Contacts of the helix formed by residues 1160 - 1170 (chain B) in PDB entry 1XTB
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 ASP1160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A ASN* 4.3 7.1 + - - -
1153B ASN* 4.5 3.6 - - - +
1155B GLY 3.5 16.8 - - - +
1156B ILE* 3.7 7.9 - - - -
1157B GLY 2.9 9.3 + - - +
1158B GLY 3.1 2.0 + - - -
1159B SER* 1.3 80.5 - - - +
1161B LEU* 1.3 80.3 + - - +
1162B GLY 3.3 1.3 - - - -
1163B PRO* 3.1 9.6 - - - +
1164B LEU* 3.1 34.3 + - - +
1182B PHE* 3.8 24.4 - - - +
1183B VAL 4.6 1.2 - - - +
1184B SER* 3.7 25.9 + - - -
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Residues in contact with LEU1161 (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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389A ALA* 4.9 5.8 - - + -
1157B GLY* 3.0 15.0 + - - +
1158B GLY* 5.6 0.2 - - - -
1160B ASP* 1.3 85.0 - - - +
1162B GLY* 1.3 57.1 + - - +
1164B LEU* 4.3 13.5 - - + -
1165B MET* 2.8 36.8 + - + +
1346B ARG* 4.7 15.0 - - + +
1349B ALA* 3.5 33.4 - - + +
1350B TYR* 3.9 25.6 - - + +
1353B GLN* 3.4 26.9 - - + +
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Residues in contact with GLY1162 (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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1158B GLY* 4.6 6.3 + - - -
1160B ASP 3.3 0.2 - - - -
1161B LEU* 1.3 79.1 - - - +
1163B PRO* 1.3 71.4 - - - +
1165B MET* 3.7 1.0 - - - +
1166B VAL* 3.0 26.8 + - - +
1275B LEU* 4.0 16.4 - - - -
1350B TYR* 3.4 25.9 - - - -
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Residues in contact with PRO1163 (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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1153B ASN* 4.7 2.9 - - - +
1158B GLY 4.6 1.6 - - - +
1159B SER 4.4 6.3 - - - +
1160B ASP* 3.1 23.3 - - - +
1162B GLY* 1.3 88.2 - - - +
1164B LEU* 1.3 54.3 + - - +
1167B THR* 2.8 35.9 + - - +
1182B PHE* 3.6 10.3 - - + -
1275B LEU* 4.3 6.7 - - + -
1279B ILE* 4.1 29.6 - - + +
1282B SER* 3.0 26.5 - - - +
1283B ILE* 3.7 19.1 - - + -
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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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1160B ASP* 3.1 35.9 + - - +
1161B LEU* 3.7 13.5 - - + +
1163B PRO* 1.3 77.5 - - - +
1165B MET* 1.3 65.2 + - - +
1167B THR* 3.0 17.2 + - - -
1168B GLU* 3.0 33.8 + - + +
1182B PHE* 3.4 36.5 - - + -
1346B ARG* 5.1 12.8 - - + +
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Residues in contact with MET1165 (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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1161B LEU* 2.8 22.5 + - + +
1162B GLY 3.7 1.1 - - - +
1164B LEU* 1.3 75.1 - - - +
1166B VAL* 1.3 67.2 + - + +
1168B GLU* 3.3 4.5 + - - +
1169B ALA* 2.9 38.4 + - - +
1343B TYR 4.6 0.9 - - - +
1344B LEU* 4.9 2.2 - - + -
1346B ARG* 3.5 46.2 - - + +
1347B PHE* 3.8 28.7 - - + +
1350B TYR* 3.8 30.7 - - + -
1486B LEU* 4.7 3.8 - - + -
1490B ILE* 3.7 28.0 - - + -
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Residues in contact with VAL1166 (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 GLY 3.0 16.3 + - - +
1165B MET* 1.3 82.5 - - - +
1167B THR* 1.3 65.4 + - - +
1169B ALA* 4.2 2.9 - - - -
1170B LEU* 2.9 46.7 + - + +
1275B LEU* 4.0 23.8 - - + -
1283B ILE* 3.8 31.6 - - + -
1295B LEU* 4.2 8.5 - - + -
1486B LEU* 3.9 6.3 - - + -
1490B ILE* 4.0 18.4 - - + -
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Residues in contact with THR1167 (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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1163B PRO 2.8 30.4 + - - +
1164B LEU* 3.0 11.4 + - - +
1166B VAL* 1.3 77.0 - - - +
1168B GLU* 1.3 62.3 + - - +
1170B LEU* 3.8 2.8 - - - -
1171B LYS* 3.4 31.0 + - - +
1180B VAL* 4.9 2.0 - - + -
1182B PHE* 3.3 28.2 - - + -
1282B SER 4.0 5.8 - - - +
1283B ILE* 3.9 30.1 - - + -
1286B HIS* 3.7 25.8 - - + +
1287B VAL* 5.7 1.8 - - + -
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Residues in contact with GLU1168 (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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1164B LEU* 3.0 35.9 + - + +
1165B MET* 3.5 6.1 - - - +
1167B THR* 1.3 80.9 + - - +
1169B ALA* 1.3 60.8 + - - +
1171B LYS* 3.1 45.4 + - - +
1343B TYR* 3.3 20.5 - - - +
1345B HIS* 2.6 42.1 + - + +
1346B ARG* 4.8 4.7 - - + +
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Residues in contact with ALA1169 (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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1165B MET* 2.9 19.3 + - - +
1166B VAL* 3.3 4.2 + - - +
1168B GLU* 1.3 79.3 - - - +
1170B LEU* 1.3 63.4 + - - +
1171B LYS 3.5 0.9 + - - -
1172B PRO* 4.2 3.1 - - - +
1173B TYR* 5.6 0.3 - - - -
1343B TYR* 3.2 31.6 + - - +
1344B LEU* 3.8 20.9 - - + -
1481B LEU* 4.2 10.5 - - + +
1486B LEU* 3.8 22.0 - - + -
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Residues in contact with LEU1170 (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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1166B VAL* 2.9 38.0 + - + +
1167B THR 3.8 3.6 - - - -
1169B ALA* 1.3 82.6 - - - +
1171B LYS* 1.3 62.9 + - - +
1172B PRO* 3.2 5.4 - - - -
1173B TYR* 2.9 25.6 + - + -
1283B ILE* 5.0 2.0 - - + -
1287B VAL* 3.6 30.7 - - + +
1291B ASN 5.6 0.7 - - - +
1295B LEU* 4.6 5.4 - - + -
1481B LEU* 4.4 6.7 - - + +
1482B THR 4.0 6.1 - - - +
1483B PRO* 3.9 44.0 - - + -
1486B LEU* 3.7 22.7 - - + -
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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