Contacts of the strand formed by residues 1060 - 1066 (chain A) in PDB entry 4OUL
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 LEU1060 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1051A MET* 3.9 29.8 - - + +
1053A LYS* 3.6 34.3 - - + +
1058A VAL 3.7 0.6 + - - -
1059A PRO* 1.3 72.9 - - - +
1061A TYR* 1.3 60.8 + - - +
1062A VAL* 3.9 11.7 - - + -
1074A ALA 3.8 0.3 - - - +
1075A TYR* 3.3 9.7 - - - -
1076A ALA* 2.8 41.0 + - + +
1086A ALA* 3.9 13.7 - - + -
1104A LEU* 3.4 33.7 - - + -
1106A ARG 3.4 3.1 - - - +
1107A GLY* 4.4 0.7 - - - -
1108A ALA 4.0 12.6 - - - +
1109A ILE* 4.1 9.0 - - + -
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Residues in contact with TYR1061 (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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1059A PRO* 3.9 17.4 - - + +
1060A LEU* 1.3 77.9 - - - +
1062A VAL* 1.3 64.5 + - - +
1063A ASN* 5.9 0.2 - - - +
1074A ALA 3.6 2.9 - - - -
1075A TYR* 3.5 35.5 - + - -
1104A LEU* 3.8 1.7 - - - +
1105A HIS* 2.9 52.9 + + + -
1106A ARG* 2.9 44.2 + - + +
1083C HIS* 5.9 1.0 - - - -
1114C TRP* 4.3 7.6 - + + -
1116C TYR* 3.4 30.1 - + - -
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Residues in contact with VAL1062 (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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1017A ILE* 3.9 21.5 - - + -
1049A PHE* 3.7 31.9 - - + -
1051A MET* 4.1 19.1 - - + -
1060A LEU* 3.9 26.9 - - + -
1061A TYR* 1.3 78.6 - - - +
1063A ASN* 1.3 71.9 + - - +
1073A SER* 3.2 6.9 - - - -
1074A ALA* 2.9 34.1 + - + +
1086A ALA* 4.4 3.8 - - + -
1102A LEU* 4.2 5.4 - - + -
1103A ARG 3.4 9.0 - - - +
1104A LEU* 4.8 0.7 - - + -
1109A ILE* 4.8 0.2 - - + -
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Residues in contact with ASN1063 (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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1062A VAL* 1.3 76.2 + - - +
1064A LEU* 1.3 60.7 + - - +
1065A MET* 3.6 20.3 + - - +
1070A VAL* 3.6 11.9 - - + +
1072A VAL 3.6 2.9 - - - -
1073A SER* 2.8 26.5 + - - -
1102A LEU* 3.3 8.7 - - - +
1103A ARG* 2.8 76.2 + - + +
1105A HIS* 3.6 12.4 - - - +
1114C TRP* 3.4 23.4 - - - -
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Residues in contact with LEU1064 (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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1047A PHE* 4.1 17.9 - - + -
1049A PHE* 4.1 10.0 - - + -
1062A VAL 4.3 0.2 + - - -
1063A ASN* 1.3 72.0 - - - +
1065A MET* 1.3 57.1 + - - +
1070A VAL* 3.8 1.4 - - - -
1071A LEU* 2.8 49.9 + - + +
1072A VAL* 2.9 27.6 + - + +
1089A HIS 5.3 0.7 - - - -
1090A ALA* 4.0 24.7 - - + +
1100A ILE* 3.5 24.5 - - + -
1101A TRP 3.7 6.3 - - - +
1102A LEU* 3.7 23.9 - - + +
1119A PHE* 3.8 15.0 - - + -
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Residues in contact with MET1065 (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 ASN* 3.6 25.6 - - - +
1064A LEU* 1.3 74.6 - - - +
1066A LYS* 1.3 58.5 + - - +
1067A ASN 3.9 1.8 - - - +
1068A GLU* 3.5 19.7 - - - +
1069A GLU 3.2 25.4 - - - +
1070A VAL* 3.7 16.4 - - + +
1071A LEU* 3.9 2.5 - - - -
1099A GLN 3.6 0.5 - - - +
1100A ILE* 3.3 11.6 - - - +
1101A TRP* 2.7 76.2 + - + +
1103A ARG* 3.7 34.8 - - + +
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Residues in contact with LYS1066 (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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1065A MET* 1.3 69.9 - - - +
1067A ASN* 1.3 81.3 + - - +
1069A GLU* 2.9 38.4 + - - +
1071A LEU* 3.5 35.6 - - + +
1092A LEU* 5.2 3.1 - - + -
1093A GLN 4.1 14.7 + - - +
1094A LEU* 3.9 15.0 - - + -
1095A PHE* 6.1 2.0 - - - -
1098A ASP* 3.7 23.8 + - - -
1099A GLN 3.4 3.8 - - - +
1100A ILE* 3.9 11.9 - - + -
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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