Contacts of the strand formed by residues 1231 - 1238 (chain B) in PDB entry 1BRW
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 ARG1231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077B VAL* 3.7 23.4 - - - +
1194B ASP* 2.9 19.2 + - + +
1195B ALA* 3.4 14.2 - - + +
1196B ILE 2.8 26.1 + - - +
1229B GLY 5.7 1.1 - - - +
1230B ARG* 1.3 68.5 - - - +
1232B THR* 1.3 58.0 + - - +
1233B MET 4.1 0.2 + - - -
1282B LEU* 3.2 44.1 + - + +
1284B GLU* 3.1 29.5 + - - +
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Residues in contact with THR1232 (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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1185B MET* 4.5 3.4 - - + -
1196B ILE* 3.6 27.2 - - + +
1198B LEU* 4.2 12.8 - - + -
1221B MET 4.2 5.2 - - - +
1222B VAL* 3.5 39.7 - - - +
1225B GLY* 3.3 20.7 - - - -
1226B LYS* 4.2 6.6 - - - +
1230B ARG* 2.9 20.8 + - - +
1231B ARG* 1.3 71.5 - - - +
1233B MET* 1.3 62.6 + - - +
1433B VAL* 3.4 18.7 - - - +
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Residues in contact with MET1233 (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 ILE 3.0 13.0 + - - +
1197B VAL* 4.3 6.5 - - + -
1198B LEU* 3.0 25.1 + - - +
1222B VAL* 4.0 5.2 - - - -
1232B THR* 1.3 74.8 - - - +
1234B ALA* 1.3 68.4 + - - +
1235B VAL* 3.6 22.7 - - + -
1278B HIS* 3.5 37.2 - - + -
1282B LEU* 3.8 31.0 - - + -
1431B THR* 3.6 31.4 - - + -
1432B ILE 3.4 10.1 - - - +
1433B VAL* 4.2 16.2 - - + +
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Residues in contact with ALA1234 (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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1198B LEU* 3.3 22.4 - - + +
1200B VAL* 4.2 4.9 - - + -
1218B ALA* 4.1 21.3 - - + -
1222B VAL* 3.8 17.5 - - + -
1233B MET* 1.3 78.6 - - - +
1235B VAL* 1.3 64.1 + - - +
1236B ILE 4.3 0.4 + - - -
1431B THR* 3.5 2.4 - - - -
1432B ILE* 2.7 39.8 + - + +
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Residues in contact with VAL1235 (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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1197B VAL* 4.9 2.5 - - + -
1198B LEU 2.8 8.9 + - - +
1199B ASP* 3.6 2.8 - - - +
1200B VAL* 2.8 26.2 + - - +
1233B MET* 3.6 21.3 - - + -
1234B ALA* 1.3 77.9 - - - +
1236B ILE* 1.3 66.6 + - - +
1237B SER* 3.6 4.1 + - - +
1274B THR* 4.7 4.9 - - + -
1275B LEU* 3.9 29.8 - - + -
1278B HIS* 4.0 15.9 - - + +
1428B ILE* 3.9 32.5 - - + -
1430B GLU 3.7 11.4 - - - +
1431B THR* 4.5 4.5 - - + +
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Residues in contact with ILE1236 (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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1200B VAL* 3.2 23.1 - - + +
1202B THR* 4.0 17.0 - - + -
1211B LEU* 3.9 24.7 - - + -
1214B ALA* 4.2 5.4 - - + +
1215B ARG* 3.8 30.3 - - + +
1218B ALA* 4.5 4.3 - - + -
1235B VAL* 1.3 76.2 - - - +
1237B SER* 1.3 55.0 + - - +
1428B ILE* 3.9 0.5 - - - -
1429B TYR* 2.9 28.5 + - + +
1430B GLU* 3.2 30.8 + - + +
1432B ILE* 3.8 28.3 - - + -
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Residues in contact with SER1237 (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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1199B ASP* 2.6 26.5 + - - -
1200B VAL 3.1 5.2 + - - +
1201B LYS* 3.4 21.2 + - - +
1202B THR* 3.1 28.1 + - - +
1235B VAL* 3.6 3.3 + - - -
1236B ILE* 1.3 75.0 - - - +
1238B ASP* 1.3 62.2 + - - +
1271B LEU* 3.8 21.8 - - - -
1427B LEU* 3.2 15.3 - - - -
1428B ILE* 4.2 4.7 - - - +
1429B TYR* 4.2 3.4 - - - -
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Residues in contact with ASP1238 (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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1201B LYS* 4.8 3.0 + - - +
1202B THR* 3.6 7.4 - - - +
1203B GLY* 5.0 0.5 - - - -
1237B SER* 1.3 75.1 + - - +
1239B MET* 1.3 74.0 + - - +
1240B SER* 2.9 33.4 + - - -
1241B GLN* 4.9 4.9 + - - +
1243B LEU* 5.5 4.5 - - - +
1425B PRO* 3.8 16.0 - - - +
1426B PRO 3.3 22.8 - - - +
1427B LEU* 3.0 20.8 + - + +
1429B TYR* 3.0 28.3 + - + -
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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