Contacts of the helix formed by residues 1177 - 1191 (chain B) in PDB entry 5XA0
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 LYS1177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1090B ARG* 2.6 29.3 - - + +
1093B VAL* 3.7 22.4 - - + +
1096B ALA* 4.8 3.4 - - - +
1132B TRP* 6.1 0.4 - - - -
1176B VAL* 1.3 71.5 - - - +
1178B GLU* 1.3 59.2 + - - +
1179B ILE 3.2 0.9 - - - -
1180B LEU* 2.6 30.5 - - + +
1181B ILE* 3.2 6.1 + - - +
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Residues in contact with GLU1178 (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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1089B GLN* 5.4 2.2 - - - -
1090B ARG* 4.2 5.5 - - - +
1095B GLN* 2.7 41.5 - - + +
1096B ALA* 3.5 16.3 - - - +
1099B GLN* 4.7 2.0 - - + -
1177B LYS* 1.3 71.2 - - - +
1179B ILE* 1.3 59.2 + - - +
1180B LEU 2.9 1.3 - - - -
1181B ILE 4.3 0.2 - - - +
1182B ARG* 2.3 52.5 + - + +
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Residues in contact with ILE1179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089B GLN* 5.0 8.8 - - + +
1125B ILE* 4.1 23.8 - - + +
1128B LYS* 5.3 2.0 - - + -
1129B SER* 3.5 7.2 - - - +
1176B VAL* 3.7 23.5 - - + +
1177B LYS 3.2 2.4 - - - +
1178B GLU* 1.3 78.5 - - - +
1180B LEU* 1.3 53.0 + - - +
1182B ARG* 4.5 0.9 - - - -
1183B LEU* 2.3 41.8 - - - +
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Residues in contact with LEU1180 (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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1129B SER* 3.7 0.9 - - - -
1133B VAL* 2.7 37.0 - - + -
1134B TYR 3.9 6.7 - - - +
1176B VAL 3.6 2.8 + - - +
1177B LYS* 2.6 26.8 + - + +
1179B ILE* 1.3 74.3 - - - +
1181B ILE* 1.3 60.1 + - + +
1183B LEU* 4.0 0.5 - - - +
1184B SER* 2.9 29.6 + - - -
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Residues in contact with ILE1181 (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 ALA* 3.6 29.2 - - + -
1177B LYS 3.2 3.9 + - - +
1180B LEU* 1.3 76.7 - - + +
1182B ARG* 1.3 61.7 + - - +
1184B SER* 3.3 8.8 - - - -
1185B LYS* 2.8 27.5 + - - +
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Residues in contact with ARG1182 (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 ALA* 5.3 0.6 - - - +
1099B GLN* 4.5 16.7 - - + +
1178B GLU* 2.3 42.9 + - + +
1179B ILE* 4.5 1.1 - - - -
1181B ILE* 1.3 72.4 - - - +
1183B LEU* 1.3 53.2 + - - +
1185B LYS* 2.6 31.0 + - - +
1186B LEU* 2.9 11.9 + - - +
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Residues in contact with LEU1183 (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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1122B LEU 5.6 0.7 - - - +
1125B ILE* 4.0 28.7 - - + +
1126B VAL* 4.6 5.6 - - + +
1129B SER* 4.5 3.8 - - - -
1134B TYR 5.7 1.1 - - - -
1179B ILE* 2.3 36.0 + - - +
1180B LEU 4.0 0.7 - - - +
1182B ARG* 1.3 73.4 - - - +
1184B SER* 1.3 62.0 + - - +
1186B LEU* 3.1 10.7 + - - +
1187B CYS* 3.1 22.7 + - - +
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Residues in contact with SER1184 (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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1134B TYR 3.4 22.1 + - - -
1180B LEU 2.9 19.6 + - - -
1181B ILE* 3.3 9.6 - - - -
1183B LEU* 1.3 77.2 - - - +
1185B LYS* 1.3 65.2 + - - +
1186B LEU 3.2 0.2 + - - -
1187B CYS* 3.3 5.7 + - - +
1188B VAL* 3.0 24.9 + - - +
1232B GLU* 5.6 9.6 - - - +
1233B ILE* 6.3 0.7 - - - +
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Residues in contact with LYS1185 (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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1103B LEU* 6.0 8.1 - - + -
1181B ILE 2.8 14.8 + - - +
1182B ARG* 2.6 22.9 + - - +
1184B SER* 1.3 71.8 - - - +
1186B LEU* 1.3 60.5 + - - +
1188B VAL* 3.3 6.7 + - - +
1189B GLN* 3.0 22.9 + - - +
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Residues in contact with LEU1186 (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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1115B ILE* 4.8 23.7 - - + +
1116B LYS* 6.2 2.2 - - + -
1122B LEU* 6.5 0.4 - - + -
1182B ARG 2.9 9.8 + - - +
1183B LEU* 3.1 12.8 + - - +
1185B LYS* 1.3 72.1 - - - +
1187B CYS* 1.3 69.0 + - - +
1189B GLN* 3.0 17.4 + - - +
1190B GLU* 3.2 11.8 + - - +
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Residues in contact with CYS1187 (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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1183B LEU 3.1 9.0 + - - +
1184B SER* 3.8 8.3 - - - +
1186B LEU* 1.3 78.2 - - - +
1188B VAL* 1.3 63.1 + - - +
1190B GLU* 2.9 14.4 + - - +
1191B SER 3.1 2.9 + - - -
1232B GLU* 4.9 12.3 - - + +
1233B ILE* 6.0 2.0 - - - -
1236B LEU* 4.6 2.5 - - + -
1237B ALA* 2.9 38.4 - - + +
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Residues in contact with VAL1188 (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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1184B SER 3.0 17.0 + - - +
1185B LYS* 3.5 7.9 - - - +
1187B CYS* 1.3 76.6 - - - +
1189B GLN* 1.3 65.5 + - - +
1190B GLU 3.3 0.3 + - - -
1191B SER* 3.4 19.3 + - - -
1192B ALA 4.9 0.5 + - - -
1232B GLU* 6.4 1.8 - - + -
1236B LEU* 4.7 6.5 - - + +
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Residues in contact with GLN1189 (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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1105B THR* 4.8 18.8 - - - -
1107B GLN 5.0 7.4 - - - +
1108B ASP* 4.5 5.4 - - - +
1112B TYR* 5.5 2.7 - - - -
1115B ILE* 5.5 9.2 - - + -
1185B LYS 3.0 11.2 + - - +
1186B LEU* 3.0 12.6 + - - +
1188B VAL* 1.3 79.8 - - - +
1190B GLU* 1.3 61.1 + - + +
1191B SER 3.4 0.7 + - - -
1192B ALA 4.7 1.4 + - - -
1193B SER* 3.8 14.7 - - - -
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Residues in contact with GLU1190 (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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1112B TYR* 3.8 32.8 - - + +
1115B ILE* 6.4 1.3 - - + -
1116B LYS* 5.7 6.3 - - + -
1186B LEU 3.2 6.2 + - - +
1187B CYS* 2.9 10.1 + - - +
1189B GLN* 1.3 78.0 - - + +
1191B SER* 1.3 64.2 + - - +
1192B ALA 3.7 0.4 - - - -
1193B SER* 4.6 3.6 - - - -
1197B SER* 3.8 6.5 - - - +
1198B ARG 3.6 13.2 + - - -
1237B ALA* 3.1 18.8 - - + +
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Residues in contact with SER1191 (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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1187B CYS 3.1 2.8 + - - -
1188B VAL* 3.6 14.1 - - - -
1189B GLN 3.3 2.8 - - - -
1190B GLU* 1.3 76.7 - - - +
1192B ALA* 1.3 63.0 + - - +
1193B SER 3.6 0.4 + - - -
1198B ARG* 3.2 27.0 - - - +
1236B LEU 2.7 26.7 - - - -
1237B ALA* 3.5 11.9 - - - +
1239B GLU* 3.5 11.5 + - - +
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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