Contacts of the helix formed by residues 1103 - 1113 (chain W) in PDB entry 5O9G
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 ASN1103 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1085W TYR* 3.2 41.3 + - + +
1100W PRO* 2.7 24.6 + - + +
1101W LYS 3.4 1.1 + - - +
1102W ASP* 1.3 76.1 + - - +
1104W PRO* 1.3 74.7 - - + +
1105W LEU* 4.1 12.4 - - - +
1106W THR* 2.6 59.9 + - - +
1107W ARG* 3.4 11.0 + - - +
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Residues in contact with PRO1104 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078W LEU* 4.6 4.7 - - + +
1081W HIS* 3.5 30.5 - - + +
1082W ALA* 3.7 25.5 - - + +
1085W TYR* 3.8 18.6 - - + -
1103W ASN* 1.3 87.6 - - + +
1105W LEU* 1.3 57.1 + - - +
1106W THR 3.4 0.2 - - - -
1107W ARG* 3.4 18.0 - - + +
1108W LEU* 2.9 31.9 + - - +
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Residues in contact with LEU1105 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082W ALA* 4.1 23.6 - - + +
1085W TYR* 3.8 31.9 - - + -
1086W ARG* 4.3 21.3 - - + -
1089W LEU* 4.4 13.5 - - + -
1103W ASN* 3.1 10.4 + - - +
1104W PRO* 1.3 76.9 - - - +
1106W THR* 1.3 58.8 + - + +
1108W LEU* 3.4 7.8 + - + +
1109W SER* 2.9 29.8 + - - -
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Residues in contact with THR1106 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100W PRO 4.9 0.2 - - - +
1101W LYS* 2.6 33.4 + - + +
1102W ASP* 4.4 0.2 - - - -
1103W ASN* 2.6 36.3 + - - +
1105W LEU* 1.3 77.2 - - + +
1107W ARG* 1.3 55.4 + - - +
1109W SER* 3.3 6.5 + - - -
1110W LEU* 2.9 39.5 + - - +
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Residues in contact with ARG1107 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078W LEU* 3.8 27.7 - - + +
1081W HIS* 5.5 6.8 + - - -
1102W ASP* 6.1 0.9 - - - -
1103W ASN 3.7 4.0 - - - +
1104W PRO* 3.4 30.1 - - + +
1106W THR* 1.3 81.3 + - - +
1108W LEU* 1.3 59.8 + - - +
1110W LEU* 3.8 8.9 - - - +
1111W LYS* 2.9 26.7 + - - +
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Residues in contact with LEU1108 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075W LEU* 4.4 18.8 - - + +
1078W LEU* 3.7 35.0 - - + +
1079W GLU* 5.1 10.3 - - + -
1082W ALA* 4.2 22.4 - - + -
1104W PRO 2.9 20.1 + - - +
1105W LEU* 3.7 9.0 - - + +
1107W ARG* 1.3 75.8 - - - +
1109W SER* 1.3 60.6 + - - +
1111W LYS* 3.0 5.1 + - - +
1112W LYS* 2.9 54.2 + - + +
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Residues in contact with SER1109 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-82J A 5.5 2.6 + - - -
1105W LEU 2.9 17.5 + - - -
1106W THR* 3.3 6.5 + - - -
1108W LEU* 1.3 75.0 - - - +
1110W LEU* 1.3 64.2 + - - +
1112W LYS* 3.2 21.6 + - - +
1113W ARG* 3.2 29.4 + - - +
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Residues in contact with LEU1110 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106W THR* 2.9 26.6 + - - +
1107W ARG* 4.1 7.9 - - - +
1109W SER* 1.3 74.4 - - - +
1111W LYS* 1.3 64.1 + - - +
1113W ARG* 3.2 27.3 - - + +
1114W GLU* 3.1 22.2 + - - +
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Residues in contact with LYS1111 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071W ARG* 3.5 27.8 - - - +
1074W ILE* 3.9 27.8 - - + -
1075W LEU* 3.8 20.2 - - + +
1078W LEU* 3.7 22.9 - - + -
1107W ARG 2.9 20.3 + - - +
1108W LEU* 3.0 8.0 + - + +
1110W LEU* 1.3 75.2 - - - +
1112W LYS* 1.3 64.1 + - - +
1114W GLU* 2.8 51.5 + - + +
1116W LYS* 4.8 8.4 - - - +
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Residues in contact with LYS1112 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-82J A 3.7 38.1 + - - +
1075W LEU* 5.8 6.8 - - + +
1108W LEU* 2.9 44.7 + - + +
1109W SER* 3.2 13.0 + - - +
1111W LYS* 1.3 78.3 - - - +
1113W ARG* 1.3 57.3 + - + +
1114W GLU* 3.3 6.5 + - - +
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Residues in contact with ARG1113 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I T 5.6 10.5 - - - +
-83J C 6.1 2.0 - - - +
-82J A 5.5 14.5 + - - -
1109W SER* 3.2 26.6 + - - +
1110W LEU* 3.2 28.2 - - + +
1111W LYS 3.3 0.2 - - - -
1112W LYS* 1.3 75.0 - - + +
1114W GLU* 1.3 63.7 + - - +
1115W LYS* 3.6 16.6 + - - +
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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