Contacts of the strand formed by residues 1099 - 1105 (chain A) in PDB entry 5J68
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 SER1099 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1037A VAL* 3.5 4.3 - - - +
1038A ASP* 2.9 29.2 + - - +
1090A ARG* 4.0 21.1 + - - +
1091A SER 3.4 6.4 + - - -
1092A HIS* 5.2 0.9 - - - -
1097A GLU* 3.2 13.8 + - - -
1098A VAL* 1.3 74.6 - - - +
1100A ILE* 1.3 64.4 + - - +
1101A TYR* 3.9 22.2 - - - -
1264A LYS* 3.0 28.4 + - - +
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Residues in contact with ILE1100 (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 GLU* 4.3 26.0 - - + +
1036A TRP 3.6 4.0 - - - +
1037A VAL* 3.8 27.1 - - + +
1089A GLY 3.8 0.9 - - - +
1090A ARG* 3.6 2.5 - - - -
1091A SER* 2.7 41.4 + - - +
1092A HIS 4.5 0.9 - - - +
1093A GLY* 3.5 25.4 - - - -
1094A GLU* 4.1 14.6 - - - +
1098A VAL 5.0 0.4 - - - +
1099A SER* 1.3 78.1 - - - +
1101A TYR* 1.3 70.4 + - - +
1102A SER* 4.8 3.4 + - - -
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Residues in contact with TYR1101 (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 GLU* 3.4 2.9 - - - +
1036A TRP* 2.9 70.4 + + + +
1038A ASP* 3.3 42.8 + - + -
1050A TYR* 3.6 8.6 - + - -
1073A PHE* 3.4 36.3 - + + -
1089A GLY 3.4 2.5 - - - -
1090A ARG* 3.5 32.9 - - + -
1099A SER* 4.0 7.0 - - - -
1100A ILE* 1.3 76.8 - - - +
1102A SER* 1.3 63.6 + - - +
1263A LEU* 3.6 31.7 - - + +
1264A LYS* 4.0 11.3 + - - +
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Residues in contact with SER1102 (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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1034A LEU 3.2 15.3 - - - -
1035A GLU* 4.3 10.8 - - - +
1036A TRP* 4.6 4.0 - - - -
1073A PHE* 3.8 2.6 - - - -
1088A ALA* 3.3 5.4 - - - +
1089A GLY* 2.8 44.5 + - - +
1100A ILE* 4.8 3.9 + - - -
1101A TYR* 1.3 78.0 - - - +
1103A VAL* 1.3 65.1 + - - +
1245A LEU* 4.9 10.0 + - - +
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Residues in contact with VAL1103 (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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1032A VAL 4.3 0.2 - - - +
1033A SER* 3.4 1.5 - - - -
1034A LEU* 2.7 47.0 + - + +
1036A TRP* 3.7 24.0 - - + -
1052A LEU* 3.7 18.4 - - + -
1077A LEU* 4.0 22.0 - - + -
1086A VAL* 3.6 23.8 - - + -
1087A ALA 3.3 13.7 - - - +
1102A SER* 1.3 76.0 - - - +
1104A ILE* 1.3 61.2 + - - +
1105A PHE* 4.1 16.7 - - + -
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Residues in contact with ILE1104 (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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1025A VAL* 5.7 0.9 - - + -
1031A VAL* 4.5 0.7 - - + -
1032A VAL 3.4 11.2 - - - +
1033A SER* 3.7 18.2 - - - -
1085A CYS 3.7 0.7 - - - +
1086A VAL* 3.3 8.3 - - - +
1087A ALA* 2.8 43.4 + - + +
1103A VAL* 1.3 74.9 - - - +
1105A PHE* 1.3 67.4 + - - +
1106A LYS* 3.9 15.7 - - + +
1244A TYR* 3.6 39.3 - - + -
1245A LEU 5.5 0.7 - - - +
1275A VAL* 3.9 27.8 - - + -
1277A MET* 4.5 13.5 - - + -
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Residues in contact with PHE1105 (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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1030A THR 4.4 0.4 - - - -
1031A VAL* 3.2 8.5 - - - +
1032A VAL 2.5 40.2 + - - +
1034A LEU* 4.2 12.1 - - + -
1052A LEU* 3.5 31.4 - - + -
1054A HIS* 3.6 35.4 - + - -
1071A LEU* 4.3 6.1 - - + -
1085A CYS 3.4 2.9 - - - +
1086A VAL* 3.8 23.6 - - + -
1103A VAL* 4.1 14.6 - - + -
1104A ILE* 1.3 75.9 - - - +
1106A LYS* 1.3 60.4 + - - +
1107A CYS 3.8 0.9 - - - +
1108A LEU* 3.8 26.2 - - + -
1116A PHE* 3.5 32.3 - + - -
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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