Contacts of the helix formed by residues 77 - 95 (chain B) in PDB entry 2JG7
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 PRO 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASP 3.4 9.4 - - - +
76B ILE* 1.3 91.9 - - + +
78B ALA* 1.3 65.5 + - - +
79B PRO* 4.1 0.2 - - + -
80B LYS* 3.0 14.3 + - + +
81B ARG* 3.0 18.0 + - - +
142C SER 3.3 21.1 - - - +
143C GLU* 3.4 26.0 - - - +
144C ARG 3.8 1.8 - - - +
145C PRO* 3.5 35.4 - - + -
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE 3.6 1.2 + - - -
77B PRO* 1.3 70.2 - - - +
79B PRO* 1.3 64.2 - - + +
81B ARG* 3.0 34.4 + - - +
82B GLY 2.9 24.4 + - - -
132B SER* 3.3 22.9 - - - +
135B ILE* 4.2 9.9 - - + -
181B THR 4.0 5.9 - - - +
141C PRO* 3.7 18.3 - - + +
142C SER 4.2 1.4 + - - -
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Residues in contact with PRO 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO 3.5 2.5 - - - -
78B ALA* 1.3 90.3 - - + +
80B LYS* 1.3 56.4 + - + +
82B GLY* 3.3 2.8 + - - -
83B GLU* 3.1 23.2 + - - +
132B SER* 3.2 26.9 + - - +
133B ARG* 3.5 40.4 + - + +
141C PRO 3.6 16.4 - - - +
142C SER 3.4 14.8 - - - +
143C GLU* 3.7 20.4 - - + +
462D GLU* 4.8 0.2 - - - +
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Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.7 16.1 - - + +
77B PRO* 3.0 21.3 + - + +
79B PRO* 1.3 77.8 - - - +
81B ARG* 1.3 64.0 + - - +
83B GLU* 3.4 21.3 - - + +
84B ILE* 3.5 12.1 + - - +
143C GLU* 3.0 38.5 + - + +
144C ARG* 5.2 0.4 - - - +
145C PRO* 5.2 7.2 - - + +
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A PRO* 6.2 0.4 - - - +
73B TRP* 3.7 38.3 + - + -
74B ALA 4.0 12.1 + - - -
76B ILE* 2.9 30.4 + - + +
77B PRO* 3.0 14.9 + - - +
78B ALA* 3.3 29.2 - - - +
80B LYS* 1.3 73.9 - - - +
82B GLY* 1.3 60.3 + - - +
84B ILE* 3.1 8.5 + - - +
85B VAL* 3.0 29.0 + - - +
135B ILE* 4.7 1.8 - - - +
155B PRO* 4.6 7.3 - - - +
180B LEU 3.2 20.2 - - - +
181B THR* 2.5 34.2 + - - +
182B CYS* 3.5 5.1 + - - +
183B GLY* 3.1 27.0 - - - +
488B MET* 5.7 1.8 - - - +
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA 2.9 13.2 + - - -
79B PRO 3.3 6.2 + - - -
81B ARG* 1.3 77.0 - - - +
83B GLU* 1.3 50.3 + - - +
85B VAL* 3.1 11.4 + - - +
86B ARG* 2.7 35.2 + - - +
129B VAL* 3.6 14.6 - - - +
132B SER* 3.8 18.8 - - - -
181B THR* 4.8 2.2 + - - -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PRO 3.1 11.6 + - - +
80B LYS* 3.4 15.7 - - + +
81B ARG 3.2 0.4 - - - -
82B GLY* 1.3 73.4 - - - +
84B ILE* 1.3 68.2 + - + +
86B ARG* 2.6 43.9 + - - +
87B GLN* 2.9 42.7 + - - +
129B VAL* 5.9 0.9 - - - -
212B ASN* 5.8 0.2 - - - +
93D ARG* 5.2 0.7 + - - -
123D ASP* 5.7 0.9 - - - +
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TRP* 4.0 18.4 - - + -
76B ILE* 6.3 0.7 - - + -
80B LYS 3.5 14.1 + - - +
81B ARG 3.1 9.3 + - - +
83B GLU* 1.3 78.5 - - + +
85B VAL* 1.3 65.2 + - - +
87B GLN* 3.0 17.7 + - - +
88B ILE* 3.0 21.3 + - + +
180B LEU* 5.3 3.1 - - + -
208B VAL* 4.2 10.7 - - + +
209B LEU* 4.1 25.1 - - + -
212B ASN* 3.6 34.5 - - + +
214B LEU* 3.7 20.6 - - + -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG 3.0 13.8 + - - +
82B GLY* 3.1 10.3 + - - +
84B ILE* 1.3 74.2 - - + +
86B ARG* 1.3 62.8 + - - +
88B ILE* 3.2 11.3 + - + +
89B GLY 3.0 18.2 + - - -
125B CYS* 3.7 42.3 - - + +
128B ALA* 3.9 11.0 - - + -
129B VAL* 4.9 0.2 - - + -
176B ASN* 6.2 0.4 - - - +
177B ALA* 3.9 13.7 - - + +
180B LEU* 3.9 25.6 - - + -
181B THR* 3.6 18.8 - - - +
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Residues in contact with ARG 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY 2.7 19.7 + - - +
83B GLU* 2.6 50.6 + - - +
84B ILE 3.2 0.2 - - - -
85B VAL* 1.3 74.2 - - - +
87B GLN* 1.3 68.8 + - - +
89B GLY* 3.2 5.2 + - - +
90B ASP* 3.0 47.1 + - - +
93B ARG* 5.8 0.2 + - - -
125B CYS* 5.2 0.9 - - - -
126B ASP* 4.7 14.8 - - - +
129B VAL* 3.7 23.7 - - + +
90D ASP* 5.2 1.4 + - - -
93D ARG* 3.5 42.6 - - - +
126D ASP* 3.5 25.6 - - - -
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Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLU* 2.9 39.7 + - - +
84B ILE* 3.0 10.3 + - - +
86B ARG* 1.3 86.0 - - - +
88B ILE* 1.3 56.3 + - - +
90B ASP* 3.2 8.5 + - + +
91B ALA* 2.8 35.9 + - - +
208B VAL* 3.8 14.1 - - + +
211B GLN* 5.4 2.1 - - - +
212B ASN* 3.0 36.9 + - - -
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ILE* 3.0 23.9 + - + +
85B VAL* 3.2 13.7 + - + +
87B GLN* 1.3 75.0 - - - +
89B GLY* 1.3 63.6 + - - +
91B ALA* 3.3 2.7 + - - +
92B LEU* 3.0 40.9 + - + +
121B TYR* 3.8 20.6 - - + +
125B CYS* 4.2 2.2 - - - -
176B ASN* 3.9 8.3 - - - +
180B LEU* 3.8 28.3 - - + -
204B ILE* 5.8 1.1 - - + -
205B VAL* 3.9 27.6 - - + +
208B VAL* 4.0 23.3 - - + +
209B LEU* 5.6 1.8 - - + -
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Residues in contact with GLY 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 VAL 3.0 11.1 + - - -
86B ARG 3.2 6.0 + - - -
88B ILE* 1.3 76.8 - - - +
90B ASP* 1.3 56.4 + - - +
92B LEU* 3.5 7.7 + - - +
93B ARG* 3.1 28.7 + - - +
122B VAL* 3.8 16.5 - - - +
125B CYS* 3.8 24.0 - - - -
126B ASP* 5.5 1.1 - - - -
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG* 3.0 35.4 + - - +
87B GLN* 3.2 10.7 + - + +
89B GLY* 1.3 72.2 - - - +
91B ALA* 1.3 66.6 + - - +
92B LEU 3.2 0.2 - - - -
93B ARG* 3.2 32.1 + - - +
94B LYS* 3.1 39.0 + - - +
86D ARG* 5.1 2.6 + - - -
90D ASP* 5.1 9.7 - - - +
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Residues in contact with ALA 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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87B GLN 2.8 21.1 + - - +
88B ILE 3.7 3.6 - - - +
90B ASP* 1.3 72.7 - - - +
92B LEU* 1.3 62.7 + - - +
94B LYS* 3.5 13.6 + - - +
95B LYS* 3.5 23.2 + - - +
204B ILE* 3.7 17.5 - - + +
208B VAL* 3.6 24.5 - - + -
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Residues in contact with LEU 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 ILE* 3.0 34.1 + - + +
89B GLY* 3.5 9.4 - - - +
91B ALA* 1.3 74.9 - - - +
93B ARG* 1.3 65.0 + - - +
95B LYS* 2.9 16.0 + - - +
96B ILE* 3.0 14.4 + - - +
99B LEU* 3.8 27.3 - - + +
118B VAL* 4.3 9.1 - - + +
121B TYR* 3.5 52.5 - - + -
122B VAL* 3.8 13.2 - - + +
169B VAL* 5.2 0.9 - - + -
201B VAL* 5.3 4.9 - - + -
204B ILE* 4.3 17.7 - - + -
205B VAL* 6.0 0.9 - - + -
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Residues in contact with ARG 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG 5.8 0.4 + - - -
89B GLY 3.1 14.4 + - - +
90B ASP* 3.2 32.0 + - - +
92B LEU* 1.3 76.3 - - - +
94B LYS* 1.3 60.8 + - + +
96B ILE* 3.2 30.5 - - + +
119B GLN* 4.5 9.3 - - - +
122B VAL* 3.4 33.5 - - + +
123B ASP* 5.4 1.4 + - - -
126B ASP* 3.2 30.9 + - - -
83D GLU* 5.2 1.0 + - - -
86D ARG* 3.5 41.0 - - - +
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Residues in contact with LYS 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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90B ASP* 3.1 24.5 + - - +
91B ALA* 3.7 13.2 - - - +
92B LEU 3.2 0.2 - - - -
93B ARG* 1.3 78.8 - - + +
95B LYS* 1.3 64.9 + - + +
96B ILE* 3.4 1.8 + - - +
97B LYS 5.3 0.2 + - - -
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Residues in contact with LYS 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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15B GLU* 3.3 32.4 + - + +
16B LEU* 4.5 5.4 - - + +
91B ALA 3.5 13.0 + - - +
92B LEU 2.9 8.8 + - - +
94B LYS* 1.3 81.9 - - + +
96B ILE* 1.3 64.7 + - - +
97B LYS 3.2 3.0 + - - -
98B VAL* 3.4 21.6 - - + +
99B LEU* 3.0 24.3 + - + +
204B ILE* 4.1 31.6 - - + -
207B GLU* 6.0 1.6 - - - -
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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) + - + + + + + -
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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