Contacts of the helix formed by residues 1091 - 1102 (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 THR1091 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1081B LYS* 3.9 10.8 - - - +
1089B ASP* 2.9 30.9 + - - -
1090B THR* 1.3 73.4 - - - +
1092B THR* 1.3 66.6 + - - +
1094B VAL* 2.9 7.8 + - - +
1095B LEU* 2.9 36.4 + - + +
1199B ASP* 4.5 2.0 + - - +
1243B LEU* 3.5 4.2 - - - +
1268B LEU* 3.9 12.9 - - - +
1271B LEU* 3.5 17.4 - - + +
1272B CYS* 4.2 7.4 - - - -
1275B LEU* 3.8 27.8 - - + -
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Residues in contact with THR1092 (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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1081B LYS* 3.0 21.9 + - - +
1089B ASP 4.8 1.8 + - - -
1090B THR 3.2 1.0 + - - -
1091B THR* 1.3 79.4 - - - +
1093B LEU* 1.3 56.3 + - - +
1095B LEU* 4.4 8.7 - - + -
1096B GLY* 2.9 26.5 + - - +
1097B PRO* 3.9 1.4 - - - +
1108B LYS* 3.7 22.0 - - + -
1120B THR* 3.9 18.6 - - + -
1150B ILE* 3.9 21.9 - - + +
2002B PO4 2.6 28.4 + - - +
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Residues in contact with LEU1093 (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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1090B THR* 2.9 31.1 + - + +
1092B THR* 1.3 77.1 - - + +
1094B VAL* 1.3 58.8 + - - +
1097B PRO* 3.1 22.6 - - - +
1120B THR* 4.6 11.7 - - + +
1123B LYS* 4.3 23.8 - - + -
1124B LEU* 3.5 37.7 - - + -
1150B ILE* 5.9 1.6 - - + -
1252B GLU 4.3 0.4 - - - -
1253B VAL* 4.0 33.0 - - + +
1256B ALA* 3.7 13.5 - - + -
1260B LEU* 4.1 1.2 - - - +
1309B PHE* 3.6 19.9 - - + -
1312B PHE* 5.6 2.5 - - + -
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Residues in contact with VAL1094 (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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1090B THR 4.3 5.8 - - - +
1091B THR 2.9 7.0 + - - +
1093B LEU* 1.3 73.3 - - - +
1095B LEU* 1.3 62.2 + - - +
1096B GLY 3.2 2.8 + - - -
1097B PRO* 3.2 4.7 - - - +
1098B LEU* 3.0 34.7 + - + +
1256B ALA* 3.8 31.6 - - + +
1259B THR* 4.1 23.6 - - + +
1260B LEU* 3.6 28.0 - - + +
1268B LEU* 4.6 7.4 - - + -
1272B CYS* 3.9 24.5 - - + -
1300B ILE* 6.1 2.5 - - + -
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Residues in contact with LEU1095 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081B LYS* 3.8 24.0 - - + -
1091B THR* 2.9 28.4 + - + +
1092B THR* 4.4 6.1 - - + +
1094B VAL* 1.3 77.8 - - - +
1096B GLY* 1.3 71.7 + - - +
1098B LEU* 3.9 11.2 - - - -
1099B VAL* 3.2 25.7 + - + +
1108B LYS* 6.3 1.1 - - + -
1272B CYS* 4.4 13.0 - - + +
1275B LEU* 3.5 34.1 - - + -
1276B GLY 4.1 4.7 - - - +
1279B MET* 3.7 32.5 - - + -
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Residues in contact with GLY1096 (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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1092B THR* 2.9 19.8 + - - -
1095B LEU* 1.3 87.5 - - - +
1097B PRO* 1.3 66.5 - - - +
1099B VAL* 3.5 5.1 - - - +
1100B ALA* 3.4 21.0 + - - +
1106B VAL* 4.0 8.5 - - - +
1148B ILE* 3.5 13.0 - - - +
1150B ILE* 4.5 8.1 - - - -
1279B MET* 5.9 0.2 - - - -
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Residues in contact with PRO1097 (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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1092B THR 3.9 1.1 - - - +
1093B LEU* 3.1 18.6 - - - +
1094B VAL 3.2 4.7 - - - +
1096B GLY* 1.3 88.2 - - - +
1098B LEU* 1.3 65.7 + - - +
1100B ALA* 3.9 2.6 - - + -
1101B SER* 3.1 15.8 + - - -
1148B ILE* 4.0 10.1 - - + -
1150B ILE* 5.2 0.7 - - + -
1260B LEU* 4.8 2.5 - - + -
1305B ALA 4.2 4.4 - - - +
1308B ALA* 3.5 15.9 - - + +
1309B PHE* 3.4 50.9 - - + +
1312B PHE* 3.9 20.0 - - + -
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Residues in contact with LEU1098 (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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1094B VAL* 3.0 22.8 + - + +
1095B LEU* 3.8 8.3 - - - +
1097B PRO* 1.3 76.1 - - - +
1099B VAL* 1.3 65.3 + - + +
1101B SER* 2.5 26.8 + - - -
1102B VAL* 3.8 4.7 + - - +
1260B LEU* 4.6 4.7 - - + +
1272B CYS* 4.1 33.0 - - + +
1273B LEU* 4.5 9.9 - - + -
1296B LEU* 3.9 33.0 - - + +
1299B ALA* 4.6 2.0 - - + -
1300B ILE* 3.8 30.5 - - + -
1305B ALA* 4.0 15.7 - - + -
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Residues in contact with VAL1099 (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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1095B LEU* 3.2 21.1 + - + +
1096B GLY 3.5 5.6 - - - +
1098B LEU* 1.3 75.4 - - + +
1100B ALA* 1.3 64.1 + - - +
1102B VAL* 3.0 23.2 + - - +
1104B VAL* 3.5 17.4 + - + +
1106B VAL* 3.9 17.0 - - + -
1276B GLY* 3.7 37.9 - - - +
1279B MET* 4.0 22.2 - - + -
1280B VAL* 4.4 7.9 - - + -
1296B LEU* 4.1 15.9 - - + -
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Residues in contact with ALA1100 (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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1096B GLY 3.4 15.8 + - - +
1097B PRO* 3.9 5.2 - - + +
1098B LEU 3.2 0.8 - - - -
1099B VAL* 1.3 81.0 - - - +
1101B SER* 1.3 62.1 + - - +
1102B VAL 3.2 0.4 + - - -
1103B GLY* 3.6 9.2 + - - -
1104B VAL 3.4 13.6 - - - +
1106B VAL* 4.1 2.7 - - + -
1146B ASN 5.2 4.3 - - - +
1147B GLY* 3.7 21.4 - - - +
1148B ILE* 3.9 19.7 - - + -
1308B ALA* 5.2 2.0 - - + -
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Residues in contact with SER1101 (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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1097B PRO 3.1 11.9 + - - -
1098B LEU 2.5 21.6 + - - -
1100B ALA* 1.3 79.4 - - - +
1102B VAL* 1.3 56.4 + - - +
1103B GLY 3.3 2.8 + - - -
1299B ALA* 3.6 20.0 - - - +
1304B ALA* 3.5 33.4 - - - +
1305B ALA* 4.0 3.0 - - - -
1308B ALA* 3.7 8.3 - - - +
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Residues in contact with VAL1102 (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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1099B VAL* 3.0 21.1 - - - +
1101B SER* 1.3 88.8 - - - +
1103B GLY* 1.3 55.3 + - - +
1104B VAL* 4.1 3.4 - - + -
1280B VAL* 3.9 27.6 - - + -
1285B LYS* 4.5 11.3 - - - +
1295B LEU* 3.8 45.5 - - + +
1296B LEU* 4.1 10.5 - - + -
1299B ALA* 3.9 10.5 - - + -
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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