Contacts of the strand formed by residues 1097 - 1105 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962D MET* 4.0 14.6 - - + -
1071D LEU* 6.2 0.7 - - + -
1072D ILE 3.5 15.3 - - - +
1073D SER* 3.8 18.6 - - - -
1074D ASP 4.3 0.7 - - - +
1089D LEU* 2.8 44.7 + - + +
1096D VAL* 1.3 89.0 - - - +
1098D CYS* 1.3 64.5 + - - +
1132D ARG* 3.9 50.3 + - + +
1133D PHE* 3.5 42.7 - + + -
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Residues in contact with CYS1098 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070D GLU 3.6 0.3 - - - +
1071D LEU* 3.6 5.0 - - - +
1072D ILE* 2.9 38.4 + - + +
1074D ASP* 4.4 16.2 - - - -
1077D ALA* 3.8 24.2 - - - -
1086D LEU* 3.9 19.7 - - + -
1087D PHE 3.2 10.3 - - - +
1088D ASP* 3.5 23.3 - - - +
1089D LEU* 4.3 3.3 - - - +
1096D VAL* 5.0 2.5 - - - -
1097D TYR* 1.3 79.8 - - - +
1099D ILE* 1.3 64.3 + - - +
1100D ASP 3.9 0.2 - - - -
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Residues in contact with ILE1099 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956D ASN* 4.2 12.1 - - - +
1067D TYR* 3.5 36.9 - - + +
1069D GLY* 3.3 41.7 - - - +
1070D GLU 3.6 3.4 - - - +
1071D LEU* 4.1 11.4 - - + -
1085D TYR 3.5 2.9 - - - +
1086D LEU* 3.5 1.1 - - - -
1087D PHE* 2.7 42.5 + - + +
1089D LEU* 3.7 31.9 - - + -
1098D CYS* 1.3 77.0 - - - +
1100D ASP* 1.3 56.7 + - - +
1134D PRO 4.8 4.3 - - - +
1136D ILE* 4.1 15.5 - - + +
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Residues in contact with ASP1100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069D GLY* 4.4 0.4 - - - -
1070D GLU* 2.9 40.9 + - - +
1072D ILE* 3.8 12.3 - - + -
1080D ARG* 2.8 39.8 + - - +
1082D ASP 4.6 6.4 - - - +
1085D TYR* 3.7 10.4 - - - +
1086D LEU* 3.6 22.9 - - + +
1098D CYS 3.9 0.6 - - - -
1099D ILE* 1.3 70.5 - - - +
1101D ALA* 1.3 59.9 + - - +
1102D ARG* 3.0 30.8 + - - +
1103D TYR* 4.6 2.2 + - - -
1104D TYR 3.5 2.8 + - - +
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Residues in contact with ALA1101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067D TYR* 3.6 25.8 - - + +
1068D VAL 3.7 20.2 - - - +
1069D GLY* 4.3 0.7 - - - -
1085D TYR* 2.9 13.5 + - + +
1099D ILE 3.9 0.6 + - - -
1100D ASP* 1.3 72.2 - - - +
1102D ARG* 1.3 60.8 + - - +
1103D TYR 3.6 0.9 - - - -
1104D TYR 3.3 15.5 + - - +
1105D GLY* 4.1 0.7 - - - -
1109D ARG* 2.9 45.3 + - + -
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Residues in contact with ARG1102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949D ASP* 2.7 43.3 + - - +
950D TYR* 3.6 2.6 - - - +
1082D ASP* 3.3 41.1 + - + +
1085D TYR* 3.4 24.7 - - + +
1100D ASP* 3.0 22.1 + - - +
1101D ALA* 1.3 76.3 - - - +
1103D TYR* 1.3 99.5 + - + +
1109D ARG* 2.9 20.3 + - - +
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Residues in contact with TYR1103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949D ASP 5.2 0.2 - - - -
950D TYR* 3.5 5.1 - - - +
951D LYS* 2.9 25.0 + - - +
1070D GLU* 4.3 4.9 + - - +
1080D ARG* 4.1 33.0 - - + +
1081D GLU* 4.5 20.4 + - - +
1082D ASP* 5.5 2.3 - - - +
1100D ASP* 4.6 3.0 + - - -
1102D ARG* 1.3 118.2 + - + +
1104D TYR* 1.3 84.7 + - + +
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Residues in contact with TYR1104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968A ILE* 3.6 40.4 - - + +
969A THR* 3.5 21.5 + - + +
1020A ALA* 6.4 0.7 - - + -
951D LYS* 3.4 32.8 - - + -
953D ILE* 3.6 19.3 - - + -
957D CYS* 3.7 16.8 - - - -
959D THR* 4.5 10.3 - - + -
1069D GLY* 3.2 16.6 - - - -
1070D GLU* 4.3 12.8 - - + +
1100D ASP 3.5 2.9 + - - +
1101D ALA* 3.3 13.3 - - - -
1103D TYR* 1.3 94.7 - - + +
1105D GLY* 1.3 58.3 + - - +
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Residues in contact with GLY1105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950D TYR* 3.8 5.5 - - - -
951D LYS 3.2 6.7 + - - +
952D TYR* 3.3 9.2 - - - -
953D ILE* 3.0 28.0 + - - +
1068D VAL 3.2 14.4 - - - -
1101D ALA* 4.1 11.4 + - - -
1104D TYR* 1.3 75.1 - - - +
1106D ASN* 1.3 64.1 + - - -
1109D ARG* 4.3 5.6 - - - -
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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