Contacts of the helix formed by residues 1159 - 1169 (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 PRO1159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1029B THR* 3.8 21.3 - - + -
1065B SER* 3.1 23.1 - - - +
1066B GLY* 3.6 14.4 - - - +
1154B THR* 5.0 5.4 - - - -
1156B ASP* 4.5 13.7 - - - +
1157B LEU 3.6 2.2 - - - +
1158B THR* 1.3 90.0 - - - +
1160B ALA* 1.3 59.7 + - - +
1162B LYS* 3.3 12.0 + - + +
1163B LYS* 3.2 26.9 + - + +
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Residues in contact with ALA1160 (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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1025B VAL* 3.7 22.4 - - + -
1028B TYR* 4.5 5.1 - - + -
1029B THR* 3.2 25.2 + - - +
1062B MET* 4.0 13.9 - - + -
1065B SER* 3.3 13.7 + - - +
1158B THR 3.2 0.6 - - - -
1159B PRO* 1.3 78.3 - - - +
1161B ASP* 1.3 60.2 + - - +
1163B LYS* 3.4 4.8 + - - +
1164B LEU* 2.9 31.8 + - - +
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Residues in contact with ASP1161 (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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1062B MET* 3.3 26.4 - - + +
1153B GLN* 3.3 13.3 + - - +
1158B THR* 3.3 21.8 + - - +
1160B ALA* 1.3 74.8 - - - +
1162B LYS* 1.3 60.7 + - - +
1164B LEU* 4.5 3.0 - - - +
1165B TYR* 2.8 41.2 + - - +
1168B ARG* 4.8 0.7 + - - -
1183B SER* 2.8 36.3 + - - -
1186B SER* 4.1 1.8 - - - +
1187B LYS* 3.0 31.9 + - - +
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Residues in contact with LYS1162 (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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1133B GLU* 4.9 9.5 + - - -
1153B GLN* 3.7 18.5 + - + +
1154B THR* 1.2 161.9 + - + -
1158B THR 3.2 10.4 + - - +
1159B PRO* 3.3 12.8 - - + +
1161B ASP* 1.3 79.1 + - - +
1163B LYS* 1.3 62.8 + - + +
1165B TYR* 3.8 2.1 - - - +
1166B ALA* 3.4 20.6 + - - +
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Residues in contact with LYS1163 (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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1028B TYR* 2.6 65.5 + - + +
1029B THR* 4.2 22.3 + - + +
1031B GLY* 4.4 9.7 - - - -
1033B ILE 5.2 0.8 + - - -
1035B ASP* 5.0 4.8 + - - -
1159B PRO* 3.2 13.3 + - + +
1160B ALA 3.8 3.8 - - - +
1161B ASP 3.2 0.2 - - - -
1162B LYS* 1.3 77.7 - - + +
1164B LEU* 1.3 65.6 + - - +
1166B ALA* 3.2 7.8 + - - +
1167B LEU* 3.1 17.5 + - - +
1368B LYS* 6.1 0.5 - - - -
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Residues in contact with LEU1164 (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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1025B VAL* 6.5 0.7 - - + -
1028B TYR* 3.7 11.3 - - + -
1038B MET* 4.0 39.5 - - + -
1042B ALA* 5.0 9.0 - - + -
1058B LEU* 5.5 6.5 - - + -
1062B MET* 4.5 21.3 - - + -
1160B ALA 2.9 21.9 + - - +
1161B ASP* 4.3 3.4 - - - +
1163B LYS* 1.3 72.4 - - - +
1165B TYR* 1.3 57.3 + - - +
1167B LEU* 3.4 8.9 + - + -
1168B ARG* 2.9 58.1 + - + +
1179B LEU* 4.7 16.2 - - + -
1182B SER* 6.0 0.4 - - - +
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Residues in contact with TYR1165 (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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1082B HIS* 6.0 0.2 - - - -
1111B GLY* 3.8 10.2 - - - -
1112B ARG* 2.7 46.7 + - + -
1113B GLY 3.9 11.4 - - - -
1114B LEU* 3.7 26.1 - - + +
1118B GLY 5.3 0.7 + - - -
1119B GLY* 5.3 0.5 - - - -
1153B GLN* 4.1 9.9 - - - +
1161B ASP* 2.8 29.2 + - - +
1162B LYS 3.8 3.4 - - - +
1164B LEU* 1.3 74.0 - - - +
1166B ALA* 1.3 65.6 + - - +
1168B ARG* 3.4 15.2 + - - +
1169B ASP* 3.1 24.1 + - + +
1183B SER* 3.7 16.8 - - - -
1187B LYS* 4.2 8.7 - - - -
5001B URA 3.3 32.4 + + - -
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Residues in contact with ALA1166 (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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1162B LYS 3.4 11.0 + - - +
1163B LYS* 3.2 10.2 + - - +
1165B TYR* 1.3 83.2 - - + +
1167B LEU* 1.3 62.4 + - - +
1169B ASP* 3.4 19.7 - - - +
1170B VAL* 3.6 13.2 - - - +
1368B LYS* 4.1 16.8 - - + +
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Residues in contact with LEU1167 (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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36A TYR* 3.8 35.4 - - + -
1028B TYR* 3.5 19.3 - - - +
1035B ASP* 3.7 30.1 - - - +
1038B MET* 3.9 20.0 - - + -
1039B SER* 3.9 10.1 - - - +
1042B ALA* 6.2 0.4 - - + -
1163B LYS 3.1 15.0 + - - +
1164B LEU* 3.7 9.9 - - + +
1166B ALA* 1.3 74.9 - - - +
1168B ARG* 1.3 66.6 + - - +
1170B VAL* 3.3 8.4 + - - +
1171B THR* 3.0 32.1 + - + +
1173B THR* 5.9 0.2 - - - +
1368B LYS* 4.1 11.4 - - + +
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Residues in contact with ARG1168 (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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1042B ALA* 5.1 1.6 - - + -
1114B LEU* 4.1 6.3 - - + +
1161B ASP* 4.8 0.6 + - - -
1164B LEU* 2.9 47.8 + - + +
1165B TYR* 3.8 21.9 - - - +
1167B LEU* 1.3 75.4 - - + +
1169B ASP* 1.3 64.5 + - - +
1170B VAL 3.2 0.7 + - - -
1171B THR 3.2 9.5 + - - -
1172B ALA 3.4 9.9 + - - -
1173B THR* 3.3 38.7 + - - +
1174B VAL* 3.1 36.2 + - + +
1179B LEU* 3.7 27.0 + - + +
1180B ILE* 3.9 4.6 - - - +
1183B SER* 3.6 28.3 + - - -
5001B URA 2.8 27.3 + - - -
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Residues in contact with ASP1169 (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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4A VAL* 4.9 5.0 - - - +
1113B GLY 3.4 18.2 - - - +
1114B LEU* 3.5 16.9 + - + +
1115B GLY* 2.9 34.1 + - - +
1165B TYR* 3.1 14.2 + - + +
1166B ALA* 3.4 15.4 - - - +
1168B ARG* 1.3 78.3 - - - +
1170B VAL* 1.3 71.2 + - - +
1171B THR 3.8 0.3 + - - -
1172B ALA* 4.5 2.9 + - - -
1174B VAL* 4.0 3.8 - - - +
1365B ARG* 4.2 29.0 + - - +
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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