Contacts of the strand formed by residues 1097 - 1105 (chain C) in PDB entry 2O8J
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962C MET* 3.7 27.1 + - + -
1071C LEU* 6.0 0.7 - - + -
1072C ILE 3.4 15.5 - - - +
1073C SER* 3.6 20.0 - - - -
1074C ASP 4.4 0.2 - - - +
1088C ASP* 4.3 0.3 - - - -
1089C LEU* 3.2 41.0 + - + +
1095C GLU* 2.6 52.6 + - + +
1096C VAL* 1.3 78.6 - - - +
1098C CYS* 1.3 69.8 + - - +
1132C ARG* 3.8 21.1 + - + +
1133C PHE* 3.5 35.6 - + + -
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Residues in contact with CYS1098 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070C GLU 3.7 0.2 - - - +
1071C LEU* 3.6 5.7 - - - +
1072C ILE* 2.9 35.5 + - + +
1074C ASP* 4.2 24.9 - - - -
1077C ALA* 4.3 15.3 - - - -
1086C LEU* 3.7 20.9 - - + -
1087C PHE 3.3 12.6 - - - +
1088C ASP* 3.6 22.2 - - - -
1089C LEU* 4.2 4.3 - - - -
1096C VAL* 5.0 2.0 - - - -
1097C TYR* 1.3 80.4 - - - +
1099C ILE* 1.3 65.2 + - - +
1100C ASP 4.0 0.2 - - - -
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Residues in contact with ILE1099 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956C ASN* 4.0 15.3 - - - +
1067C TYR* 3.3 35.4 - - + +
1068C VAL 3.8 4.5 - - - -
1069C GLY* 3.3 39.9 - - - +
1070C GLU 3.5 2.2 - - - -
1071C LEU* 3.8 17.7 - - + -
1085C TYR 3.5 4.2 - - - +
1086C LEU* 4.3 1.8 - - - -
1087C PHE* 2.8 41.2 + - + +
1089C LEU* 3.7 24.7 - - + -
1098C CYS* 1.3 74.8 - - - +
1100C ASP* 1.3 57.8 + - - +
1134C PRO 4.8 2.5 - - - +
1136C ILE* 4.2 15.5 - - + +
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Residues in contact with ASP1100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070C GLU* 2.8 39.3 + - + +
1072C ILE* 3.9 8.0 - - + +
1080C ARG* 2.9 43.2 + - - +
1082C ASP 4.5 9.2 - - - +
1085C TYR* 3.7 10.2 - - - +
1086C LEU* 3.7 19.9 + - + +
1098C CYS 4.0 0.8 - - - -
1099C ILE* 1.3 71.6 - - - +
1101C ALA* 1.3 60.0 + - - +
1102C ARG* 2.9 36.3 + - - +
1103C TYR* 4.8 1.7 + - - -
1104C TYR 3.5 2.8 + - - +
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Residues in contact with ALA1101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067C TYR* 3.7 24.2 - - + +
1068C VAL 3.7 21.8 - - - +
1069C GLY* 4.4 0.2 - - - -
1085C TYR* 2.9 13.3 + - + +
1099C ILE 3.8 0.8 + - - -
1100C ASP* 1.3 70.3 - - - +
1102C ARG* 1.3 63.5 + - - +
1103C TYR 3.5 2.1 + - - -
1104C TYR 3.1 16.1 - - - +
1105C GLY* 4.1 1.3 - - - -
1109C ARG* 2.9 44.0 + - + -
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Residues in contact with ARG1102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949C ASP* 2.8 43.7 + - - +
950C TYR* 3.6 2.6 - - - +
1082C ASP* 3.6 37.3 + - + +
1085C TYR* 3.4 24.9 - - + +
1100C ASP* 2.9 22.5 + - - +
1101C ALA* 1.3 77.6 - - - +
1103C TYR* 1.3 97.2 + - + +
1109C ARG* 2.9 18.5 + - - +
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Residues in contact with TYR1103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950C TYR* 3.6 4.1 - - - +
951C LYS* 2.9 27.2 + - - +
1070C GLU* 4.2 4.5 + - - +
1080C ARG* 4.2 32.3 - - + +
1081C GLU* 5.9 4.2 + - - +
1082C ASP* 5.9 2.1 - - - +
1100C ASP* 4.8 3.0 + - - -
1102C ARG* 1.3 119.0 + - + +
1104C TYR* 1.3 81.5 + - + +
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Residues in contact with TYR1104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968B ILE* 3.8 45.9 - - + +
969B THR* 3.9 14.1 - - + +
1020B ALA* 6.4 0.4 - - + -
951C LYS* 3.3 33.4 - - + -
953C ILE* 3.6 19.3 - - + -
957C CYS* 3.8 13.9 - - - -
959C THR* 4.4 11.7 - - + -
1069C GLY* 3.2 9.5 - - - -
1070C GLU* 4.0 16.4 + - + +
1100C ASP 3.5 2.6 + - - +
1101C ALA* 3.1 21.7 - - - -
1103C TYR* 1.3 93.0 - - + +
1105C GLY* 1.3 59.5 + - - +
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Residues in contact with GLY1105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950C TYR* 3.8 5.3 - - - -
951C LYS 3.1 7.5 + - - -
952C TYR* 3.2 9.7 - - - -
953C ILE* 3.0 27.6 + - - +
1068C VAL 3.3 12.8 - - - -
1101C ALA* 4.1 12.3 + - - -
1104C TYR* 1.3 75.5 - - - +
1106C ASN* 1.3 63.2 + - - -
1109C ARG* 4.3 6.3 - - - -
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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