Contacts of the helix formed by residues 1160 - 1166 (chain B) in PDB entry 4Z4Q
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 PRO1160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1159B PHE* 1.4 87.2 - - + +
1161B ASN* 1.3 64.6 + - - +
1162B LEU* 3.3 4.2 + - - -
1163B LEU* 3.4 6.2 + - + +
1164B VAL* 3.3 23.7 + - + +
1186B VAL* 3.8 24.9 - - + -
1187B ILE* 4.1 21.1 - - + -
1190B ALA* 4.9 8.5 - - + -
1345B ILE* 6.3 1.6 - - + -
1346B LEU* 5.0 4.9 - - + -
1349B TYR* 3.6 42.6 - - + -
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Residues in contact with ASN1161 (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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1034B ARG 5.0 2.2 + - - -
1035B ASP* 2.9 28.4 + - - +
1036B GLY 4.0 5.9 + - - -
1037B LEU* 3.6 22.0 - - - +
1098B LEU* 4.2 5.2 - - - +
1130B LEU* 3.8 20.3 - - + +
1159B PHE* 3.0 31.9 + - + -
1160B PRO* 1.3 70.7 - - - +
1162B LEU* 1.3 65.2 + - - +
1164B VAL* 4.5 0.2 - - - -
1165B ASN* 2.9 54.6 + - - +
1166B GLY 3.8 1.3 + - - +
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Residues in contact with LEU1162 (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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1031B PRO* 4.2 13.5 - - + -
1032B ASP 4.3 5.8 - - - +
1033B ILE* 4.3 13.0 - - + +
1034B ARG 5.4 1.1 + - - +
1035B ASP 4.1 1.0 + - - -
1036B GLY* 3.7 31.7 - - - +
1160B PRO* 3.3 1.5 - - + -
1161B ASN* 1.3 76.5 - - - +
1163B LEU* 1.3 60.5 + - + +
1166B GLY* 2.9 30.9 + - - +
1167B SER* 4.3 8.5 - - - -
1178B ILE* 3.4 34.9 - - + +
1331B ALA* 4.3 16.4 - - + -
1345B ILE* 4.1 34.8 - - + -
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Residues in contact with LEU1163 (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 PRO* 3.4 4.4 + - + +
1161B ASN 3.3 0.4 - - - -
1162B LEU* 1.3 78.1 - - - +
1164B VAL* 1.3 64.2 + - - +
1165B ASN 3.5 0.2 + - - -
1178B ILE* 4.5 10.5 - - + -
1179B PRO 3.5 3.5 - - - +
1180B PRO* 3.4 1.9 - - - +
1181B HIS* 2.8 52.1 + - + +
1186B VAL* 4.0 24.7 - - + -
1208B LEU* 4.6 5.2 - - + -
1329B MET* 4.9 4.0 - - - -
1342B ILE* 3.7 30.5 - - + -
1345B ILE* 3.7 40.8 - - + -
1346B LEU* 3.8 20.6 - - + -
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Residues in contact with VAL1164 (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 ARG* 3.3 8.7 - - + +
1096B GLU* 4.0 26.5 - - + -
1159B PHE* 4.1 23.6 - - + -
1160B PRO* 3.3 17.7 + - + +
1161B ASN 3.3 2.8 + - - +
1163B LEU* 1.3 76.8 - - - +
1165B ASN* 1.3 59.2 + - - +
1180B PRO* 3.3 8.5 - - - +
1181B HIS* 2.9 34.4 + - - +
1183B LEU* 4.0 33.0 - - + +
1186B VAL* 4.1 14.6 - - + -
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Residues in contact with ASN1165 (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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1087B ARG* 5.9 0.7 + - - -
1093B LYS 4.5 5.4 - - - +
1094B ASN* 3.4 24.3 + - - +
1095B ARG* 2.9 13.9 + - - +
1096B GLU* 2.8 52.1 + - - +
1098B LEU* 3.8 15.5 - - + +
1159B PHE* 4.8 1.6 - - - -
1161B ASN* 2.9 37.6 + - - +
1164B VAL* 1.3 76.2 - - - +
1166B GLY* 1.3 66.5 + - - +
1180B PRO* 4.0 15.4 - - - +
1261B TYR* 4.7 2.4 + - - -
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Residues in contact with GLY1166 (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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1036B GLY 4.4 9.0 - - - +
1161B ASN* 3.8 1.4 + - - +
1162B LEU* 2.9 23.5 + - - +
1163B LEU 3.9 0.8 + - - -
1164B VAL 3.6 1.0 - - - -
1165B ASN* 1.3 84.1 - - - +
1167B SER* 1.3 65.7 + - - -
1178B ILE* 3.1 21.5 - - - -
1179B PRO 4.0 6.7 - - - -
1180B PRO* 5.1 0.2 - - - -
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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