Contacts of the strand formed by residues 181 - 188 (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 GLY 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B PHE* 3.6 11.9 - - - -
86B ILE 3.1 14.4 - - - -
88B ARG 4.0 4.3 - - - -
125B GLU* 3.3 8.9 - - - +
126B ALA 2.8 35.3 + - - +
179B ARG* 2.9 6.3 + - - +
180B SER* 1.3 80.0 + - - +
182B PHE* 1.3 61.5 + - - +
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Residues in contact with PHE 182 (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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31B LEU* 4.7 1.3 - - + -
85B PHE* 3.7 4.5 - - - -
86B ILE* 2.8 71.4 + - + +
87B ARG 4.6 0.2 - - - -
88B ARG* 4.5 16.2 - - + -
94B ILE* 3.8 29.8 - - + -
123B TYR* 4.9 2.9 - - + -
124B TYR 3.2 17.9 - - - +
125B GLU* 3.9 11.9 - - + +
126B ALA 4.4 0.9 - - - +
174B PHE* 4.0 17.9 - + - -
177B VAL* 4.9 8.3 - - + -
181B GLY* 1.3 78.4 - - - +
183B TYR* 1.3 66.2 + - - +
184B LEU* 3.9 19.7 - - + -
200B VAL* 3.7 24.0 - - + -
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Residues in contact with TYR 183 (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 ARG* 4.2 10.3 - - + -
83B THR* 3.5 25.6 - - - +
84B LYS* 3.7 6.5 - - - -
85B PHE* 3.6 32.8 - + + -
86B ILE* 5.1 0.2 - - - -
123B TYR* 3.2 8.8 - - - +
124B TYR* 2.9 47.0 + + - +
126B ALA* 4.1 14.8 - - + -
129B ASP* 2.6 27.3 + - - -
130B SER* 3.1 17.4 + - - -
131B ALA* 3.1 26.7 + - + -
136B PRO* 5.5 0.9 - - + -
143B TRP* 3.6 21.5 - + + -
182B PHE* 1.3 77.1 - - - +
184B LEU* 1.3 64.9 + - - +
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Residues in contact with LEU 184 (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* 4.6 2.5 - - + -
82B ARG* 3.4 7.3 - - - +
83B THR* 3.0 43.5 + - + +
86B ILE* 4.4 9.2 - - + +
96B VAL* 3.6 33.9 - - + -
121B LEU* 4.3 6.1 - - + -
122B TYR 3.3 6.5 - - - +
123B TYR* 3.7 18.6 - - + -
143B TRP* 3.8 2.0 - - - -
174B PHE* 3.8 17.5 - - + -
182B PHE* 3.9 9.0 - - + -
183B TYR* 1.3 80.8 - - - +
185B ALA* 1.3 60.5 + - - +
186B PHE* 4.1 10.5 - - + -
198B VAL* 4.2 8.5 - - + -
200B VAL* 3.7 22.0 - - + -
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Residues in contact with ALA 185 (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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80B TRP* 3.6 32.8 - - + -
81B LEU 3.2 9.0 - - - +
82B ARG* 4.8 0.9 - - + -
120B ASN 3.5 1.2 - - - +
121B LEU* 3.4 6.1 - - - +
122B TYR* 2.8 39.8 + - + -
143B TRP* 3.5 25.4 - - + -
184B LEU* 1.3 75.1 - - - +
186B PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 186 (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* 4.0 5.4 - + - -
51B TRP* 3.6 14.5 + - + -
79B ASN 3.6 1.2 - - - +
80B TRP* 3.4 4.6 - - - -
81B LEU* 2.8 53.9 + - + +
83B THR* 3.8 24.2 - - + -
98B MET* 4.2 17.0 - - + -
119B PHE* 3.8 22.9 - + + -
120B ASN 3.3 5.4 - - - +
121B LEU* 3.4 29.2 - - + -
184B LEU* 4.1 9.4 - - + -
185B ALA* 1.3 74.7 - - - +
187B GLN* 1.3 59.4 + - - +
195B LEU* 3.7 23.6 - - + -
198B VAL* 3.9 26.5 - - + -
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Residues in contact with GLN 187 (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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51B TRP* 4.6 0.9 - - - -
78B ASN* 2.8 28.1 + - - +
79B ASN 3.2 3.4 - - - -
80B TRP* 3.5 21.9 - - + +
119B PHE* 3.4 9.5 - - - +
120B ASN* 2.8 47.7 + - + +
122B TYR* 2.8 37.2 + - + -
185B ALA 4.1 0.2 + - - -
186B PHE* 1.3 74.1 - - - +
188B ASP* 1.3 65.4 + - - +
189B TYR* 3.7 12.9 - - + +
411B SO4 3.5 26.1 + - - -
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Residues in contact with ASP 188 (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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51B TRP* 4.0 11.3 - - + +
69B VAL* 3.5 30.0 - - + +
71B ASN 5.4 0.7 + - - -
77B GLN* 5.0 0.2 - - - +
78B ASN* 3.5 2.8 + - - -
79B ASN* 2.8 62.8 + - + +
118B THR 4.9 1.0 - - - +
119B PHE* 4.8 2.9 - - - -
187B GLN* 1.3 75.6 - - - +
189B TYR* 1.3 66.7 + - - +
190B GLY* 3.2 8.9 + - - -
191B GLY* 2.9 32.7 + - - +
193B MET* 3.7 13.7 - - + +
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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