Contacts of the helix formed by residues 1168 - 1177 (chain A) in PDB entry 6O0Z
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 ILE1168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1101A GLN 4.2 15.0 - - - +
1102A THR* 4.4 6.5 - - + -
1103A GLY 4.2 17.7 - - - +
1104A GLY 3.7 24.9 - - - +
1105A PHE* 4.1 22.9 - - + -
1138A THR* 3.6 24.0 - - + +
1140A ALA* 4.2 12.3 - - + +
1167A THR* 1.3 73.8 - - + +
1169A MET* 1.3 63.1 + - - +
1171A ARG* 3.0 30.7 + - - +
1172A SER* 3.1 14.2 + - - -
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Residues in contact with MET1169 (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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1105A PHE* 3.7 48.2 - - + -
1120A ILE* 4.3 28.5 - - + -
1167A THR* 3.4 11.2 - - + -
1168A ILE* 1.3 74.0 - - - +
1170A GLU* 1.3 66.3 + - + +
1172A SER* 3.3 6.9 + - - -
1173A SER* 3.1 22.3 + - - -
52B A 3.8 50.3 - - + +
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Residues in contact with GLU1170 (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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1165A GLY 4.2 4.7 - - - +
1166A ILE* 3.7 7.7 - - + +
1167A THR* 2.8 40.6 + - - +
1169A MET* 1.3 78.8 - - + +
1171A ARG* 1.3 59.2 + - - +
1173A SER* 3.8 7.4 - - - +
1174A PHE* 2.8 34.5 + - - +
1181A PHE* 3.8 27.5 - - + -
1185A LYS* 4.1 14.9 + - - -
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Residues in contact with ARG1171 (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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1100A VAL* 4.1 19.8 - - - +
1101A GLN 5.5 0.9 - - - -
1102A THR* 5.9 8.1 - - - +
1140A ALA* 3.9 20.0 - - + -
1141A TYR* 3.8 22.9 - - + +
1166A ILE* 3.7 12.1 - - + -
1167A THR 2.5 24.6 + - - +
1168A ILE* 3.0 21.0 + - - +
1170A GLU* 1.3 68.8 - - - +
1172A SER* 1.3 62.7 + - - +
1174A PHE* 4.0 3.1 - - - +
1175A GLU* 2.9 55.0 + - - +
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Residues in contact with SER1172 (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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1168A ILE 3.1 9.8 + - - -
1169A MET* 3.7 8.5 - - - -
1171A ARG* 1.3 81.4 - - - +
1173A SER* 1.3 63.4 + - - +
1175A GLU* 3.9 5.8 - - - +
1176A LYS* 3.1 24.6 + - - +
52B A 5.2 10.7 + - - -
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Residues in contact with SER1173 (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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1169A MET 3.1 16.3 + - - -
1170A GLU* 4.1 7.2 - - - -
1172A SER* 1.3 78.1 + - - +
1174A PHE* 1.3 57.6 + - - +
1176A LYS* 3.9 8.6 - - - +
1177A ASN* 3.7 16.5 + - - +
1181A PHE* 4.2 17.3 - - - +
52B A 6.4 0.7 - - - -
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Residues in contact with PHE1174 (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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1141A TYR* 3.4 35.4 - + - -
1143A VAL* 4.0 21.5 - - + -
1166A ILE* 4.4 15.9 - - + -
1170A GLU 2.8 18.3 + - - +
1171A ARG 4.5 1.6 - - - -
1173A SER* 1.3 76.9 - - - +
1175A GLU* 1.3 67.5 + - - +
1176A LYS 3.2 1.8 - - - -
1177A ASN 3.2 22.1 - - - -
1178A PRO* 3.3 41.0 - - + +
1181A PHE* 3.5 33.7 - + + -
1182A LEU* 4.7 13.2 - - + -
1195A ILE* 4.8 10.1 - - + -
1197A LYS* 5.8 2.0 - - + -
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Residues in contact with GLU1175 (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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1141A TYR* 5.0 8.9 + - - +
1171A ARG* 2.9 47.6 + - - +
1172A SER* 4.0 5.1 - - - +
1174A PHE* 1.3 77.7 - - - +
1176A LYS* 1.3 64.9 + - - +
1178A PRO* 5.1 4.4 - - - +
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Residues in contact with LYS1176 (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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1172A SER 3.1 17.3 + - - +
1173A SER* 3.9 9.6 - - - +
1175A GLU* 1.3 79.6 - - - +
1177A ASN* 1.3 62.6 + - + +
1178A PRO* 4.5 1.2 - - - +
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Residues in contact with ASN1177 (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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1173A SER 3.7 7.3 + - - +
1174A PHE 3.2 5.0 + - - +
1176A LYS* 1.3 84.2 - - + +
1178A PRO* 1.3 71.0 - - - +
1179A ILE* 3.4 18.6 - - - +
1180A ASP* 3.4 28.6 - - + +
1181A PHE* 3.4 19.1 + - - +
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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