Contacts of the helix formed by residues 1167 - 1181 (chain D) in PDB entry 4OIP
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 SER1167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920D LEU* 6.4 1.8 - - - -
1145D TYR* 4.2 2.7 - - - -
1164D ARG* 5.0 1.0 + - - -
1165D TYR 3.4 3.6 + - - -
1166D LEU* 1.3 76.3 - - - +
1168D MET* 1.3 65.8 + - - +
1169D ASP* 3.6 12.4 + - - +
1170D ASP* 2.9 44.9 + - - +
1171D VAL* 3.0 11.8 + - - +
1207D TYR* 4.2 15.5 - - - -
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Residues in contact with MET1168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916D TYR* 3.8 31.8 + - + +
917D GLN* 5.9 2.7 - - - +
920D LEU* 5.5 4.2 - - + +
1141D GLU* 3.5 37.5 - - + +
1145D TYR* 3.7 34.9 - - + -
1167D SER* 1.3 72.5 - - - +
1169D ASP* 1.3 62.5 + - - +
1171D VAL* 3.0 25.6 + - + +
1172D HIS* 2.9 59.6 + - + +
1362D LYS* 6.4 0.9 - - - -
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Residues in contact with ASP1169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917D GLN* 5.3 8.9 + - - +
920D LEU* 5.9 4.3 - - - +
1167D SER* 3.1 11.1 + - - +
1168D MET* 1.3 80.3 - - - +
1170D ASP* 1.3 58.9 + - - +
1172D HIS* 3.3 14.2 + - - +
1173D LEU* 2.9 29.5 + - - +
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Residues in contact with ASP1170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160D LEU* 3.8 10.3 - - + +
1164D ARG* 2.8 46.0 + - - -
1165D TYR 3.7 1.7 - - - +
1166D LEU* 3.7 17.7 - - + -
1167D SER* 2.9 38.3 + - - +
1169D ASP* 1.3 77.3 - - - +
1171D VAL* 1.3 57.1 + - - +
1173D LEU* 3.3 11.9 + - - +
1174D LEU* 2.9 33.7 + - - +
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Residues in contact with VAL1171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140D ILE* 4.4 7.6 - - + -
1141D GLU* 4.4 15.0 - - + -
1144D LEU* 4.1 25.8 - - + -
1145D TYR* 3.6 34.8 - - + +
1166D LEU* 4.5 7.6 - - + -
1167D SER 3.0 13.4 + - - +
1168D MET* 3.0 22.1 + - + +
1170D ASP* 1.3 73.8 - - - +
1172D HIS* 1.3 60.4 + - - +
1174D LEU* 3.1 11.1 + - - +
1175D ILE* 2.9 31.2 + - + +
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Residues in contact with HIS1172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137D ARG* 4.0 26.7 + - - +
1141D GLU* 3.2 26.9 - - - -
1168D MET* 2.9 43.9 + - + +
1169D ASP* 3.3 16.4 + - - +
1171D VAL* 1.3 75.0 - - - +
1173D LEU* 1.3 58.1 + - - +
1175D ILE* 3.2 15.1 + - + +
1176D LYS* 2.9 30.9 + - - +
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Residues in contact with LEU1173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155D VAL* 4.8 6.7 - - + -
1156D LEU* 3.8 24.0 - - + -
1158D VAL* 3.9 40.4 - - + -
1160D LEU* 4.4 23.3 - - + -
1169D ASP 2.9 14.3 + - - +
1170D ASP* 3.4 12.1 - - - +
1172D HIS* 1.3 76.3 - - - +
1174D LEU* 1.3 57.7 + - - +
1176D LYS* 3.2 15.9 + - + +
1177D ALA* 2.9 27.5 + - - +
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Residues in contact with LEU1174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122D LEU* 4.0 8.1 - - + +
1144D LEU* 4.0 22.0 - - + -
1149D LEU* 5.4 1.1 - - + -
1153D VAL* 4.3 8.7 - - + -
1155D VAL* 4.4 7.4 - - + -
1160D LEU* 3.8 21.8 - - + -
1166D LEU* 4.0 32.8 - - + -
1170D ASP 2.9 18.7 + - - +
1171D VAL* 3.4 9.6 - - - +
1173D LEU* 1.3 77.3 - - - +
1175D ILE* 1.3 57.8 + - - +
1177D ALA* 3.4 5.2 + - - +
1178D ALA* 2.9 28.1 + - - +
1183D ILE* 4.3 25.4 - - + +
1186D VAL* 4.0 15.7 - - + -
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Residues in contact with ILE1175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122D LEU* 5.6 1.3 - - + -
1134D LEU* 4.3 21.5 - - + -
1137D ARG* 3.4 52.3 - - + +
1140D ILE* 4.3 36.3 - - + -
1141D GLU* 5.2 1.8 - - + -
1171D VAL* 2.9 24.8 + - + +
1172D HIS* 3.2 15.9 + - - +
1174D LEU* 1.3 74.5 - - - +
1176D LYS* 1.3 60.0 + - - +
1178D ALA* 3.1 9.0 + - - +
1179D GLU* 2.9 33.9 + - - +
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Residues in contact with LYS1176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137D ARG* 6.3 1.3 - - - +
1156D LEU* 4.1 20.1 - - + +
1172D HIS 2.9 13.6 + - - +
1173D LEU* 3.5 18.1 - - + +
1175D ILE* 1.3 76.8 - - - +
1177D ALA* 1.3 58.0 + - - +
1179D GLU* 3.2 18.6 + - - +
1180D ALA* 2.9 27.4 + - - +
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Residues in contact with ALA1177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155D VAL* 3.7 26.5 - - + -
1156D LEU* 4.0 17.0 - - + +
1173D LEU 2.9 16.3 + - - +
1174D LEU* 3.6 6.5 - - - +
1175D ILE 3.2 0.2 - - - -
1176D LYS* 1.3 75.7 - - - +
1178D ALA* 1.3 57.6 + - - +
1180D ALA* 3.1 5.5 + - - +
1181D GLY 2.9 22.2 + - - -
1182D GLU* 3.0 14.0 + - - +
1183D ILE* 3.7 18.2 - - + -
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Residues in contact with ALA1178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122D LEU* 3.7 12.6 - - + -
1123D PHE* 3.1 30.6 - - + -
1134D LEU* 3.9 14.1 - - + -
1174D LEU 2.9 14.7 + - - +
1175D ILE* 3.4 10.3 - - - +
1177D ALA* 1.3 77.8 - - - +
1179D GLU* 1.3 57.0 + - - +
1181D GLY* 3.0 16.3 + - - -
1183D ILE* 3.5 24.0 - - - +
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Residues in contact with GLU1179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123D PHE* 5.2 1.8 - - - -
1134D LEU* 3.8 28.0 - - + +
1137D ARG* 5.2 3.7 + - - -
1175D ILE* 2.9 21.8 + - - +
1176D LYS* 3.5 23.2 + - - +
1178D ALA* 1.3 76.9 - - - +
1180D ALA* 1.3 60.9 + - - +
1181D GLY* 3.1 1.7 + - - -
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Residues in contact with ALA1180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156D LEU* 4.2 19.7 - - + -
1176D LYS 2.9 13.3 + - - +
1177D ALA 3.1 10.1 + - - +
1179D GLU* 1.3 76.9 - - - +
1181D GLY* 1.3 60.2 + - - +
1182D GLU* 3.3 9.7 + - + +
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Residues in contact with GLY1181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123D PHE* 5.5 2.7 - - - -
1177D ALA 2.9 3.0 + - - -
1178D ALA 3.0 14.8 + - - -
1179D GLU 3.1 1.2 - - - -
1180D ALA* 1.3 79.7 - - - +
1182D GLU* 1.3 62.3 + - - +
1183D ILE 3.5 1.6 - - - -
1184D GLN* 3.7 12.4 - - - +
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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