Contacts of the strand formed by residues 1160 - 1169 (chain A) in PDB entry 1YO8
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 VAL1160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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989A VAL* 3.3 3.8 - - - -
990A GLN* 2.8 38.5 + - + +
1014A PHE* 4.5 8.1 - - + -
1015A TYR 3.8 4.9 - - - +
1016A VAL* 4.2 8.1 - - + +
1025A ALA* 3.7 20.0 - - + -
1154A VAL* 4.8 1.8 - - + -
1157A GLN* 3.5 38.4 - - + +
1158A GLU 3.6 7.6 - - - +
1159A MSE 1.3 76.2 - - - +
1161A TYR* 1.3 66.6 + - - +
1162A PHE* 3.4 37.6 - - + -
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Residues in contact with TYR1161 (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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723A LEU* 4.1 16.1 - - + +
724A PRO* 3.6 29.8 - - + -
739A ALA 4.9 2.6 + - - -
982A ARG* 3.5 28.5 + - - -
987A GLU* 4.8 3.1 - - - -
988A LEU 3.8 3.6 - - - -
989A VAL* 3.5 30.2 - - + +
1013A THR 3.1 4.9 - - - +
1014A PHE* 3.5 2.3 - - - -
1015A TYR* 2.7 46.6 + + + +
1017A ASN* 3.1 45.7 + - + -
1159A MSE 3.8 12.6 - - - -
1160A VAL* 1.3 79.1 - - - +
1162A PHE* 1.3 61.8 + - - +
1163A SER* 3.7 2.5 - - - +
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Residues in contact with PHE1162 (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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979A TRP* 3.6 24.2 - + - -
987A GLU* 3.3 5.8 - - - +
988A LEU 2.7 39.9 + - - +
990A GLN* 4.4 0.2 - - + -
1013A THR 3.2 6.7 - - - -
1014A PHE* 4.6 4.9 - + - -
1025A ALA* 4.1 1.8 - - + -
1026A GLY* 3.1 28.3 - - - -
1112A TRP* 3.8 13.7 - + - -
1152A LEU* 3.2 41.5 - - + -
1153A PHE 3.6 22.4 - - - -
1154A VAL* 4.0 6.1 - - + -
1160A VAL* 3.4 37.0 - - + -
1161A TYR* 1.3 72.1 - - - +
1163A SER* 1.3 59.8 + - - +
1165A LEU* 3.5 12.3 - - + +
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Residues in contact with SER1163 (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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698A ASP* 4.0 3.2 - - - +
724A PRO* 3.6 25.1 - - - +
726A SER* 3.0 12.0 + - - -
987A GLU* 2.5 29.9 + - - -
1012A GLY* 3.6 1.2 - - - -
1013A THR* 2.6 49.9 + - - -
1161A TYR* 5.0 2.0 - - - -
1162A PHE* 1.3 74.5 - - - +
1164A ASP* 1.3 73.2 + - - +
1165A LEU 3.2 3.1 + - - -
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Residues in contact with ASP1164 (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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697A LEU 4.4 0.7 - - - +
698A ASP* 3.8 22.7 - - - +
699A GLY* 3.9 16.1 + - - -
714A HIS* 5.0 6.9 - - - -
726A SER* 3.0 22.7 + - - -
983A HIS* 4.1 15.8 - - - -
986A LYS* 3.3 4.7 + - - +
1111A ARG* 2.9 33.6 + - - +
1163A SER* 1.3 77.4 + - - +
1165A LEU* 1.3 66.8 + - - +
1166A LYS* 3.3 29.9 + - - +
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Residues in contact with LEU1165 (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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957A THR* 3.2 15.6 - - + +
959A PHE* 3.8 32.5 - - + -
985A GLY 4.6 0.2 - - - +
986A LYS* 2.8 36.2 + - - +
987A GLU* 4.1 2.9 - - - +
988A LEU* 4.3 3.4 - - + +
1010A PHE* 4.3 5.2 - - + -
1011A SER 3.7 3.8 - - - +
1012A GLY* 3.8 20.4 - - - -
1112A TRP* 3.8 21.8 - - + -
1152A LEU* 3.8 22.4 - - + -
1162A PHE 3.5 23.3 - - - +
1163A SER 4.2 1.3 - - - +
1164A ASP* 1.3 77.9 - - - +
1166A LYS* 1.3 67.1 + - - +
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Residues in contact with LYS1166 (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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679A GLU* 5.0 19.2 + - - +
699A GLY* 5.9 0.8 - - - -
714A HIS* 5.0 12.9 + - - -
947A VAL* 6.2 2.0 - - + -
957A THR* 3.3 9.6 - - - +
986A LYS* 6.0 1.3 - - + -
1009A ASP 4.6 0.2 - - - -
1010A PHE* 3.1 5.9 - - - -
1011A SER* 2.9 44.5 + - - +
1111A ARG* 3.3 17.9 - - - +
1164A ASP* 3.3 34.2 + - - +
1165A LEU* 1.3 80.6 - - - +
1167A TYR* 1.3 62.5 + - - +
1168A GLU* 5.5 8.7 - - + +
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Residues in contact with TYR1167 (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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947A VAL* 3.0 27.9 - - + +
954A ILE* 4.2 6.3 - - + -
956A GLU 3.7 4.3 - - - -
957A THR* 2.8 33.0 + - + -
958A ASP 2.9 27.8 + - - -
959A PHE* 3.7 32.8 - + - -
1003A ASP* 2.4 30.4 + - + +
1005A PHE* 3.3 28.7 - + + -
1008A VAL* 4.3 1.6 - - + -
1009A ASP 3.2 9.9 - - - +
1010A PHE* 4.0 3.4 - + + -
1150A LEU* 3.4 35.2 - - + -
1166A LYS* 1.3 75.0 - - - +
1168A GLU* 1.3 66.7 + - - +
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Residues in contact with GLU1168 (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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668A LEU* 5.4 1.9 - - - +
677A LYS* 3.7 22.8 + - - -
679A GLU* 4.6 4.0 - - - +
946A ASP 5.7 0.4 - - - -
947A VAL* 3.2 27.7 - - + +
948A CYS* 4.5 0.9 - - - -
1005A PHE* 5.1 0.4 - - - -
1008A VAL* 3.4 8.3 - - - +
1009A ASP* 2.8 36.9 + - + +
1166A LYS* 5.5 10.1 - - + +
1167A TYR* 1.3 80.7 - - - +
1169A CYS* 1.3 66.5 + - - +
1170A ARG* 2.7 45.4 + - - +
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Residues in contact with CYS1169 (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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883A ASN* 5.8 2.5 - - - -
947A VAL 2.8 11.4 + - - +
948A CYS* 2.1 51.6 - - + -
949A PRO* 4.8 7.9 - - + +
950A GLU 6.1 0.7 - - - +
951A ASN* 5.1 9.9 - - + -
954A ILE* 5.1 0.9 - - - -
1004A GLU 5.5 0.7 - - - -
1005A PHE* 3.8 18.6 - - - -
1007A SER 3.9 9.6 - - - +
1168A GLU* 1.3 74.1 - - - +
1170A ARG* 1.3 68.1 + - - +
1171A ASP* 3.6 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