Contacts of the strand formed by residues 181 - 186 (chain B) in PDB entry 2PMW
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B SER 6.0 0.4 - - - +
179B LEU 4.3 0.4 + - - -
180B VAL* 1.3 80.5 - - - +
182B VAL* 1.3 64.6 + - - +
183B TYR* 4.1 8.1 + - + -
246B SER* 3.7 20.4 - - - +
248B ARG* 2.7 48.2 + - + -
280B VAL* 3.7 31.4 - - + +
282B PRO 3.3 5.7 + - - -
283B LEU* 3.5 20.0 - - + +
284B VAL 3.0 24.3 + - - +
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Residues in contact with VAL 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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180B VAL* 4.5 2.5 - - + +
181B GLU* 1.3 77.7 - - - +
183B TYR* 1.3 72.1 + - - +
234B VAL* 4.3 23.8 - - + -
245B ALA* 5.1 5.6 - - + -
246B SER 2.9 15.3 + - - +
247B MET* 3.0 19.9 - - + +
248B ARG 2.8 25.2 + - - +
284B VAL* 3.2 24.7 - - + +
286B LEU* 4.6 9.6 - - + -
393B ALA* 4.7 4.7 - - + +
397B ALA* 4.2 25.4 - - + -
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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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181B GLU* 4.3 4.5 + - + -
182B VAL* 1.3 78.6 - - - +
184B LEU* 1.3 58.6 - - - +
185B LEU* 4.7 1.6 - - + -
203B THR* 4.6 4.7 - - + -
248B ARG* 3.2 43.9 + - + -
250B LEU* 3.5 27.8 - - + -
270B PHE* 5.4 3.8 - + - -
271B ILE* 3.7 50.4 + - + -
274B SER* 3.9 20.6 - - - -
275B GLN 5.4 0.5 + - - -
283B LEU* 3.9 31.8 - - + +
284B VAL 2.8 14.0 + - - +
285B VAL* 4.3 5.4 - - + -
286B LEU* 2.8 31.6 + - - +
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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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183B TYR* 1.3 75.3 - - - +
185B LEU* 1.3 58.1 + - - +
186B ASP* 4.0 15.3 - - + -
189B ILE* 4.7 8.3 - - + -
227B GLY* 3.7 24.2 - - - +
230B LEU* 4.4 6.3 - - + -
231B ALA* 4.2 9.9 - - + +
247B MET* 3.9 25.4 - - + -
248B ARG 2.8 12.1 + - - +
249B SER* 3.3 9.4 - - - -
250B LEU* 2.7 34.3 + - - +
286B LEU* 3.5 35.4 - - + -
288B PRO* 4.0 19.1 - - + -
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Residues in contact with LEU 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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183B TYR* 4.7 0.2 - - + -
184B LEU* 1.3 76.1 - - - +
186B ASP* 1.3 60.2 + - - +
250B LEU* 3.6 16.6 - - + -
252B VAL* 3.8 24.9 - - + -
264B THR* 4.2 11.2 - - + +
267B GLY* 4.2 5.4 - - - -
268B LEU* 4.1 26.5 - - + +
271B ILE* 3.7 15.0 - - + -
285B VAL* 3.6 30.7 - - + -
286B LEU 3.2 8.0 + - - +
287B LEU* 3.9 22.9 - - + -
288B PRO* 3.0 23.5 - - - +
289B LEU* 3.7 8.7 - - + +
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Residues in contact with ASP 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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184B LEU* 3.8 18.9 + - + -
185B LEU* 1.3 74.3 - - - +
187B THR* 1.3 78.4 + - - +
226B HIS* 2.6 44.4 + - - +
227B GLY* 2.9 23.3 + - - -
230B LEU* 3.9 1.6 - - - -
250B LEU 3.1 6.7 + - - -
251B ARG* 3.4 2.3 - - - -
252B VAL* 2.9 24.6 + - - +
253B LEU* 3.1 24.4 + - - +
288B PRO* 3.1 15.4 - - + +
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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