Contacts of the helix formed by residues 1226 - 1238 (chain B) in PDB entry 2WIN
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 PHE1226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189B LEU* 4.3 26.9 - - + -
1195B LYS* 3.4 57.7 - - + -
1198B TRP* 3.8 25.1 - + - -
1218B LEU* 3.8 21.0 - - + +
1223B ASP* 3.2 25.5 + - - +
1225B ASP* 1.3 80.9 - - - +
1227B VAL* 1.3 61.7 + - - +
1229B PRO* 3.7 12.4 - - + +
1230B VAL* 3.2 20.8 - - + +
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Residues in contact with VAL1227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1215B LEU* 3.7 9.2 - - + -
1218B LEU* 4.0 19.3 - - + -
1219B LEU* 4.0 21.3 - - + -
1223B ASP 3.1 21.3 - - - +
1224B PHE* 3.9 12.3 - - + -
1226B PHE* 1.3 78.3 - - - +
1228B PRO* 1.3 74.7 - - + +
1229B PRO 3.3 0.4 - - - -
1230B VAL* 2.9 17.0 + - - +
1231B VAL* 3.0 32.0 + - + -
1260B TYR* 3.8 20.0 - - + -
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Residues in contact with PRO1228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968B MET* 5.2 14.6 - - + -
970B GLU* 3.4 28.4 - - + +
1224B PHE 3.2 22.0 - - - +
1225B ASP* 4.2 3.4 - - - +
1226B PHE 3.8 1.6 - - - +
1227B VAL* 1.3 94.1 - - + +
1229B PRO* 1.3 69.0 - - + +
1231B VAL* 3.5 2.8 + - + -
1232B ARG* 3.1 28.4 + - - +
1260B TYR* 5.6 3.4 - - + +
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Residues in contact with PRO1229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195B LYS 3.6 20.0 - - - +
1196B ASN* 3.5 15.7 - - + +
1225B ASP 4.5 6.3 - - - +
1226B PHE* 3.7 16.2 - - + +
1227B VAL 3.4 3.8 - - - -
1228B PRO* 1.3 101.0 - - + +
1230B VAL* 1.3 60.1 + - - +
1232B ARG* 3.3 19.7 + - - +
1233B TRP* 3.4 15.2 + - - +
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Residues in contact with VAL1230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195B LYS 4.7 0.7 - - - +
1196B ASN* 3.8 17.4 - - - +
1198B TRP* 3.9 25.4 - - + -
1211B THR* 3.7 26.7 - - + +
1215B LEU* 4.2 25.4 - - + -
1218B LEU* 4.1 7.4 - - + -
1226B PHE* 3.2 25.4 - - + +
1227B VAL 2.9 6.8 + - - +
1229B PRO* 1.3 74.3 - - - +
1231B VAL* 1.3 67.2 + - - +
1233B TRP* 3.1 14.2 + - - +
1234B LEU* 3.3 13.0 + - + +
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Residues in contact with VAL1231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970B GLU* 4.0 11.9 - - + +
971B ASP 5.3 0.2 - - - +
1215B LEU* 3.8 17.5 - - + -
1227B VAL* 3.0 38.1 + - + +
1228B PRO* 4.0 4.3 - - + +
1230B VAL* 1.3 74.8 - - - +
1232B ARG* 1.3 62.9 + - - +
1234B LEU* 3.1 19.9 + - - +
1235B ASN* 3.1 23.1 + - - +
1257B LEU* 4.0 20.0 - - + -
1260B TYR* 3.7 32.8 - - + -
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Residues in contact with ARG1232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970B GLU* 3.0 31.2 + - - +
1228B PRO* 3.1 16.3 + - - +
1229B PRO* 3.3 37.9 + - - +
1230B VAL 3.2 0.2 - - - -
1231B VAL* 1.3 75.9 - - - +
1233B TRP* 1.3 63.8 + - - +
1235B ASN* 3.5 5.6 + - - +
1236B GLU* 3.2 52.3 + - + +
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Residues in contact with TRP1233 (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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1196B ASN* 3.2 48.0 - - - +
1197B ARG* 3.3 37.5 - - + +
1198B TRP 6.3 0.2 - - - -
1199B GLU* 5.7 2.2 - - + -
1207B ASN* 4.7 14.8 - - + -
1208B VAL* 4.6 15.0 - - + -
1211B THR* 3.5 24.7 - - + -
1229B PRO 3.4 7.3 + - - +
1230B VAL 3.1 4.2 + - - +
1232B ARG* 1.3 78.8 - - - +
1234B LEU* 1.3 82.5 + - + +
1236B GLU* 3.6 9.7 + - + +
1237B GLN* 3.1 64.4 + - + +
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Residues in contact with LEU1234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208B VAL* 4.6 16.2 - - + +
1211B THR* 3.6 34.5 - - + +
1212B SER* 5.0 1.8 - - - +
1215B LEU* 3.8 31.2 - - + -
1230B VAL* 3.6 14.1 - - + +
1231B VAL* 3.1 8.1 + - - +
1233B TRP* 1.3 90.3 - - + +
1235B ASN* 1.3 69.7 + - - +
1237B GLN* 3.1 21.5 + - + +
1238B ARG 3.7 2.6 + - - -
1239B TYR* 4.8 2.4 + - - +
1253B VAL* 4.9 11.9 - - + -
1256B ALA* 5.3 3.4 - - + -
1257B LEU* 4.1 19.7 - - + -
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Residues in contact with ASN1235 (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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970B GLU* 4.8 6.7 + - - +
971B ASP 3.0 26.8 + - - +
972B ALA 4.9 8.9 + - - -
973B VAL* 5.3 2.3 - - - +
1231B VAL* 3.1 25.4 + - - +
1232B ARG* 4.1 5.3 - - - +
1233B TRP 3.5 0.2 - - - -
1234B LEU* 1.3 75.4 - - - +
1236B GLU* 1.3 62.8 + - + +
1238B ARG* 3.2 23.3 + - - +
1257B LEU* 3.9 25.8 - - - +
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Residues in contact with GLU1236 (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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1232B ARG* 3.2 41.4 + - + +
1233B TRP* 4.0 9.7 - - + +
1234B LEU 3.2 0.2 - - - -
1235B ASN* 1.3 75.4 - - + +
1237B GLN* 1.3 64.1 + - - +
1238B ARG* 2.9 41.7 + - - +
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Residues in contact with GLN1237 (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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1204B GLN* 4.8 12.1 + - - -
1208B VAL* 5.3 10.4 - - + +
1233B TRP* 3.1 68.3 + - + +
1234B LEU* 3.1 11.6 + - + +
1236B GLU* 1.3 79.1 - - - +
1238B ARG* 1.3 68.9 + - - +
1239B TYR* 3.3 13.1 + - + +
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Residues in contact with ARG1238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234B LEU 3.7 2.2 + - - -
1235B ASN 3.2 16.1 + - - +
1236B GLU* 2.9 39.4 + - - +
1237B GLN* 1.3 81.3 - - - +
1239B TYR* 1.3 58.5 + - - +
1240B TYR* 3.2 43.8 - - + +
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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