Contacts of the helix formed by residues 81 - 103 (chain D) in PDB entry 5GQQ
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 ASN 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D PHE* 3.8 2.9 - - - -
41D GLY 3.9 16.8 - - - +
42D VAL* 4.7 4.7 - - + +
74D ARG* 4.0 7.3 - - - +
75D GLU* 3.7 22.8 + - - -
77D LYS* 3.5 6.8 - - - +
80D VAL* 1.3 75.2 - - - +
82D PHE* 1.3 52.8 + - - +
83D SER* 2.9 14.4 + - - -
84D GLU* 2.6 38.1 + - - +
85D PHE* 2.7 32.9 + - - +
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Residues in contact with PHE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU* 3.7 13.0 - - + -
29D TRP* 3.6 57.0 - + + -
32D PHE* 3.5 40.9 - + + -
41D GLY 4.6 0.6 + - - -
81D ASN* 1.3 72.4 - - - +
83D SER* 1.3 70.5 + - - +
85D PHE* 3.0 12.4 + + - +
86D THR* 3.1 34.4 + - + +
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Residues in contact with SER 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ARG* 3.8 18.3 + - - -
81D ASN* 2.9 19.2 + - - -
82D PHE* 1.3 83.4 - - - +
84D GLU* 1.3 58.7 + - - +
86D THR* 2.6 28.7 + - - -
87D GLY 3.8 1.6 + - - -
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Residues in contact with GLU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D PHE* 3.5 28.1 - - - +
73D ASP* 4.0 0.4 - - - -
74D ARG* 3.0 45.7 + - - +
75D GLU* 2.8 24.0 - - - +
77D LYS* 2.8 11.2 + - - -
79D GLY 3.6 0.7 - - - +
80D VAL* 3.0 14.6 - - + -
81D ASN* 2.6 46.2 + - - +
83D SER* 1.3 78.3 + - - +
85D PHE* 1.3 60.3 + - - +
87D GLY* 3.1 6.9 + - - -
88D VAL* 3.1 19.4 + - - +
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Residues in contact with PHE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 3.8 38.1 - + - -
28D LEU* 4.2 17.9 - - + -
31D VAL* 4.0 22.9 - - + -
32D PHE* 3.8 29.8 - + + -
35D VAL* 4.7 2.7 - - + -
43D ILE* 3.5 21.5 - - + -
48D LEU* 4.5 5.8 - - + -
80D VAL* 4.2 10.5 - - + +
81D ASN 2.7 18.6 + - - +
82D PHE* 3.0 8.7 + + - +
84D GLU* 1.3 71.7 - - - +
86D THR* 1.3 59.7 + - - +
88D VAL* 3.5 18.6 - - + +
89D TRP* 2.7 43.0 + + + +
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Residues in contact with THR 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 3.9 28.4 - - + +
82D PHE* 3.1 40.0 + - + +
83D SER* 2.6 21.8 + - - +
85D PHE* 1.3 77.4 - - - +
87D GLY* 1.3 60.9 + - - +
89D TRP* 3.5 4.0 + - - +
90D LYS* 3.2 23.6 + - - +
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Residues in contact with GLY 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D PHE* 3.7 21.3 - - - -
83D SER 3.8 1.0 + - - -
84D GLU 3.1 8.8 + - - -
86D THR* 1.3 80.7 + - - +
88D VAL* 1.3 64.1 + - - +
90D LYS* 3.3 6.7 + - - +
91D TYR* 2.9 25.1 + - - +
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Residues in contact with VAL 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 4.6 0.4 - - + -
48D LEU* 4.3 12.3 - - + -
68D ILE* 3.7 24.7 - - + +
69D ILE* 5.2 0.9 - - - -
72D PHE* 3.6 36.5 - - + -
80D VAL* 4.1 19.3 - - + -
84D GLU 3.1 7.0 + - - +
85D PHE* 3.1 25.8 + - + +
87D GLY* 1.3 74.0 - - - +
89D TRP* 1.3 64.5 + - - +
91D TYR* 3.3 1.0 + - - +
92D ILE* 3.1 37.8 + - + +
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Residues in contact with TRP 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 3.7 39.8 - + - +
27D PHE* 4.3 24.7 - + - -
28D LEU* 3.4 40.1 - - + +
31D VAL* 4.8 5.2 - - + +
85D PHE* 2.7 30.3 + + + +
86D THR 3.7 5.2 - - - +
88D VAL* 1.3 74.7 - - - +
90D LYS* 1.3 66.7 + - + +
92D ILE* 3.4 1.6 + - - +
93D THR* 2.8 63.7 + - + -
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Residues in contact with LYS 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D THR 3.2 13.9 + - - +
87D GLY* 3.3 6.3 + - - +
89D TRP* 1.3 92.8 - - + +
91D TYR* 1.3 57.4 + - - +
93D THR* 3.2 1.8 + - - -
94D ASP* 2.8 63.6 + - - +
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Residues in contact with TYR 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ILE* 4.1 28.3 - - + -
71D MET* 3.4 31.8 - - + +
72D PHE* 3.5 29.6 - + + -
87D GLY 2.9 17.1 + - - +
88D VAL 3.8 2.2 - - - +
90D LYS* 1.3 79.1 - - - +
92D ILE* 1.3 65.5 + - + +
94D ASP* 3.8 6.1 + - + +
95D TRP* 3.1 64.0 + + - -
152D ILE* 4.7 3.1 - - + -
156D ILE* 3.5 16.0 - - + +
159D GLN* 5.8 0.9 + - - -
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Residues in contact with ILE 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PRO* 3.8 26.7 - - + -
100B PHE* 4.0 9.4 - - + -
48D LEU* 5.0 0.4 - - + -
52D LEU* 3.7 35.9 - - + -
60D PHE* 5.6 2.0 - - + -
68D ILE* 3.7 27.4 - - + -
88D VAL* 3.1 33.5 + - + +
89D TRP 4.1 2.0 - - - +
91D TYR* 1.3 78.7 - - + +
93D THR* 1.3 61.8 + - - +
95D TRP* 3.1 7.3 + - - +
96D GLN* 2.9 26.5 + - - +
148D PHE* 3.6 14.3 - - + -
152D ILE* 5.1 2.9 - - + -
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Residues in contact with THR 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PRO* 5.3 1.4 - - - +
100B PHE* 5.2 4.2 - - - -
89D TRP* 2.8 62.0 + - + -
90D LYS* 3.6 3.8 - - - -
92D ILE* 1.3 74.4 - - - +
94D ASP* 1.3 68.1 + - - +
96D GLN* 3.0 33.8 + - - +
97D ASN* 3.0 24.6 + - - +
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Residues in contact with ASP 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D LYS* 2.8 56.1 + - - +
91D TYR* 4.0 6.6 - - - +
93D THR* 1.3 76.4 - - - +
95D TRP* 1.3 62.1 + - + +
97D ASN* 3.3 16.2 + - - +
98D VAL* 3.1 27.2 + - + +
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Residues in contact with TRP 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D TYR* 3.1 64.7 + + - -
92D ILE* 3.1 10.6 + - - +
94D ASP* 1.3 77.4 - - + +
96D GLN* 1.3 59.6 + - - +
98D VAL* 3.3 13.2 + - + +
99D PHE* 2.9 24.4 + - - +
122D PHE* 4.3 14.8 - + - -
148D PHE* 3.4 19.6 - - + -
151D PHE* 3.5 33.7 - + - -
152D ILE* 3.7 33.0 - - + +
155D CYS* 3.4 32.3 - - + -
156D ILE* 4.9 4.0 - - + -
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Residues in contact with GLN 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLY* 3.7 2.9 - - - -
99B PRO* 3.1 40.3 - - + +
92D ILE 2.9 12.7 + - - +
93D THR* 3.2 28.4 + - - +
95D TRP* 1.3 77.8 - - - +
97D ASN* 1.3 59.7 + - - +
99D PHE* 3.2 4.1 + - + +
100D ARG* 2.6 75.6 + - + +
148D PHE* 3.4 12.5 - - + -
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Residues in contact with ASN 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D THR* 3.0 27.2 + - - +
94D ASP* 3.6 18.5 + - - +
95D TRP 3.2 0.2 - - - -
96D GLN* 1.3 83.4 + - - +
98D VAL* 1.3 66.5 + - + +
100D ARG* 3.3 10.6 + - - +
101D THR* 3.0 29.2 + - - +
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ASP* 3.1 15.8 + - + +
95D TRP* 3.7 16.8 - - + +
97D ASN* 1.3 77.5 - - + +
99D PHE* 1.3 64.3 + - - +
101D THR* 3.3 5.2 + - - -
102D TYR* 3.1 43.7 + - + -
122D PHE* 3.6 38.1 - - + -
151D PHE* 4.3 8.7 - - + -
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Residues in contact with PHE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D TRP 2.9 17.2 + - - +
96D GLN* 3.4 5.4 - - + +
97D ASN 3.2 0.2 - - - -
98D VAL* 1.3 78.2 - - - +
100D ARG* 1.3 69.5 + - + +
102D TYR* 3.3 2.8 + - - -
103D ASP* 2.9 39.5 + - - +
108D GLY* 3.3 36.8 - - - -
109D MET* 4.1 0.4 - - - -
110D ILE* 3.5 37.1 - - + +
146D ILE 3.8 9.2 - - - -
147D ALA 4.0 2.0 - - - -
148D PHE* 3.6 49.1 - + + -
151D PHE* 3.9 19.3 - + + -
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Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B SER* 3.2 34.1 + - - -
98B GLY* 4.2 0.8 - - - -
96D GLN* 2.6 57.4 + - + +
97D ASN* 3.9 9.6 + - - +
99D PHE* 1.3 83.7 - - + +
101D THR* 1.3 66.6 + - - +
103D ASP* 3.6 20.0 + - + +
104D ARG* 5.3 0.2 - - - -
106D ASN* 4.4 8.8 - - - +
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Residues in contact with THR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ASN* 3.0 15.8 + - - +
98D VAL* 3.4 11.3 - - - -
100D ARG* 1.3 79.3 - - - +
102D TYR* 1.3 85.6 - - + +
104D ARG* 3.3 25.4 + - - +
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Residues in contact with TYR 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D VAL* 3.1 42.8 + - + +
99D PHE 4.4 1.6 - - - +
101D THR* 1.3 93.4 - - + +
103D ASP* 1.3 61.9 + - - +
104D ARG* 3.0 24.5 + - - +
110D ILE* 4.4 8.7 - - + -
114D GLU* 3.2 27.1 - - - +
117D GLN* 3.4 26.1 - - + +
118D ALA* 3.4 43.7 - - + -
121D GLY* 3.8 20.6 + - - -
122D PHE* 4.6 4.5 - + - -
151D PHE* 5.6 0.4 - + - -
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Residues in contact with ASP 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D PHE* 2.9 27.8 + - + +
100D ARG* 3.6 12.6 + - + +
101D THR 3.4 0.6 - - - -
102D TYR* 1.3 72.5 - - - +
104D ARG* 1.3 59.9 + - - +
105D ASP* 2.9 5.7 - - - +
106D ASN* 3.0 29.3 + - - +
107D SER* 3.0 8.0 + - - -
108D GLY* 2.6 30.2 + - - -
109D MET 2.8 12.5 - - - +
110D ILE* 4.4 4.2 - - + +
114D GLU* 3.4 3.8 - - - -
202D CA 2.3 32.1 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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