Contacts of the strand formed by residues 1060 - 1066 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1051E MET* 3.8 34.3 - - + +
1053E LYS* 3.7 31.7 - - + +
1059E PRO* 1.3 70.8 - - - +
1061E TYR* 1.3 60.8 + - - +
1062E VAL* 3.7 13.2 - - + -
1075E TYR* 3.3 9.5 - - - -
1076E ALA* 2.8 41.3 + - + +
1086E ALA* 3.8 14.1 - - + +
1104E LEU* 3.4 21.5 - - + -
1106E ARG 3.3 16.2 - - - +
1107E GLY* 4.3 2.7 - - - -
1108E ALA 4.2 7.0 - - - +
1109E ILE* 4.2 10.8 - - + -
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Residues in contact with TYR1061 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083D HIS* 5.6 2.8 - - - -
1114D TRP* 4.3 11.7 - + + -
1116D TYR* 3.3 30.1 - + - -
1059E PRO* 4.0 16.9 - - + +
1060E LEU* 1.3 75.3 - - - +
1062E VAL* 1.3 66.5 + - - +
1074E ALA 3.5 4.0 - - - -
1075E TYR* 3.5 35.4 - + - -
1104E LEU* 3.9 1.0 - - - +
1105E HIS* 2.9 47.3 + + + -
1106E ARG* 3.0 43.0 + - + +
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Residues in contact with VAL1062 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017E ILE* 3.8 22.2 - - + -
1049E PHE* 3.8 27.7 - - + -
1051E MET* 4.1 18.2 - - + -
1060E LEU* 3.7 26.0 - - + -
1061E TYR* 1.3 78.9 - - - +
1063E ASN* 1.3 73.4 + - - +
1073E SER* 3.2 6.6 - - - -
1074E ALA* 2.8 38.3 + - + +
1086E ALA* 4.6 3.8 - - + -
1102E LEU* 4.2 8.7 - - + -
1103E ARG 3.4 9.4 - - - +
1104E LEU* 4.8 1.1 - - + -
1109E ILE* 4.9 0.2 - - + -
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Residues in contact with ASN1063 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114D TRP* 3.5 22.8 - - - -
1061E TYR* 5.8 0.2 - - - +
1062E VAL* 1.3 77.8 + - - +
1064E LEU* 1.3 60.7 + - - +
1065E MET* 3.6 21.1 + - - +
1070E VAL* 3.7 12.1 - - + +
1072E VAL 3.6 3.1 - - - -
1073E SER* 2.8 26.3 + - - -
1102E LEU* 3.3 4.7 - - - +
1103E ARG* 2.7 69.3 + - + +
1105E HIS* 3.6 11.4 - - - +
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Residues in contact with LEU1064 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047E PHE* 4.2 14.4 - - + -
1049E PHE* 4.0 15.0 - - + -
1062E VAL 4.3 0.2 + - - -
1063E ASN* 1.3 71.7 - - - +
1065E MET* 1.3 59.8 + - - +
1070E VAL* 3.9 1.0 - - - -
1071E LEU* 2.9 41.1 + - + +
1072E VAL* 2.8 28.7 + - + +
1090E ALA* 3.8 30.7 - - + +
1092E LEU* 4.6 3.4 - - + -
1100E ILE* 3.6 27.8 - - + -
1101E TRP 3.7 2.0 - - - +
1102E LEU* 3.6 20.3 - - + +
1119E PHE* 3.9 14.6 - - + -
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Residues in contact with MET1065 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063E ASN* 3.6 25.1 - - - +
1064E LEU* 1.3 73.9 - - - +
1066E LYS* 1.3 60.4 + - - +
1067E ASN 3.9 1.1 - - - +
1068E GLU* 3.6 28.5 - - - +
1069E GLU 3.3 14.8 - - - +
1070E VAL* 3.7 17.0 - - + +
1071E LEU* 4.2 2.6 - - - +
1100E ILE* 3.4 13.0 - - - +
1101E TRP* 2.7 77.8 + - + +
1103E ARG* 3.7 33.2 - - + +
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Residues in contact with LYS1066 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065E MET* 1.3 71.9 - - - +
1067E ASN* 1.3 77.8 + - - +
1068E GLU 3.0 0.5 + - - -
1069E GLU* 2.9 42.4 + - - +
1071E LEU* 3.3 35.6 - - + +
1092E LEU* 5.4 2.0 - - + +
1093E GLN 4.0 16.0 + - - -
1094E LEU* 3.9 14.8 - - + -
1098E ASP* 4.0 18.8 + - - -
1099E GLN 3.5 3.6 - - - +
1100E ILE* 3.8 10.3 - - + -
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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