Contacts of the helix formed by residues 1183 - 1187 (chain A) in PDB entry 1SIW
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 ILE1183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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718A GLY* 4.7 14.4 - - - +
719A SER 5.1 0.2 - - - +
724A HIS* 3.0 47.8 - - + +
1144A LEU* 3.5 14.1 - - - +
1161A MET* 5.3 4.3 - - + -
1166A GLU* 3.5 25.1 - - - +
1167A ARG* 3.4 34.1 - - + +
1182A GLY* 1.3 77.5 - - - +
1184A HIS* 1.3 75.4 + - + +
1185A ASN* 3.5 11.0 - - + +
1186A SER* 2.8 32.8 + - - +
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Residues in contact with HIS1184 (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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719A SER* 3.1 33.2 + - - -
1088A PHE* 3.8 12.4 - - + -
1090A THR* 4.2 22.9 - - + -
1144A LEU* 3.8 11.6 - - - +
1161A MET* 3.8 28.1 - - + +
1163A HIS* 3.4 17.9 + - + -
1164A ALA* 3.5 31.7 - - + +
1165A GLN 5.0 1.8 + - - -
1166A GLU 5.6 0.2 + - - -
1183A ILE* 1.3 82.1 - - - +
1185A ASN* 1.3 73.6 + - + +
1186A SER 3.2 0.2 - - - -
1187A VAL* 3.1 24.9 - - - +
1188A THR* 3.9 6.9 - - + +
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Residues in contact with ASN1185 (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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719A SER* 2.5 37.3 + - - +
720A SER 3.6 4.2 + - - -
721A GLY 3.3 29.4 + - - +
722A LYS* 3.7 11.3 + - - +
723A GLY* 3.5 2.3 + - - -
724A HIS* 2.9 27.3 + - + -
1183A ILE* 3.1 7.4 - - + +
1184A HIS* 1.3 91.8 + - - +
1186A SER* 1.3 58.4 + - - +
1187A VAL 3.1 5.8 + - - -
1188A THR* 2.9 32.7 + - - +
1217A ASN* 4.7 2.1 + - - -
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Residues in contact with SER1186 (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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724A HIS* 4.0 5.8 - - - -
725A GLU* 2.9 26.6 + - - -
1141A ASN* 2.9 31.2 - - - +
1142A GLY* 3.0 5.9 + - - -
1143A ALA 3.5 24.0 - - - -
1182A GLY* 3.3 2.3 - - - -
1183A ILE* 2.8 40.9 + - - +
1185A ASN* 1.3 78.7 - - - +
1187A VAL* 1.3 59.0 + - - +
1188A THR 3.6 0.4 - - - -
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Residues in contact with VAL1187 (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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1088A PHE* 3.5 31.9 - - + -
1137A VAL 4.0 8.7 - - - +
1138A PHE* 3.9 17.5 - - - +
1139A ASN* 2.9 30.5 + - - +
1141A ASN* 3.2 9.6 + - - -
1142A GLY 3.5 22.0 - - - +
1143A ALA* 4.2 2.7 - - - -
1144A LEU* 4.3 9.9 - - + -
1184A HIS 3.1 18.6 - - - +
1186A SER* 1.3 81.3 - - - +
1188A THR* 1.3 57.6 + - + +
1220A GLU* 3.6 8.1 - - - +
1222A VAL* 4.0 8.1 - - + -
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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