Contacts of the helix formed by residues 1154 - 1163 (chain B) in PDB entry 4DDG
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 SER1154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1105B LEU* 4.7 0.4 - - - -
1152B GLN* 3.4 13.7 - - - +
1153B THR* 1.3 80.9 + - - +
1155B VAL* 1.3 68.7 + - - +
1156B ALA* 2.9 15.7 + - - +
1157B ASP* 3.0 27.0 + - - +
1158B LEU 3.9 0.9 + - - -
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Residues in contact with VAL1155 (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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1051B ARG* 4.8 13.7 - - - +
1083B ARG* 5.0 6.3 - - - +
1098B PHE* 4.6 1.9 - - + -
1102B GLU* 3.3 41.3 - - + +
1105B LEU* 3.6 20.4 - - + +
1153B THR 3.6 0.8 + - - -
1154B SER* 1.3 72.9 - - - +
1156B ALA* 1.3 61.2 + - + +
1158B LEU* 3.3 13.0 - - + +
1159B LEU* 2.9 30.1 + - - +
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Residues in contact with ALA1156 (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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1154B SER* 2.9 11.7 + - - +
1155B VAL* 1.3 86.0 - - + +
1157B ASP* 1.3 57.5 + - - +
1159B LEU* 3.5 16.1 - - + +
1160B ALA* 2.9 26.2 + - - +
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Residues in contact with ASP1157 (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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1148B GLN* 4.1 2.6 - - - +
1153B THR* 3.0 32.0 + - + +
1154B SER* 3.0 12.5 + - - +
1156B ALA* 1.3 76.1 - - - +
1158B LEU* 1.3 59.9 + - - +
1159B LEU 3.2 1.1 - - - -
1160B ALA* 3.1 12.0 + - - +
1161B SER* 2.9 27.9 + - - -
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Residues in contact with LEU1158 (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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1098B PHE* 3.6 23.8 - - + -
1101B LEU* 3.9 32.5 - - + -
1102B GLU* 4.5 11.0 - - + +
1105B LEU* 4.2 13.5 - - + -
1145B LEU* 4.9 7.4 - - + +
1148B GLN* 3.8 20.8 + - + +
1149B VAL* 4.9 8.3 - - + -
1153B THR* 4.4 11.5 - - + +
1154B SER 3.9 1.8 + - - -
1155B VAL* 3.3 31.2 + - - +
1157B ASP* 1.3 75.8 - - - +
1159B LEU* 1.3 57.6 + - - +
1161B SER* 3.1 4.8 + - - -
1162B PHE* 2.9 47.9 + - + -
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Residues in contact with LEU1159 (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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1048B VAL* 3.9 18.4 - - + +
1049B SER 3.7 15.5 - - - +
1050B GLU* 4.5 8.1 - - + +
1083B ARG* 3.3 28.9 - - - +
1098B PHE* 3.6 15.0 - - + -
1155B VAL 2.9 20.5 + - - +
1156B ALA* 3.5 17.0 - - + +
1157B ASP 3.2 0.2 - - - -
1158B LEU* 1.3 75.5 - - - +
1160B ALA* 1.3 69.7 + - + +
1162B PHE* 3.0 11.6 + - - +
1163B ASN* 3.0 30.7 + - - +
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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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1156B ALA 2.9 16.6 + - - +
1157B ASP* 3.1 17.4 + - - +
1159B LEU* 1.3 79.8 - - + +
1161B SER* 1.3 62.1 + - - +
1163B ASN* 3.5 13.3 + - - +
1164B ASP* 3.6 10.4 + - - +
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Residues in contact with SER1161 (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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1145B LEU* 4.1 12.8 - - - -
1148B GLN* 2.5 41.9 + - - -
1157B ASP 2.9 9.4 + - - -
1158B LEU* 3.3 10.1 - - - -
1159B LEU 3.1 0.4 - - - -
1160B ALA* 1.3 78.1 - - - +
1162B PHE* 1.3 61.7 + - - +
1164B ASP* 3.2 24.0 + - - +
1167B THR* 3.9 15.1 - - - +
1168B SER 4.4 0.3 + - - -
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Residues in contact with PHE1162 (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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1047B LEU* 3.8 12.3 - - - +
1048B VAL* 4.1 15.7 - - + +
1094B ARG* 4.0 8.5 - - + -
1097B GLY 4.0 2.9 - - - -
1098B PHE* 3.4 57.4 - + + -
1101B LEU* 4.1 9.4 - - + -
1145B LEU* 4.5 11.2 - - + -
1158B LEU* 2.9 38.8 + - + +
1159B LEU* 3.0 8.7 + - - +
1161B SER* 1.3 77.8 - - - +
1163B ASN* 1.3 59.4 + - - +
1164B ASP 3.3 0.4 - - - -
1168B SER* 3.2 39.6 + - - +
1171B LEU* 3.6 39.7 - - + -
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Residues in contact with ASN1163 (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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1046B PRO* 3.9 6.4 - - - +
1047B LEU* 3.4 27.2 + - + +
1048B VAL* 3.0 47.0 + - - +
1159B LEU* 3.0 41.2 + - - +
1160B ALA* 4.1 7.6 - - - +
1161B SER 3.2 1.0 - - - -
1162B PHE* 1.3 76.4 - - - +
1164B ASP* 1.3 62.3 + - - +
1165B GLN 3.7 0.9 + - - -
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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