Contacts of the strand formed by residues 1188 - 1193 (chain A) 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 LEU1188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1040A ILE* 4.9 9.2 - - + -
1056A LEU* 4.0 20.0 - - + +
1057A PRO 3.3 23.8 - - - +
1058A MET* 4.0 17.2 - - - -
1059A GLY 3.6 3.8 - - - +
1060A ARG 3.5 14.4 - - - +
1062A VAL* 3.8 24.0 - - + -
1079A VAL* 5.0 3.1 - - + -
1139A ASP 2.9 12.7 + - - +
1140A VAL* 3.3 13.7 - - + -
1141A ILE 2.9 26.3 + - - +
1186A ASN 3.9 1.0 + - - -
1187A THR* 1.3 75.5 - - - +
1189A LEU* 1.3 64.3 + - - +
1190A ILE* 3.9 27.6 - - + -
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Residues in contact with LEU1189 (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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1060A ARG 3.0 9.0 + - - +
1061A ILE* 3.4 6.1 - - + +
1062A VAL* 2.9 26.7 + - - +
1129A CYS* 4.7 7.4 - - + -
1141A ILE* 3.2 21.5 - - + +
1143A VAL* 3.9 18.2 - - + -
1178A LEU* 3.7 20.9 - - + -
1182A LEU* 3.7 37.5 - - + -
1187A THR 3.8 0.4 + - - -
1188A LEU* 1.3 74.0 - - - +
1190A ILE* 1.3 76.4 + - - +
1191A PHE* 3.6 32.1 - - + -
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Residues in contact with ILE1190 (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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1056A LEU* 3.8 22.9 - - + -
1062A VAL* 3.3 17.9 - - + +
1064A ILE* 3.7 29.4 - - + -
1076A THR* 3.9 13.9 - - - +
1079A VAL* 3.9 26.0 - - + -
1140A VAL* 4.7 6.5 - - + -
1141A ILE 2.8 10.4 + - - +
1142A VAL* 3.2 12.6 - - + +
1143A VAL 2.8 27.9 + - - +
1188A LEU* 3.9 18.4 - - + -
1189A LEU* 1.3 79.1 - - - +
1191A PHE* 1.3 67.9 + - - +
1192A ILE* 4.7 0.9 - - + +
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Residues in contact with PHE1191 (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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1061A ILE* 3.7 24.0 - - + -
1062A VAL 2.7 11.8 + - - +
1063A GLU* 3.3 2.9 - - - +
1064A ILE 2.9 25.5 + - - -
1126A LEU* 4.1 21.8 - - + -
1143A VAL* 3.8 31.4 - - + -
1146A VAL* 3.8 19.5 - - + -
1149A LEU* 4.5 4.5 - - + -
1171A MET* 4.8 2.7 - - + -
1175A MET* 3.8 30.1 - - + -
1178A LEU* 4.4 1.3 - - + -
1189A LEU* 3.6 33.7 - - + -
1190A ILE* 1.3 73.4 - - - +
1192A ILE* 1.3 62.4 + - - +
1215A LEU* 3.7 25.6 - - + -
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Residues in contact with ILE1192 (chain A).
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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1064A ILE* 3.4 7.4 - - + +
1072A LYS* 3.6 50.7 - - + +
1073A THR* 3.9 9.4 - - - -
1076A THR* 3.5 30.7 - - + +
1142A VAL* 4.4 3.6 - - + -
1143A VAL 2.9 10.4 + - - +
1144A ASP* 3.4 36.8 - - + +
1145A SER* 3.0 17.7 - - - +
1146A VAL* 2.9 27.1 + - - +
1190A ILE* 4.8 3.1 - - + -
1191A PHE* 1.3 74.3 - - - +
1193A ASN* 1.3 63.0 + - - +
1501A ALF 5.3 0.2 - - - -
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Residues in contact with ASN1193 (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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1063A GLU* 3.1 21.3 - - + +
1064A ILE 2.8 8.6 + - - +
1065A TYR* 3.3 28.9 - - + +
1066A GLY 3.7 0.5 + - - -
1072A LYS* 3.4 13.0 - - - +
1145A SER* 4.9 0.4 - - - +
1146A VAL* 3.3 20.7 - - + +
1147A ALA 3.9 3.2 - - - +
1191A PHE 3.8 0.4 + - - -
1192A ILE* 1.3 75.1 - - - +
1194A GLN* 1.3 79.3 + - - +
1209A THR* 3.0 14.1 - - - +
1210A THR* 2.9 53.4 + - - +
1215A LEU* 4.5 1.4 - - - +
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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