Contacts of the helix formed by residues 1163 - 1167 (chain A) in PDB entry 1Y1S
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 TYR1163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1161A THR* 6.1 0.2 - - - -
1162A PHE* 1.3 113.0 - + + +
1164A PRO* 1.3 77.9 - - + +
1165A GLY 3.4 1.1 - - - -
1166A GLN 3.0 8.1 + - - -
1168A ARG* 2.8 43.7 + - + +
1170A ASP 4.9 4.0 - - - -
1171A THR* 3.7 30.7 - - + -
4007F PHE* 4.1 6.6 + - + +
4008F HIS* 4.0 1.4 - - - -
4075F SER 5.3 0.7 - - - -
4076F ILE* 4.5 10.8 - - + -
4079F GLU* 3.6 28.3 - - + -
4080F GLU* 2.5 39.3 + - + +
4083F GLN* 4.1 12.4 + - - -
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Residues in contact with PRO1164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161A THR* 3.4 11.7 - - - +
1163A TYR* 1.3 94.5 - - + +
1165A GLY* 1.3 63.1 + - - +
1167A GLU* 2.8 21.0 + - - +
1168A ARG 4.5 5.6 - - - +
1171A THR* 5.4 1.1 - - + -
1175A ARG 5.2 3.1 - - - +
1176A VAL* 3.7 23.6 - - + +
1177A VAL 5.3 0.2 - - - +
1180A PHE* 3.6 15.9 - - + +
4079F GLU* 6.0 0.7 - - - +
4122F HIS* 3.1 31.2 - - + +
4123F PHE* 3.9 25.8 - - + -
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Residues in contact with GLY1165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116A LEU* 4.4 2.6 - - - +
1159A SER* 3.5 15.6 + - - -
1161A THR* 2.7 25.4 + - - -
1164A PRO* 1.3 72.2 - - - +
1166A GLN* 1.3 60.0 + - - +
1167A GLU 3.4 0.7 - - - -
1180A PHE* 4.0 21.8 - - - -
1183A SER* 5.2 0.9 + - - -
1187A TRP* 5.5 0.3 + - - -
1195A TYR* 3.7 10.9 + - - -
4122F HIS* 3.2 19.2 + - - -
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Residues in contact with GLN1166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1159A SER* 3.9 4.5 - - - -
1161A THR 3.1 23.5 + - - +
1162A PHE* 3.4 25.4 - - - +
1163A TYR 3.0 1.0 + - - -
1164A PRO 2.9 1.2 - - - -
1165A GLY* 1.3 81.9 - - - +
1167A GLU* 1.3 68.4 + - - +
1168A ARG* 3.0 12.1 + - + +
1195A TYR* 3.2 43.4 - - + +
1196A GLU 4.7 0.8 + - - -
1197A MET* 3.7 8.3 - - - +
1223A ARG* 2.9 28.1 + - - +
8001A URA 3.1 40.1 + - - +
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Residues in contact with GLU1167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1164A PRO 2.8 14.1 + - - -
1165A GLY 3.4 1.0 - - - -
1166A GLN* 1.3 77.4 - - - +
1168A ARG* 1.3 61.5 + - - +
1169A TYR* 3.0 39.3 + - + +
1176A VAL* 4.4 4.3 - - + -
1180A PHE 3.5 14.6 - - - +
1182A GLY* 2.7 30.0 + - - -
1183A SER* 3.2 8.9 + - - +
1184A MET* 3.0 39.8 + - + +
1185A GLU 4.3 1.0 + - - -
1195A TYR* 4.4 0.6 + - - -
1223A ARG* 3.2 11.3 + - - -
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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