Contacts of the strand formed by residues 1090 - 1096 (chain A) in PDB entry 2W18
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 PHE1090 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061A HIS* 3.7 29.6 - + + -
1073A VAL* 4.0 16.2 - - + -
1074A LEU 3.5 12.8 - - - -
1075A SER* 4.2 3.8 - - - -
1088A PRO 4.2 5.2 - - - -
1089A VAL* 1.3 82.0 - - + +
1091A GLN* 1.3 62.6 + - - +
1107A LEU* 4.0 1.9 - - - +
1108A TYR* 2.9 45.0 + - + +
1118A PHE* 3.8 19.1 - + - -
1121A GLY* 4.3 2.5 - - - -
1122A ASP 4.4 2.9 - - - -
1123A VAL* 4.7 0.4 - - + -
1128A ALA* 3.5 31.9 - - + -
1129A ALA 3.5 20.6 - - - -
1130A ALA* 3.6 20.2 - - + -
1140A TRP* 4.0 17.5 - + - -
1142A LEU* 5.3 0.2 - - + -
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Residues in contact with GLN1091 (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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1057A ALA* 6.5 0.7 - - - -
1072A ILE 3.6 1.2 - - - +
1073A VAL* 3.5 2.8 - - - -
1074A LEU* 2.8 43.9 + - + +
1088A PRO* 5.8 1.3 - - - +
1090A PHE* 1.3 78.2 - - - +
1092A LEU* 1.3 64.3 + - - +
1093A ILE* 3.4 35.0 + - + +
1104A GLY* 4.4 12.0 - - - -
1106A MET 3.5 11.2 - - - +
1107A LEU* 3.7 21.3 - - + +
1108A TYR* 4.2 3.1 - - - -
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Residues in contact with LEU1092 (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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1064A TYR* 4.4 6.7 - - + -
1071A PHE* 4.0 28.5 - - + -
1072A ILE 3.5 20.9 - - - +
1073A VAL* 3.8 22.9 - - + -
1091A GLN* 1.3 71.7 - - - +
1093A ILE* 1.3 66.0 + - - +
1094A VAL* 4.3 6.3 - - + -
1104A GLY* 3.8 1.0 - - - -
1105A VAL* 3.0 25.9 + - + +
1106A MET* 2.8 45.1 + - + +
1108A TYR* 3.8 15.3 - - + +
1142A LEU* 5.6 3.6 - - + +
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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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1051A ILE* 3.7 21.8 - - + -
1070A LEU 3.6 1.4 - - - +
1071A PHE* 3.5 3.6 - - - -
1072A ILE* 3.0 41.5 + - + +
1074A LEU* 3.4 27.4 - - + -
1091A GLN* 3.4 31.6 - - + +
1092A LEU* 1.3 75.3 - - - +
1094A VAL* 1.3 64.3 + - - +
1095A ILE* 3.8 22.4 - - + +
1102A SER* 4.1 10.5 - - - +
1103A VAL 3.4 17.5 - - - +
1104A GLY* 4.3 4.3 - - - +
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Residues in contact with VAL1094 (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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1069A LEU* 3.9 26.2 - - + -
1070A LEU 3.3 6.5 - - - +
1071A PHE* 3.3 42.4 - - + -
1092A LEU* 4.3 8.5 - - + -
1093A ILE* 1.3 74.3 - - - +
1095A ILE* 1.3 64.5 + - - +
1096A ASN 4.4 0.2 + - - -
1101A LEU 4.2 1.0 - - - +
1102A SER* 3.5 2.1 - - - -
1103A VAL* 3.0 31.7 + - - +
1105A VAL* 4.2 25.5 - - + +
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Residues in contact with ILE1095 (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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1035A ILE* 3.6 27.1 - - + -
1049A MET* 3.8 36.1 - - + -
1051A ILE* 4.9 6.7 - - + -
1069A LEU* 3.5 7.4 - - - -
1070A LEU* 2.8 47.7 + - + +
1072A ILE* 3.6 28.0 - - + -
1093A ILE* 3.8 7.0 - - + -
1094A VAL* 1.3 75.0 - - - +
1096A ASN* 1.3 65.8 + - - +
1097A PRO* 3.2 5.5 - - + +
1100A THR 4.5 2.0 - - - -
1101A LEU 3.8 4.3 - - - +
1102A SER* 3.3 27.6 - - - -
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Residues in contact with ASN1096 (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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1068A GLY 4.4 1.6 + - - -
1069A LEU* 3.9 17.1 - - + +
1095A ILE* 1.3 73.0 - - - +
1097A PRO* 1.3 58.6 - - - +
1098A LYS* 3.1 22.7 + - - +
1099A THR* 3.3 31.8 + - - +
1100A THR* 2.5 37.9 + - - -
1101A LEU* 3.1 13.8 + - + +
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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