Contacts of the strand formed by residues 1097 - 1105 (chain A) in PDB entry 5JHN
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 TYR1097 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962A MET* 4.0 14.9 + - - -
1072A ILE 3.4 17.5 - - - +
1073A SER* 3.7 19.3 - - - -
1074A ASP* 4.2 2.0 - - - +
1088A ASP* 3.9 1.4 - - - +
1089A LEU* 2.9 32.4 + - + +
1090A ASP* 5.2 1.2 - - - +
1095A GLU* 2.4 54.5 + - + +
1096A VAL* 1.3 83.8 - - - +
1098A CYS* 1.3 62.6 + - - +
1132A ARG* 3.9 32.7 + - + +
1133A PHE* 3.5 41.5 - + + -
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Residues in contact with CYS1098 (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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1070A GLU 3.6 0.3 - - - +
1071A LEU* 3.5 5.7 - - - +
1072A ILE* 2.8 43.7 + - + +
1073A SER 4.8 1.6 - - - +
1074A ASP* 5.1 1.8 - - - +
1077A ALA* 4.2 13.9 - - + -
1086A LEU* 3.8 22.2 - - - -
1087A PHE 3.1 37.5 - - - -
1088A ASP* 3.7 14.1 - - - +
1089A LEU* 4.2 3.4 - - - +
1097A TYR* 1.3 76.9 - - - +
1099A ILE* 1.3 66.6 + - - +
8F ARG* 4.4 0.4 - - - -
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Residues in contact with ILE1099 (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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956A ASN* 4.2 15.3 - - - +
1067A TYR* 3.3 46.4 - - + +
1069A GLY* 3.3 35.4 - - - +
1070A GLU 3.4 3.1 - - - -
1071A LEU* 3.8 17.0 - - + -
1085A TYR 3.5 1.9 - - - +
1086A LEU* 3.4 2.6 - - - -
1087A PHE* 2.8 38.1 + - + +
1089A LEU* 3.8 24.7 - - + -
1098A CYS* 1.3 76.2 - - - +
1100A ASP* 1.3 61.7 + - - +
1134A PRO 5.1 2.2 - - - +
1136A ILE* 4.4 9.2 - - + +
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Residues in contact with ASP1100 (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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1070A GLU* 2.8 39.1 + - + +
1072A ILE* 3.8 12.3 - - + -
1080A ARG* 2.8 40.7 + - - +
1082A ASP 4.7 4.1 - - - +
1085A TYR 3.5 9.5 - - - +
1086A LEU* 3.4 22.7 - - + +
1098A CYS 4.0 0.8 + - - -
1099A ILE* 1.3 73.9 - - - +
1101A ALA* 1.3 59.9 + - - +
1102A ARG* 3.0 31.3 + - - +
1103A TYR* 4.4 2.4 - - - -
1104A TYR 3.4 4.0 + - - +
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Residues in contact with ALA1101 (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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1067A TYR* 3.8 21.1 - - + +
1068A VAL 3.7 21.3 - - - +
1069A GLY* 4.3 0.2 - - - -
1085A TYR* 2.8 16.5 + - + +
1099A ILE 3.9 1.2 - - - -
1100A ASP* 1.3 70.4 - - - +
1102A ARG* 1.3 58.6 + - - +
1103A TYR 3.5 1.7 + - - -
1104A TYR 3.2 14.6 - - - +
1105A GLY* 4.1 0.9 - - - -
1109A ARG* 2.8 50.0 + - + +
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Residues in contact with ARG1102 (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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949A ASP* 2.7 47.0 + - - +
950A TYR* 3.4 4.3 - - - +
1082A ASP* 3.2 41.6 + - + +
1085A TYR* 3.6 23.2 - - + +
1100A ASP* 3.0 20.0 + - - +
1101A ALA* 1.3 76.2 - - - +
1103A TYR* 1.3 100.8 + - + +
1109A ARG* 2.8 24.5 + - - +
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Residues in contact with TYR1103 (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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949A ASP 5.4 0.2 - - - -
950A TYR* 3.5 3.5 - - - +
951A LYS* 2.7 34.1 + - - +
1070A GLU* 4.2 3.3 + - - +
1080A ARG* 4.0 33.0 - - - -
1081A GLU* 5.7 3.6 + - - +
1082A ASP* 4.7 12.7 + - + +
1100A ASP* 4.4 3.4 + - - -
1102A ARG* 1.3 122.8 + - + +
1104A TYR* 1.3 77.4 + - + +
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Residues in contact with TYR1104 (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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951A LYS* 3.3 32.1 - - + -
953A ILE* 3.6 20.4 - - + -
957A CYS* 3.6 14.6 - - - -
959A THR* 4.1 15.3 - - + -
1069A GLY* 3.2 9.7 - - - -
1070A GLU* 3.8 15.9 - - + -
1100A ASP 3.4 2.4 + - - +
1101A ALA* 3.2 20.3 - - - -
1103A TYR* 1.3 93.0 - - + +
1105A GLY* 1.4 57.7 + - - +
968B ILE* 3.8 33.3 - - + +
969B THR* 3.9 20.6 - - - +
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Residues in contact with GLY1105 (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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950A TYR* 3.9 4.8 - - - -
951A LYS 3.0 6.3 + - - -
952A TYR* 3.3 9.9 - - - -
953A ILE* 3.0 27.2 + - - +
1068A VAL 3.3 13.5 - - - -
1101A ALA* 4.1 12.1 + - - -
1104A TYR* 1.4 75.3 - - - +
1106A ASN* 1.3 62.9 + - - -
1109A ARG* 4.3 6.1 - - - -
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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