Contacts of the helix formed by residues 83 - 102 (chain B) in PDB entry 4GCK
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 ASP 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B GLU* 2.8 20.4 + - - +
82B LYS* 1.3 75.3 - - - +
84B THR* 1.3 67.8 + - - +
85B THR* 3.5 10.2 + - - -
86B ALA* 2.9 30.6 + - + +
87B ARG* 2.9 27.3 + - - +
147B GLU* 3.7 17.4 - - - +
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LYS 3.5 1.4 + - - -
83B ASP* 1.3 72.2 - - - +
85B THR* 1.3 65.2 + - - +
87B ARG* 3.1 13.8 + - - +
88B LEU* 3.0 24.5 + - + +
139B VAL* 4.0 23.0 + - + +
140B MET* 4.5 0.2 - - - -
143B LYS* 3.5 32.9 + - + -
146B ARG* 4.2 10.9 - - - -
147B GLU* 3.0 30.4 + - - -
151B TYR* 3.5 24.2 - - + +
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ASP* 3.5 10.2 + - - -
84B THR* 1.3 78.3 - - - +
86B ALA* 1.3 57.9 + - - +
88B LEU* 3.2 9.5 + - - +
89B ARG* 2.9 26.9 + - - +
143B LYS* 4.5 11.3 + - - -
147B GLU* 4.9 1.0 + - - -
151B TYR* 4.5 7.6 + - - -
190B TRP* 4.2 19.7 - - + +
194B ALA* 4.6 11.4 - - + -
197B LEU* 4.9 7.8 - - + +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLU* 3.6 30.1 - - + +
83B ASP* 2.9 19.8 + - + +
84B THR 3.3 0.2 - - - -
85B THR* 1.3 74.0 - - - +
87B ARG* 1.3 59.4 + - - +
89B ARG* 3.6 9.0 - - - +
90B LEU* 2.9 36.1 + - + +
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ILE* 4.1 14.4 - - + -
78B LEU* 3.0 59.7 + - + +
81B GLU* 2.7 33.7 + - + +
82B LYS* 3.7 6.8 + - - +
83B ASP 2.9 21.1 + - - +
84B THR* 3.1 10.3 + - - +
86B ALA* 1.3 76.7 - - - +
88B LEU* 1.3 63.4 + - - +
90B LEU* 3.2 2.9 + - - +
91B ILE* 2.9 30.9 + - + +
139B VAL* 4.1 25.6 + - + +
142B GLU* 3.7 8.9 + - - +
146B ARG* 3.4 44.8 - - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B THR* 3.0 18.4 + - + +
85B THR* 3.5 8.5 - - - +
87B ARG* 1.3 78.0 - - - +
89B ARG* 1.3 63.2 + - - +
91B ILE* 3.3 4.6 + - + +
92B VAL* 3.0 27.4 + - - +
136B LEU* 3.8 26.9 - - + +
139B VAL* 3.6 23.1 - - + -
140B MET* 4.0 26.7 - - + -
151B TYR* 3.5 17.9 - - - +
162B LEU* 4.1 5.8 - - + -
190B TRP* 3.8 12.6 - - + -
197B LEU* 3.4 27.6 - - + -
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B THR 2.9 10.8 + - - +
86B ALA* 3.6 12.1 - - - +
88B LEU* 1.3 77.5 - - - +
90B LEU* 1.3 65.6 + - + +
92B VAL* 3.3 1.7 + - - +
93B LEU* 2.8 45.0 + - - +
186B PHE* 3.7 24.5 - - + -
187B GLU* 3.6 28.7 + - - +
190B TRP* 3.4 58.9 - - + +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ILE* 3.7 28.2 - - + +
80B ASP* 6.2 1.3 - - + -
81B GLU* 4.0 28.5 - - + +
86B ALA* 2.9 22.0 + - + +
87B ARG 3.7 3.1 - - - +
89B ARG* 1.3 83.2 - - + +
91B ILE* 1.3 57.6 + - - +
93B LEU* 3.7 16.7 - - + +
94B LEU* 2.8 31.2 + - - +
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Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ILE* 3.8 42.0 - - + -
77B ILE* 4.0 17.0 - - + -
78B LEU* 4.5 6.7 - - + -
87B ARG 2.9 24.2 + - - +
88B LEU* 3.8 4.0 - - - +
90B LEU* 1.3 75.2 - - - +
92B VAL* 1.3 64.1 + - + +
94B LEU* 3.2 3.9 + - - +
95B ILE* 2.9 39.5 + - + +
132B ILE* 5.0 1.1 - - + -
135B GLN* 4.8 4.0 - - + -
136B LEU* 3.9 32.1 - - + -
139B VAL* 4.4 19.1 - - + -
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU 3.0 19.6 + - - +
89B ARG 3.8 3.4 - - - +
91B ILE* 1.3 77.9 - - + +
93B LEU* 1.3 64.8 + - - +
95B ILE* 3.1 5.0 + - + +
96B LEU* 2.9 44.2 + - + +
136B LEU* 5.6 3.4 - - + -
162B LEU* 4.0 24.9 - - + +
165B PHE* 4.0 14.1 - - + -
166B CYS* 3.7 24.2 - - - -
186B PHE* 4.0 8.3 - - + -
190B TRP* 4.0 18.4 - - + -
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ARG* 2.8 32.9 + - - +
90B LEU* 3.7 16.6 - - + +
92B VAL* 1.3 77.2 - - - +
94B LEU* 1.3 52.8 + - - +
96B LEU* 4.6 1.3 - - - +
97B GLY* 2.7 34.8 + - - -
183B THR* 4.2 19.3 - - + -
186B PHE* 3.8 44.6 - - + -
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 3.8 22.0 - - + +
73B ARG* 3.6 43.7 - - + +
74B ILE* 3.6 31.6 - - + -
77B ILE* 4.0 12.1 - - + -
90B LEU 2.8 19.0 + - - +
91B ILE 3.3 5.2 - - - +
93B LEU* 1.3 74.0 - - - +
95B ILE* 1.3 62.0 + - + +
97B GLY* 5.0 0.4 - - - -
98B PHE* 2.8 32.7 + - + +
101B ARG* 4.6 12.8 - - - +
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Residues in contact with ILE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 4.4 19.7 - - + -
74B ILE* 5.4 1.8 - - + -
91B ILE* 2.9 31.8 + - + +
92B VAL* 3.7 5.8 - - + +
94B LEU* 1.3 75.9 - - + +
96B LEU* 1.3 65.1 + - + +
98B PHE* 3.9 2.3 - - - +
99B GLY* 3.1 19.2 + - - -
109B LEU* 5.5 6.3 - - + +
129B PHE* 5.9 5.2 - - + -
132B ILE* 4.0 36.3 - - + -
136B LEU* 5.6 2.0 - - + -
163B LEU* 4.3 13.5 - - + -
166B CYS* 4.1 27.1 - - + -
170B LEU* 4.2 20.1 - - + +
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B VAL* 2.9 38.5 + - + +
93B LEU* 3.9 2.2 - - - +
95B ILE* 1.3 77.1 - - + +
97B GLY* 1.3 58.1 + - - +
99B GLY* 3.2 2.4 + - - -
100B GLU* 2.9 28.8 + - - +
165B PHE* 3.9 15.3 - - + -
166B CYS* 4.0 38.4 - - + +
169B MET* 4.1 8.7 - - + -
170B LEU* 4.5 5.4 - - + -
182B PRO* 3.6 34.4 - - + +
183B THR* 3.6 15.3 - - + -
186B PHE* 4.0 15.9 - - + -
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Residues in contact with GLY 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 2.7 23.0 + - - -
94B LEU* 3.8 0.9 - - - -
96B LEU* 1.3 71.5 - - - +
98B PHE* 1.3 64.3 + - - +
100B GLU* 3.3 3.2 + - - +
101B ARG* 3.0 40.9 + - - +
183B THR* 3.5 15.0 - - - +
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Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PHE* 4.2 7.6 - + - -
66B ILE* 4.0 15.9 - - + -
69B SER* 3.4 35.9 - - - -
70B LEU* 3.6 33.4 - - + -
73B ARG* 4.8 9.4 - - - -
94B LEU* 2.8 22.7 + - + +
95B ILE 3.9 3.4 - - - +
97B GLY* 1.3 72.7 - - - +
99B GLY* 1.3 66.3 + - - +
101B ARG* 3.5 22.4 - - - +
102B ASN* 2.9 51.0 + - + +
105B LEU* 4.0 26.9 - - + -
109B LEU* 5.1 7.9 - - + -
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE 3.1 12.7 + - - -
96B LEU 3.6 3.8 - - - -
97B GLY 3.2 0.4 - - - -
98B PHE* 1.3 85.0 - - - +
100B GLU* 1.3 61.9 + - - +
102B ASN 3.2 13.6 + - - -
106B THR* 2.7 29.7 + - - -
109B LEU* 5.4 4.3 - - - -
170B LEU* 4.2 10.1 - - - -
173B PHE* 3.3 8.8 - - - -
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LEU 2.9 12.2 + - - +
97B GLY* 3.3 9.4 + - - +
99B GLY* 1.3 78.7 - - - +
101B ARG* 1.3 62.6 + - + +
102B ASN 3.3 0.5 + - - -
103B PRO* 3.4 17.2 - - - +
173B PHE* 3.8 10.8 - - - -
181B ARG* 3.4 46.2 + - - +
182B PRO* 3.5 9.2 - - + +
183B THR* 2.7 45.3 + - - -
184B ASP* 3.9 3.5 - - - +
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ARG* 5.1 12.9 - - - +
94B LEU* 4.5 14.1 + - - +
97B GLY* 3.0 25.0 + - - +
98B PHE* 3.5 30.3 - - - +
100B GLU* 1.3 77.0 - - + +
102B ASN* 1.3 78.9 + - - +
103B PRO* 3.5 6.2 - - - +
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Residues in contact with ASN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PHE* 4.8 5.2 - - - -
98B PHE* 2.9 50.8 + - + +
99B GLY 3.2 3.8 + - - -
101B ARG* 1.3 97.6 - - - +
103B PRO* 1.3 65.9 - - - +
104B GLY 3.3 2.7 - - - -
105B LEU* 3.0 34.9 + - + +
106B THR* 2.9 20.4 + - - -
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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