Contacts of the strand formed by residues 94 - 100 (chain B) in PDB entry 6GJH
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 ARG 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ARG 4.4 1.0 - - - +
90B HIS* 3.6 1.7 - - - -
91B THR* 2.8 42.7 + - - +
93B ASP* 1.3 94.3 + - + +
95B TRP* 1.3 62.9 + - - +
96B ARG* 3.8 15.6 + - - +
152B GLN 5.2 1.6 + - - -
154B SER* 5.4 1.8 - - - -
166B GLU* 3.3 28.0 + - - +
167B ALA* 3.4 34.9 - - - +
168B PRO* 4.0 21.6 - - - +
169B MET* 3.5 6.6 - - - +
146C PRO* 3.2 38.9 - - - +
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Residues in contact with TRP 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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90B HIS* 3.1 34.3 + + - -
94B ARG* 1.3 72.1 - - - +
96B ARG* 1.3 60.6 + - - +
97B VAL* 3.6 29.4 - - + -
118B VAL* 4.4 7.0 - - + -
142B TYR* 4.0 26.0 - + + -
143B THR 4.3 8.9 + - - -
144B LEU* 3.7 28.9 - - + -
145B PRO* 3.8 27.7 - - + +
148B VAL* 5.8 2.5 - - + -
153B VAL* 5.9 0.4 - - + -
165B VAL* 3.9 30.5 - - + -
166B GLU* 3.1 7.7 - - - +
167B ALA* 2.8 49.1 + - + +
168B PRO 5.6 0.4 - - - -
169B MET* 3.7 19.7 - - - +
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Residues in contact with ARG 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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89B ARG* 3.0 91.3 + - + +
90B HIS* 3.1 16.0 + - - -
91B THR* 4.2 15.8 - - - +
94B ARG* 3.8 27.6 + - + +
95B TRP* 1.3 75.2 - - - +
97B VAL* 1.3 66.9 + - - +
164B THR* 4.0 12.8 - - + -
165B VAL 3.4 5.8 - - - +
166B GLU* 3.5 31.4 + - + -
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Residues in contact with VAL 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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87B GLU 3.8 7.9 - - - +
88B ILE* 4.2 14.8 - - + -
89B ARG* 4.6 1.1 - - - +
90B HIS* 3.5 19.3 - - + +
95B TRP* 3.6 30.1 - - + -
96B ARG* 1.3 83.0 - - - +
98B SER* 1.3 64.0 + - - +
99B LEU* 6.2 0.4 - - + -
120B ILE* 5.6 0.4 - - + -
142B TYR* 4.1 33.7 - - + -
163B LEU 4.0 0.3 - - - +
164B THR* 3.5 4.2 - - - +
165B VAL* 2.9 47.5 + - + +
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 3.3 15.9 - - - -
86B SER* 3.2 3.5 - - - -
87B GLU* 2.9 39.2 + - - +
88B ILE* 5.6 0.9 - - - +
89B ARG* 3.9 20.5 + - - +
97B VAL* 1.3 74.2 + - - +
99B LEU* 1.3 63.3 + - - +
142B TYR* 4.2 7.8 + - - -
162B THR* 3.8 13.1 - - - +
163B LEU 3.3 5.4 - - - -
164B THR* 3.5 16.3 + - - +
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Residues in contact with LEU 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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131A HIS* 6.4 1.1 - - + -
85B VAL 3.6 5.8 - - - -
86B SER* 3.6 20.0 - - - +
97B VAL* 6.2 0.7 - - + -
98B SER* 1.3 76.3 - - - +
100B ASP* 1.3 65.4 + - - +
101B VAL* 3.5 22.1 + - + -
120B ILE* 4.3 19.1 - - + -
138B PHE* 4.4 12.3 - - + -
140B ARG* 4.1 41.1 - - + +
142B TYR* 3.9 17.3 - - + +
162B THR* 3.5 2.1 - - - -
163B LEU* 2.8 45.4 + - + +
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Residues in contact with ASP 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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84B GLY* 2.7 45.4 + - - +
85B VAL* 3.7 0.8 + - - -
86B SER* 2.9 21.1 + - - +
99B LEU* 1.3 75.1 - - - +
101B VAL* 1.3 67.7 + - - +
102B ASN* 2.7 33.8 + - - -
161B GLY 3.6 2.9 - - - +
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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