Contacts of the helix formed by residues 1189 - 1193 (chain A) in PDB entry 5G04
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 ALA1189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1155A SER* 3.7 13.1 + - - +
1187A LYS 4.8 0.4 - - - -
1188A LEU* 1.3 77.0 - - - +
1190A THR* 1.3 59.4 + - - +
1191A LEU* 2.5 23.9 + - - +
1192A ASN* 3.1 29.2 + - - +
89R GLU* 5.3 2.6 - - - +
92R SER* 5.8 3.8 - - - +
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Residues in contact with THR1190 (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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1188A LEU 2.9 13.1 + - - -
1189A ALA* 1.3 69.1 - - - +
1191A LEU* 1.3 58.9 + - + +
1192A ASN 3.0 2.5 - - - -
1193A ILE* 2.7 47.9 + - - +
1194A HIS* 3.6 21.0 + - - -
1223A SER* 4.8 12.7 - - - -
1224A ILE* 5.8 3.7 - - - +
89R GLU* 3.8 22.9 - - - +
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Residues in contact with LEU1191 (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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1189A ALA 2.5 10.4 + - - +
1190A THR* 1.3 77.6 + - + +
1192A ASN* 1.3 55.3 + - - -
1193A ILE 3.3 3.0 + - - -
1194A HIS* 3.9 12.6 + - + +
1195A ASP* 3.7 19.4 + - - +
89R GLU* 4.8 14.4 - - + +
90R VAL* 3.7 30.5 - - + +
93R PHE* 3.7 41.2 - - + -
121R ASN* 3.6 31.6 - - + +
123R PHE* 5.5 3.1 - - + -
125R VAL* 3.9 10.1 - - + -
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Residues in contact with ASN1192 (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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1155A SER* 4.8 3.7 + - - -
1159A VAL* 5.2 9.7 - - - +
1188A LEU* 3.8 25.7 - - + +
1189A ALA* 3.1 25.9 + - + +
1190A THR 2.9 1.8 + - - -
1191A LEU* 1.3 75.8 - - - +
1193A ILE* 1.3 57.3 + - - +
1195A ASP* 2.9 36.7 - - - +
1196A TYR* 3.3 19.3 + - + -
92R SER* 5.7 1.8 + - - -
93R PHE* 4.1 29.7 - - - +
96R SER* 4.8 12.8 + - - -
97R LYS* 5.8 1.0 - - - +
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Residues in contact with ILE1193 (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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1185A LEU* 4.2 20.2 - - + +
1186A THR 5.9 0.2 - - - +
1188A LEU* 3.9 20.4 - - + +
1190A THR* 2.7 36.2 + - - +
1192A ASN* 1.3 74.2 - - - +
1194A HIS* 1.3 54.4 - - + +
1195A ASP 3.0 3.4 - - - -
1196A TYR* 2.8 32.7 + - - +
1197A LEU* 3.3 29.6 + - + +
1208A LEU* 3.6 19.5 - - + +
1212A VAL* 3.9 20.9 - - + -
1224A ILE* 5.7 7.6 - - + -
1227A LEU* 4.1 10.8 - - + -
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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