Contacts of the helix formed by residues 1086 - 1093 (chain A) in PDB entry 2PC0
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 GLY1086 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025A ASP 3.8 4.5 - - - -
1028A ALA* 3.4 14.4 - - - -
1030A ASP 3.5 17.8 + - - -
1031A THR* 3.0 10.9 + - - -
1084A ILE 3.7 2.8 + - - -
1085A ILE* 1.3 73.1 - - - +
1087A ARG* 1.3 65.3 + - - -
1088A ASN* 3.1 5.7 + - - -
1089A LEU* 3.1 4.2 + - - -
1090A LEU* 3.0 24.4 + - - +
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Residues in contact with ARG1087 (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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1026A THR* 3.6 31.4 + - + +
1027A GLY 5.7 0.4 - - - -
1028A ALA 2.8 20.7 + - - +
1029A ASP* 2.8 40.7 + - - +
1086A GLY* 1.3 72.7 - - - -
1088A ASN* 1.3 63.3 + - - +
1090A LEU* 4.0 10.3 - - + -
1091A THR* 2.9 36.3 + - + +
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Residues in contact with ASN1088 (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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1029A ASP 3.3 13.0 + - - +
1030A ASP* 3.7 6.8 - - - +
1031A THR* 2.8 36.2 + - - +
1073A GLY* 4.8 0.6 - - - -
1074A THR* 2.9 45.8 + - - +
1086A GLY 3.8 0.2 - - - +
1087A ARG* 1.3 77.2 - - - +
1089A LEU* 1.3 63.0 + - - +
1091A THR* 3.0 16.4 + - - -
1092A GLN* 3.3 17.0 - - - +
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Residues in contact with LEU1089 (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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1031A THR* 3.4 37.7 - - + +
1062A ILE 5.9 0.2 - - - +
1064A ILE* 4.1 28.7 - - + -
1066A ILE* 4.0 6.1 - - + -
1071A ALA* 4.3 14.1 - - + -
1072A ILE 4.1 6.5 - - - +
1073A GLY* 3.9 32.3 - - - +
1074A THR 4.3 5.6 - - - +
1075A VAL* 4.3 6.7 - - + -
1085A ILE* 4.0 11.7 - - + -
1086A GLY 3.1 1.8 + - - -
1088A ASN* 1.3 86.9 - - - +
1090A LEU* 1.3 67.9 + - - +
1091A THR 3.2 1.8 - - - -
1092A GLN* 3.1 4.4 + - + +
1093A ILE* 3.1 27.0 + - - +
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Residues in contact with LEU1090 (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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1024A LEU* 3.8 32.8 - - + -
1025A ASP 4.0 23.3 - - - +
1026A THR* 4.1 17.3 - - + -
1085A ILE* 3.9 19.1 - - + +
1086A GLY 3.0 22.4 + - - +
1087A ARG* 3.9 9.6 - - + +
1089A LEU* 1.3 78.7 - - - +
1091A THR* 1.3 60.6 + - + +
1093A ILE* 3.3 11.2 - - + +
1094A GLY 3.2 3.5 + - - -
1095A CYS* 2.9 57.0 + - + +
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Residues in contact with THR1091 (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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1087A ARG* 2.9 28.8 + - + +
1088A ASN* 3.0 15.4 + - - -
1090A LEU* 1.3 73.4 - - + +
1092A GLN* 1.3 72.3 + - - +
1094A GLY* 2.9 14.4 + - - -
1095A CYS 4.9 5.2 - - - +
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Residues in contact with GLN1092 (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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907A PGR 5.9 2.1 - - - -
1070A LYS 5.0 2.1 - - - +
1071A ALA* 3.7 20.0 - - + +
1072A ILE* 3.6 25.5 + - - +
1073A GLY* 5.2 1.1 - - - -
1088A ASN 3.3 16.9 - - - +
1089A LEU* 3.1 13.7 + - + +
1091A THR* 1.3 83.9 + - - +
1093A ILE* 1.3 59.8 + - - +
1094A GLY 3.3 0.6 + - - -
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Residues in contact with ILE1093 (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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1024A LEU* 5.5 2.7 - - + -
1066A ILE* 4.0 36.6 - - + +
1069A HIS* 4.0 42.1 + - + +
1070A LYS 4.2 3.8 - - - +
1071A ALA* 3.7 23.3 - - + -
1089A LEU 3.1 10.1 + - - +
1090A LEU* 3.3 22.2 - - + +
1092A GLN* 1.3 74.6 - - - +
1094A GLY* 1.3 59.4 + - - +
1095A CYS* 3.9 15.9 - - + -
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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