Contacts of the strand formed by residues 1008 - 1016 (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 VAL1008 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1005A PHE* 3.8 34.5 - - + -
1006A GLY 3.9 7.6 - - - +
1007A SER* 1.3 75.2 - - - +
1009A ASP* 1.3 74.5 + - - +
1029A PHE* 5.4 0.9 - - + -
1114A LEU* 3.8 12.6 - - + +
1116A HIS* 2.8 58.5 + - + +
1117A ARG* 2.9 7.9 + - - +
1150A LEU* 4.3 19.3 - - + -
1167A TYR* 4.3 2.0 - - + -
1168A GLU 3.4 14.8 - - - +
1170A ARG* 4.6 1.6 - - - +
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Residues in contact with ASP1009 (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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1008A VAL* 1.3 73.2 - - - +
1010A PHE* 1.3 61.8 + - - +
1011A SER* 5.6 0.4 - - - -
1113A HIS* 3.9 26.7 + - - +
1114A LEU 3.1 4.5 - - - +
1115A THR* 3.5 10.3 - - - +
1117A ARG* 2.8 39.1 + - - -
1166A LYS 4.6 0.4 - - - -
1167A TYR* 3.2 5.7 - - - +
1168A GLU* 2.8 38.7 + - + +
1170A ARG* 3.6 31.1 + - - +
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Residues in contact with PHE1010 (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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959A PHE* 3.7 35.7 - + - -
1008A VAL* 4.8 0.9 - - + -
1009A ASP* 1.3 76.9 - - - +
1011A SER* 1.3 69.7 + - - +
1027A PHE* 4.1 28.3 - + + -
1028A VAL 4.2 0.9 - - - -
1112A TRP* 3.5 19.2 - + - -
1113A HIS* 3.6 1.3 + - - -
1114A LEU* 2.6 51.1 + - + -
1150A LEU* 3.7 36.1 - - + -
1151A GLY 4.2 13.2 - - - -
1152A LEU* 4.3 8.1 - - + -
1165A LEU* 4.3 6.3 - - + -
1166A LYS 3.1 19.3 - - - -
1167A TYR* 4.0 8.1 - + + -
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Residues in contact with SER1011 (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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1009A ASP 5.6 0.2 - - - -
1010A PHE* 1.3 80.9 + - - +
1012A GLY* 1.3 57.1 + - - +
1111A ARG* 3.4 22.5 + - - -
1112A TRP* 3.0 26.7 - - - +
1113A HIS* 3.6 21.8 - - - -
1165A LEU* 3.7 1.4 - - - -
1166A LYS* 2.9 37.6 + - - +
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Residues in contact with GLY1012 (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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1011A SER* 1.3 79.1 - - - +
1013A THR* 1.3 62.3 + - - -
1111A ARG* 3.4 16.0 - - - -
1112A TRP* 3.0 51.4 + - - -
1163A SER 3.7 5.4 - - - -
1164A ASP 4.2 0.4 - - - -
1165A LEU* 3.8 5.2 - - - -
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Residues in contact with THR1013 (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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696A ASP 3.6 22.4 - - - +
697A LEU* 2.5 27.0 + - + +
724A PRO* 4.3 9.6 - - + -
1012A GLY* 1.3 72.7 - - - -
1014A PHE* 1.3 64.7 + - - +
1015A TYR* 4.8 0.4 - - + -
1109A ALA* 4.7 0.4 - - + -
1110A TYR 3.2 13.2 - - - +
1111A ARG* 3.0 16.8 + - - -
1112A TRP* 4.0 2.0 - - - -
1161A TYR 3.1 5.9 - - - +
1162A PHE* 3.2 4.2 - - - -
1163A SER* 2.6 57.2 + - - +
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Residues in contact with PHE1014 (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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1012A GLY 3.8 0.4 + - - -
1013A THR* 1.3 72.9 - - - +
1015A TYR* 1.3 63.5 + - - +
1016A VAL* 3.8 21.1 - - + -
1025A ALA* 3.4 43.1 - - + -
1026A GLY* 4.6 5.2 - - - -
1042A TRP* 4.0 15.9 - + + -
1104A TRP* 3.8 43.3 - + + -
1108A THR 3.4 1.4 - - - +
1110A TYR* 2.8 58.4 + + + +
1112A TRP* 3.9 26.5 - + + +
1160A VAL* 4.5 2.5 - - + -
1161A TYR 3.5 2.7 - - - -
1162A PHE* 4.6 9.0 - + - -
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Residues in contact with TYR1015 (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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696A ASP* 5.4 0.9 - - + -
722A HIS 3.3 20.9 + - - -
723A LEU* 3.6 25.0 - - + +
724A PRO* 3.6 33.9 - - + -
1013A THR* 4.8 1.1 - - + -
1014A PHE* 1.3 78.8 - - - +
1016A VAL* 1.3 64.6 + - - +
1017A ASN* 3.7 20.6 + - + -
1107A TYR* 3.3 42.3 + - - +
1108A THR 3.3 7.4 - - - -
1109A ALA* 3.3 29.4 - - + -
1160A VAL* 3.7 0.6 - - - -
1161A TYR* 2.7 48.4 + - + +
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Residues in contact with VAL1016 (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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1014A PHE* 3.8 26.9 - - + -
1015A TYR* 1.3 78.1 - - - +
1017A ASN* 1.3 59.2 + - - +
1018A THR* 3.1 30.1 + - + +
1104A TRP* 3.6 44.6 - - + -
1105A LYS 5.0 1.4 + - - +
1107A TYR* 2.9 30.6 + - - +
1108A THR 4.5 3.0 + - - -
1157A GLN* 3.9 2.2 - - + +
1158A GLU 3.9 7.2 - - - +
1159A MSE 3.4 9.4 - - - +
1160A VAL* 4.2 15.0 - - + -
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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