP* 2.8 49.3 + + + +
101A LEU* 1.3 104.1 - - + +
103A ARG* 1.3 88.6 + - - +
104A THR 5.4 0.4 - - - -
105A LYS* 5.5 6.2 - - - -
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TRP* 3.3 44.1 + - + -
99A VAL* 2.9 18.2 + - + +
102A PHE* 1.3 106.2 + - - +
104A THR* 1.3 65.9 + - - +
105A LYS* 3.5 13.5 + - - +
350A ASP* 4.3 8.7 - - - +
354A HIS* 3.3 34.3 + - + +
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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