Contacts of the strand formed by residues 192 - 202 (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 CYS 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B VAL 3.4 3.4 - - - -
70B CYS* 2.0 45.8 - - - -
72B VAL* 4.0 1.1 - - + -
102B VAL* 3.9 2.1 - - - +
103B ARG* 2.9 43.0 + - + +
108B ILE* 3.7 22.4 - - + -
116B LYS 4.0 4.0 + - - -
191B GLY* 1.3 73.6 - - - -
193B MET* 1.3 64.6 + - - +
5D ILE* 3.7 24.0 - - - -
7D PRO* 5.2 0.2 - - - -
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Residues in contact with MET 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TRP* 4.0 16.8 - - + -
68B GLN* 3.4 4.3 - - - +
69B VAL* 3.0 42.5 + - + +
100B PHE* 5.9 2.2 - - + -
101B SER 3.2 14.8 - - - +
102B VAL* 4.1 11.2 - - + -
117B GLU* 4.7 5.4 - - - +
118B THR 3.5 28.7 - - - +
119B PHE* 3.8 36.3 - - + -
188B ASP* 3.7 19.7 - - - +
191B GLY* 4.3 4.3 - - - -
192B CYS* 1.3 88.1 - - - +
194B SER* 1.3 64.1 + - - +
5D ILE* 3.7 9.7 - - - +
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Residues in contact with SER 194 (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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66B THR* 4.0 7.3 + - - +
67B TYR 3.4 7.7 + - - -
68B GLN* 3.7 20.8 + - - +
100B PHE* 3.2 6.8 - - - +
101B SER* 2.8 35.9 + - - -
193B MET* 1.3 78.2 - - - +
195B LEU* 1.3 62.1 + - - +
196B ILE* 3.6 16.5 + - - +
4D TRP* 3.8 25.3 - - - -
5D ILE* 3.8 3.8 - - - +
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Residues in contact with LEU 195 (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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43B TRP* 4.5 3.1 - - + -
51B TRP* 3.8 15.2 - - + -
66B THR* 3.4 4.7 - - - -
67B TYR* 2.8 37.8 + - + +
81B LEU* 3.8 17.7 - - + -
98B MET* 4.5 9.9 - - + -
99B LYS 3.9 13.9 - - - +
100B PHE* 4.2 9.2 - - + -
119B PHE* 4.4 17.5 - - + -
186B PHE* 3.7 39.5 - - + -
194B SER* 1.3 71.7 - - - +
196B ILE* 1.3 58.9 + - - +
197B ALA 4.1 10.3 - - - +
198B VAL* 4.1 15.3 - - + -
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Residues in contact with ILE 196 (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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34B SER* 4.1 1.6 + - - -
57B TYR 3.4 22.7 - - - +
58B ASP* 4.1 8.1 - - + -
64B ILE* 3.4 27.0 - - + +
65B ARG 3.6 12.7 - - - +
66B THR* 3.7 10.4 - - + +
99B LYS* 2.8 23.4 + - + +
100B PHE* 4.0 9.2 - - - -
101B SER* 3.2 28.7 - - - +
165B MET* 5.4 0.4 - - - -
167B ILE* 3.7 23.6 - - + -
194B SER* 3.7 17.5 - - - +
195B LEU* 1.3 72.6 - - - +
197B ALA* 1.3 58.6 + - + +
4D TRP* 5.1 7.4 - - + -
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Residues in contact with ALA 197 (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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34B SER* 3.2 7.0 - - - -
35B THR* 3.2 27.8 - - + -
58B ASP* 6.2 0.7 - - + -
64B ILE* 4.7 0.7 - - + -
97B GLU 4.2 1.3 - - - +
98B MET* 3.4 4.0 - - - -
99B LYS* 2.9 52.7 + - + +
195B LEU* 3.8 2.5 - - - +
196B ILE* 1.3 81.2 - - + +
198B VAL* 1.3 71.2 + - - +
199B ARG 5.3 0.4 - - - +
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Residues in contact with VAL 198 (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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32B MET* 3.4 28.1 - - + +
33B ASP* 3.4 3.6 - - - -
34B SER* 2.8 32.8 + - - +
43B TRP* 3.8 22.2 - - + -
96B VAL* 3.8 26.9 - - + -
97B GLU 3.2 4.7 - - - +
98B MET* 4.8 1.3 - - + -
184B LEU* 4.2 0.9 - - + -
186B PHE* 3.9 26.0 - - + -
195B LEU* 4.1 16.6 - - + -
197B ALA* 1.3 81.2 - - - +
199B ARG* 1.3 57.7 + - - +
200B VAL* 4.1 1.1 - - + -
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Residues in contact with ARG 199 (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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28B GLU* 3.1 30.5 + - - +
30B THR* 3.7 21.5 + - + -
32B MET 3.5 10.1 - - - +
33B ASP* 3.2 27.8 - - + +
95B HIS 3.7 0.7 - - - +
96B VAL* 3.5 2.4 - - - +
97B GLU* 2.7 68.8 + - + +
197B ALA* 4.2 1.2 - - + +
198B VAL* 1.3 74.0 - - - +
200B VAL* 1.3 64.4 + - - +
201B PHE* 3.5 41.4 - - - +
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Residues in contact with VAL 200 (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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30B THR* 3.5 1.7 - - - +
31B LEU* 2.6 40.4 + - + -
32B MET* 2.8 49.6 + - + +
86B ILE* 3.9 4.3 - - + -
94B ILE* 3.6 27.4 - - + -
95B HIS 3.3 3.8 - - - +
96B VAL* 4.4 2.9 - - + -
182B PHE* 3.7 19.5 - - + -
184B LEU* 3.7 20.9 - - + -
198B VAL* 4.2 1.8 - - + -
199B ARG* 1.3 75.7 - - - +
201B PHE* 1.3 60.1 + - - +
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Residues in contact with PHE 201 (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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28B GLU* 3.3 43.1 - - + -
29B GLU 3.2 17.5 - - - +
30B THR* 4.1 0.4 - - - -
31B LEU* 4.2 6.1 - - - +
94B ILE* 3.6 3.1 - - - +
95B HIS* 2.6 80.7 + + + +
97B GLU* 4.4 14.6 - - + -
171B VAL* 4.7 11.0 - - + -
199B ARG* 3.5 42.6 - - - +
200B VAL* 1.3 76.9 - - - +
202B TYR* 1.3 65.9 + - - +
203B ARG* 4.5 8.7 - - - -
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Residues in contact with TYR 202 (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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28B GLU* 3.2 5.2 - - - +
29B GLU* 2.4 62.9 + - + +
31B LEU* 3.7 29.6 - - + -
89B ARG* 3.6 17.7 + - - +
90B GLY 5.2 2.0 - - - -
91B ALA* 3.5 32.5 - - + -
92B HIS 5.4 0.7 - - - +
93B ARG 3.3 23.8 - - - +
94B ILE* 5.0 0.2 - - + -
95B HIS* 4.0 4.0 - - - -
201B PHE* 1.3 77.5 - - - +
203B ARG* 1.3 90.6 + - + +
401B SO4 4.8 0.7 - - - +
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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