Contacts of the strand formed by residues 1140 - 1143 (chain D) in PDB entry 3CMT
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 VAL1140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1040D ILE* 5.5 4.5 - - + -
1058D MET* 5.5 2.0 - - + -
1079D VAL* 4.5 14.4 - - + -
1080D ILE* 4.3 20.4 - - + -
1083D ALA* 3.8 17.9 - - + -
1088D LYS* 5.0 2.5 - - + -
1089D THR 3.3 1.2 + - - -
1090D CYS* 3.1 29.1 - - - +
1091D ALA 2.9 23.7 + - - +
1138D VAL* 3.6 1.1 - - - +
1139D ASP* 1.3 86.8 - - + +
1141D ILE* 1.3 71.0 + - - +
1142D VAL* 4.3 4.7 - - + -
1188D LEU* 3.3 23.1 - - + +
1190D ILE* 4.7 2.0 - - + -
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Residues in contact with ILE1141 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1091D ALA* 3.4 16.4 - - + +
1093D ILE* 4.0 24.7 - - + -
1129D CYS* 3.9 29.4 - - + +
1132D LEU* 3.8 27.4 - - + -
1133D ALA* 4.2 3.6 - - - +
1138D VAL* 3.8 15.9 - - + -
1140D VAL* 1.3 77.5 - - - +
1142D VAL* 1.3 67.1 + - - +
1182D LEU* 4.8 7.2 - - + -
1187D THR* 3.9 20.6 - - + -
1188D LEU 2.9 8.3 + - - +
1189D LEU* 3.2 11.7 - - + +
1190D ILE* 2.8 24.6 + - - +
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Residues in contact with VAL1142 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1076D THR* 3.3 33.7 - - + +
1080D ILE* 3.4 36.3 - - + -
1091D ALA 3.0 6.9 + - - +
1092D PHE* 3.6 15.0 - - + -
1093D ILE* 2.7 34.0 + - - +
1140D VAL* 4.3 7.0 - - + -
1141D ILE* 1.3 76.6 - - - +
1143D VAL* 1.3 67.3 + - - +
1144D ASP 4.3 0.7 - - - +
1190D ILE* 3.2 20.0 - - + +
1192D ILE* 4.4 4.7 - - + -
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Residues in contact with VAL1143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093D ILE* 3.6 16.8 - - + +
1095D ALA* 5.1 0.2 - - + -
1125D ALA* 5.5 1.6 - - + -
1126D LEU* 5.6 1.6 - - + -
1129D CYS* 3.7 30.1 - - - -
1141D ILE* 4.7 0.2 - - + -
1142D VAL* 1.3 76.2 - - - +
1144D ASP* 1.3 59.7 + - - +
1145D SER 3.4 8.1 + - - +
1149D LEU* 4.0 38.4 - - + -
1189D LEU* 3.9 15.3 - - + -
1190D ILE 2.8 8.9 + - - +
1191D PHE* 3.7 19.9 - - + -
1192D ILE* 2.9 28.6 + - - +
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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