Contacts of the strand formed by residues 94 - 102 (chain B) in PDB entry 2QBX
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 ILE 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B LEU* 3.8 26.5 - - + -
88B ARG* 5.2 0.7 - - + -
91B ALA* 3.8 20.2 - - + -
93B ARG* 1.3 74.5 - - - +
95B HIS* 1.3 67.0 + - - +
96B VAL* 4.3 0.4 - - + -
172B ARG 4.0 0.2 - - - +
173B SER* 3.2 5.9 - - - -
174B PHE* 3.0 72.2 + - + -
177B VAL* 3.7 22.4 - - + -
182B PHE* 3.8 15.9 - - + -
200B VAL* 3.6 26.2 - - + -
201B PHE 3.7 1.6 - - - +
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Residues in contact with HIS 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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93B ARG* 4.0 10.3 - - + +
94B ILE* 1.3 74.9 - - - +
96B VAL* 1.3 61.6 + - - +
97B GLU 4.0 0.4 - - - -
171B VAL* 4.5 7.5 - - + +
172B ARG 3.6 3.1 + - - +
173B SER* 3.4 26.2 - - - -
200B VAL* 3.3 4.5 - - - +
201B PHE* 2.6 79.9 + + + +
202B TYR* 4.0 11.4 - - - -
203B ARG* 3.7 16.9 - - - -
401B SO4 2.6 40.3 + - - -
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 4.3 4.0 - - + -
95B HIS* 1.3 76.7 - - - +
97B GLU* 1.3 60.0 + - - +
98B MET* 3.7 18.6 - - + +
121B LEU* 4.4 17.5 - - + -
171B VAL* 3.4 5.6 - - - -
172B ARG 2.7 36.4 + - - +
174B PHE* 3.7 31.4 - - + -
184B LEU* 3.6 29.8 - - + -
198B VAL* 3.8 18.8 - - + -
199B ARG 3.5 2.7 - - - +
200B VAL* 4.4 2.0 - - + -
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Residues in contact with GLU 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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95B HIS 4.0 1.4 - - - -
96B VAL* 1.3 70.7 - - - +
98B MET* 1.3 64.5 + - - +
99B LYS* 3.4 20.2 + - + -
169B THR* 3.3 25.1 - - + +
170B GLU 3.8 2.5 - - - -
171B VAL* 3.7 22.8 - - + +
197B ALA 3.7 0.9 - - - +
198B VAL* 3.2 6.6 - - - +
199B ARG* 2.7 77.4 + - + +
201B PHE* 4.4 8.4 - - + -
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Residues in contact with MET 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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96B VAL* 3.7 22.7 - - + +
97B GLU* 1.3 77.2 - - - +
99B LYS* 1.3 61.6 + - - +
100B PHE* 4.0 14.2 - - + -
119B PHE* 4.1 25.8 - - - -
121B LEU* 4.0 20.4 - - + -
149B ILE* 3.7 24.0 - - + -
168B ASN 3.7 0.9 - - - +
169B THR* 3.3 6.8 - - - +
170B GLU* 2.9 49.8 + - + +
172B ARG* 4.0 13.0 - - + -
186B PHE* 4.2 15.0 - - + -
195B LEU* 4.5 9.6 - - + -
197B ALA 3.4 5.6 - - - +
198B VAL* 4.8 2.2 - - + -
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Residues in contact with LYS 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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58B ASP* 6.1 3.1 - - + -
59B GLU* 3.1 33.2 + - + -
97B GLU* 3.4 24.0 + - - +
98B MET* 1.3 75.0 - - - +
100B PHE* 1.3 62.7 + - - +
167B ILE* 4.2 10.3 - - + -
168B ASN 3.3 4.9 - - - +
169B THR* 2.5 39.7 + - + +
195B LEU* 3.8 2.4 - - - +
196B ILE* 2.8 31.1 + - + -
197B ALA* 2.9 36.7 + - + +
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Residues in contact with PHE 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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98B MET* 4.0 11.2 - - + -
99B LYS* 1.3 76.3 - - - +
101B SER* 1.3 65.6 + - - +
102B VAL* 3.9 20.9 - - + -
119B PHE* 3.9 22.7 - + + -
149B ILE* 3.8 19.3 - - + -
150B ALA* 3.9 12.3 - - - -
151B ALA* 3.9 18.8 - - + -
167B ILE* 3.5 4.9 - - - +
168B ASN* 2.9 59.0 + - + +
170B GLU* 3.7 26.2 - - + -
193B MET* 5.9 2.0 - - + -
194B SER 3.2 14.1 - - - +
195B LEU* 4.2 12.1 - - + -
196B ILE* 4.0 5.6 - - - -
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Residues in contact with SER 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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100B PHE* 1.3 70.8 + - - +
102B VAL* 1.3 63.0 + - - +
165B MET* 4.4 0.7 - - - +
166B LYS 3.0 23.0 + - - -
167B ILE* 3.7 4.3 - - - +
168B ASN* 5.1 0.7 - - - -
193B MET* 3.2 4.9 - - - +
194B SER 2.8 33.2 + - - -
196B ILE* 3.2 21.2 - - - +
2D ASN* 3.6 16.8 + - - -
4D TRP* 3.9 18.9 - - - -
5D ILE* 3.7 3.3 - - - +
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Residues in contact with VAL 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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100B PHE* 3.9 26.1 - - + -
101B SER* 1.3 76.4 - - - +
103B ARG* 1.3 74.5 + - - +
104B ASP* 3.7 4.0 + - + +
116B LYS 5.2 0.2 - - - +
117B GLU* 3.6 46.2 - - + +
118B THR* 5.6 0.4 - - - -
119B PHE* 5.6 1.3 - - + -
150B ALA* 5.7 0.4 - - - -
151B ALA* 4.5 15.3 - - + +
166B LYS* 4.8 3.3 + - - +
168B ASN* 5.0 3.8 + - - -
192B CYS 3.9 7.2 - - - +
193B MET* 4.1 14.6 - - + -
1D SER* 4.2 5.4 + - - +
2D ASN* 2.7 25.9 + - - +
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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