Contacts of the helix formed by residues 1052 - 1063 (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 GLU1052 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051B THR* 1.3 73.1 - - - +
1053B GLU* 1.3 58.6 + - - +
1055B THR* 3.4 7.2 + - - -
1056B ALA* 3.0 29.9 + - - +
1220B VAL* 4.0 42.0 - - - +
1223B ASP* 4.2 6.7 - - - +
1224B ILE* 5.0 2.2 - - - +
1227B ARG* 2.7 43.5 + - - +
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Residues in contact with GLU1053 (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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1018B LYS* 6.0 2.8 - - + +
1051B THR* 3.1 9.7 + - - +
1052B GLU* 1.3 76.8 - - - +
1054B GLU* 1.3 65.8 + - + +
1056B ALA* 3.4 6.9 + - - +
1057B ALA* 3.1 23.5 + - + +
1227B ARG* 5.8 0.7 - - - +
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Residues in contact with GLU1054 (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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1010B LYS* 2.8 28.3 + - - -
1015B ALA* 3.4 22.4 - - + +
1016B LEU 3.0 32.6 + - - +
1021B ILE* 3.6 12.7 - - + +
1050B MET* 3.3 26.0 - - + +
1051B THR* 2.8 42.9 + - - +
1053B GLU* 1.3 77.0 - - + +
1055B THR* 1.3 63.9 + - - +
1057B ALA* 3.2 4.5 + - - +
1058B LEU* 3.0 23.9 + - - +
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Residues in contact with THR1055 (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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1050B MET* 3.9 8.9 + - - +
1051B THR 2.8 18.8 + - - -
1052B GLU* 3.6 7.2 - - - -
1054B GLU* 1.3 77.4 - - - +
1056B ALA* 1.3 59.9 + - - +
1058B LEU* 3.4 7.2 + - - +
1059B THR* 2.8 29.6 + - - +
1177B ILE* 6.2 0.2 - - + -
1178B PRO* 3.7 41.2 - - + +
1181B ALA* 4.1 17.0 - - + -
1182B SER* 4.2 0.2 - - - -
1220B VAL* 4.4 8.3 - - + +
1224B ILE* 4.3 12.1 - - + -
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Residues in contact with ALA1056 (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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1052B GLU 3.0 16.4 + - - +
1053B GLU* 3.8 6.3 - - - +
1055B THR* 1.3 72.5 - - - +
1057B ALA* 1.3 66.8 + - - +
1059B THR* 3.3 7.5 + - - -
1060B MET* 3.0 31.8 + - + +
1224B ILE* 4.7 12.9 - - + +
1227B ARG* 4.4 17.0 - - - +
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Residues in contact with ALA1057 (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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1018B LYS* 4.3 30.3 - - + +
1021B ILE* 4.1 17.8 - - + +
1022B GLU* 4.9 4.3 - - + +
1053B GLU* 3.1 15.2 + - + +
1054B GLU* 3.2 8.7 + - - +
1056B ALA* 1.3 77.5 - - - +
1058B LEU* 1.3 54.9 + - - +
1060B MET* 3.5 5.3 + - - +
1061B ALA* 2.9 29.5 + - - +
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Residues in contact with LEU1058 (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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1021B ILE* 3.7 23.5 - - + +
1024B ILE* 6.5 0.2 - - + -
1025B VAL* 3.8 18.8 - - + -
1038B MET* 6.3 3.1 - - + -
1045B ILE* 5.5 1.8 - - + -
1050B MET* 4.2 22.2 - - + -
1054B GLU 3.0 12.4 + - - +
1055B THR* 3.6 9.2 - - - +
1056B ALA 3.3 0.2 - - - -
1057B ALA* 1.3 71.7 - - - +
1059B THR* 1.3 66.3 + - - +
1061B ALA* 3.1 4.7 + - - +
1062B MET* 3.1 36.8 + - - +
1164B LEU* 5.5 7.0 - - + -
1178B PRO 4.1 7.6 - - - +
1179B LEU* 4.2 18.8 - - + -
1182B SER* 3.4 24.9 - - - +
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Residues in contact with THR1059 (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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1055B THR 2.8 18.3 + - - -
1056B ALA* 3.3 11.3 + - - -
1058B LEU* 1.3 80.4 - - - +
1060B MET* 1.3 64.7 + - - +
1062B MET* 3.4 1.5 + - - -
1063B VAL* 3.1 24.4 + - - +
1181B ALA 4.7 0.2 - - - -
1182B SER* 3.3 24.9 - - - +
1185B MET* 3.9 12.8 - - + -
1186B SER* 3.7 30.7 - - - +
1189B ILE* 4.0 16.6 - - + -
1224B ILE* 4.1 14.7 - - + +
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Residues in contact with MET1060 (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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1022B GLU* 5.6 1.3 - - - +
1056B ALA* 3.0 20.5 + - + +
1057B ALA* 4.0 5.2 - - - +
1059B THR* 1.3 79.0 - - - +
1061B ALA* 1.3 60.4 + - - +
1063B VAL* 3.1 22.9 + - + +
1064B GLN* 2.8 56.4 + - + +
1068B MET* 4.9 7.2 - - + -
1189B ILE* 4.0 30.1 - - + -
1224B ILE* 6.1 1.3 - - - -
1228B VAL* 4.6 16.2 - - + -
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Residues in contact with ALA1061 (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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1021B ILE* 4.5 1.3 - - + -
1022B GLU* 4.1 21.0 + - + -
1025B VAL* 3.7 31.9 - - + +
1057B ALA 2.9 18.3 + - - +
1058B LEU* 3.1 7.4 + - - +
1060B MET* 1.3 73.9 - - - +
1062B MET* 1.3 62.1 + - - +
1064B GLN* 3.2 15.0 + - - +
1065B SER* 3.1 21.0 + - - -
6001B MES 4.4 5.3 - - - +
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Residues in contact with MET1062 (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* 4.1 11.9 - - + -
1058B LEU* 3.1 28.7 + - - +
1059B THR 3.7 7.0 - - - +
1061B ALA* 1.3 72.5 - - - +
1063B VAL* 1.3 62.7 + - - +
1065B SER* 2.6 24.9 + - - -
1158B THR* 3.5 13.4 - - - +
1160B ALA* 4.0 19.7 - - + -
1161B ASP* 3.3 44.4 - - + +
1164B LEU* 4.5 19.7 - - + -
1182B SER* 4.0 16.2 - - - +
1183B SER* 4.2 3.8 - - - -
1186B SER* 3.6 15.0 - - - +
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Residues in contact with VAL1063 (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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1059B THR 3.1 18.5 + - - +
1060B MET* 3.1 17.8 + - + +
1062B MET* 1.3 75.9 - - - +
1064B GLN* 1.3 61.0 + - + +
1065B SER 3.1 5.4 + - - -
1066B GLY* 3.1 21.0 + - - +
1067B GLU* 4.2 2.3 + - - -
1068B MET* 3.9 32.0 + - + +
1158B THR* 4.2 8.4 - - - +
1186B SER* 3.6 28.5 - - - +
1189B ILE* 4.0 20.6 - - + -
1190B ALA* 4.4 12.7 - - + +
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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