Contacts of the strand formed by residues 181 - 186 (chain A) in PDB entry 2W2Q
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 GLU 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A LEU 3.6 2.6 + - - +
180A VAL* 1.3 75.3 - - - +
182A VAL* 1.3 62.8 + - - +
183A TYR* 3.9 26.5 - - + +
246A SER* 2.7 47.2 + - - +
247A MET* 3.5 7.4 + - - -
248A ARG* 3.7 38.3 + - + +
282A PRO 3.0 12.2 + - - +
283A LEU* 3.7 8.0 - - + -
284A VAL* 3.0 26.0 + - - +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A VAL* 4.4 3.8 - - + -
181A GLU* 1.3 77.2 - - - +
183A TYR* 1.3 69.8 + - - +
234A VAL* 4.2 11.9 - - + -
245A ALA* 4.6 9.0 - - + -
246A SER 3.3 16.9 + - - +
247A MET* 3.2 27.8 - - + +
248A ARG 2.8 24.9 + - - +
284A VAL* 3.3 23.6 - - + +
286A LEU* 4.9 8.1 - - + -
393A ALA* 4.9 3.6 - - + +
397A ALA* 3.9 28.9 - - + -
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Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLU* 3.9 12.8 - - + +
182A VAL* 1.3 78.1 - - - +
184A LEU* 1.3 56.9 + - - +
185A LEU* 4.1 0.9 - - - -
203A THR* 5.3 2.0 - - + -
248A ARG* 3.2 48.3 + - + +
250A LEU* 3.8 19.7 - - + -
270A PHE* 5.5 1.8 - + - -
271A ILE* 3.8 32.8 - - + -
274A SER* 3.4 31.7 - - - -
278A GLN* 5.1 3.3 - - - +
283A LEU* 3.7 44.7 - - + +
284A VAL 2.7 14.8 + - - +
285A VAL* 3.6 3.9 - - + +
286A LEU* 2.7 35.2 + - - +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A VAL 4.0 0.4 + - - -
183A TYR* 1.3 73.4 - - - +
185A LEU* 1.3 55.9 + - - +
186A ASP* 3.8 17.9 - - + -
189A ILE* 4.5 8.5 - - + -
200A VAL* 6.3 0.4 - - + -
227A GLY* 3.7 25.4 - - - +
230A LEU* 4.5 3.4 - - + -
231A ALA* 4.1 15.7 - - + +
247A MET* 4.0 20.6 - - + -
248A ARG 2.9 11.6 + - - +
249A SER* 3.3 10.0 - - - -
250A LEU* 2.7 34.7 + - - +
286A LEU* 3.6 30.3 - - + -
288A PRO* 3.7 24.9 - - + -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TYR 4.9 0.2 - - - +
184A LEU* 1.3 71.7 - - - +
186A ASP* 1.3 58.3 + - - +
250A LEU* 3.5 16.2 - - + -
252A VAL* 3.7 32.1 - - + -
264A THR* 4.2 11.0 - - + +
267A GLY* 3.9 28.3 - - - -
268A LEU* 4.0 7.9 - - + +
271A ILE* 3.6 15.9 - - + -
285A VAL* 3.6 31.6 - - + -
286A LEU 3.3 9.2 + - - +
287A LEU* 4.0 15.3 - - + -
288A PRO* 3.2 21.8 - - - +
289A LEU* 3.9 8.9 - - + +
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Residues in contact with ASP 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 3.8 21.7 - - + -
185A LEU* 1.3 72.8 - - - +
187A THR* 1.3 79.2 + - - +
226A HIS* 2.7 34.4 + - - -
227A GLY* 3.0 19.5 + - - -
230A LEU* 4.1 2.9 - - - -
250A LEU 3.1 6.5 + - - -
251A ARG* 3.4 1.9 - - - -
252A VAL* 2.9 25.6 + - - +
253A LEU* 3.2 21.6 + - - +
288A PRO* 2.9 26.6 - - - +
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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
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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