Contacts of the strand formed by residues 988 - 994 (chain A) in PDB entry 2W18
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 GLN 988 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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980A SER* 3.1 6.9 + - - -
981A SER* 2.9 43.1 + - - +
986A ASP 3.3 8.6 + - - +
987A GLN* 1.3 77.5 - - - +
989A VAL* 1.3 64.8 + - - +
990A GLU* 3.4 22.1 - - - +
1005A PHE* 3.7 27.2 - - + -
1008A PRO* 5.0 2.0 - - - -
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Residues in contact with VAL 989 (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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978A VAL* 4.1 9.9 - - + -
979A SER 3.5 7.9 - - - +
980A SER* 3.6 13.7 - - - +
987A GLN* 4.4 13.9 - - - -
988A GLN* 1.3 79.5 - - - +
990A GLU* 1.3 64.2 + - - +
1005A PHE* 3.4 6.3 - - - +
1006A LEU* 2.8 66.2 + - + +
1008A PRO* 4.5 11.0 - - + +
1009A PRO* 4.5 0.4 - - + -
1013A ILE* 4.5 2.5 - - + -
1016A PHE* 4.1 10.1 - - + -
1038A TRP* 4.1 21.8 - - + -
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Residues in contact with GLU 990 (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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962A LYS* 3.3 28.2 + - - +
977A LEU 3.6 1.7 - - - +
978A VAL* 3.1 2.6 - - - +
979A SER* 2.8 40.5 + - - +
980A SER 6.1 0.2 - - - -
981A SER* 4.3 7.6 + - - -
988A GLN* 3.4 19.5 - - + +
989A VAL* 1.3 82.5 - - - +
991A VAL* 1.3 64.6 + - - +
992A MET 3.9 0.4 + - - -
1003A ASN* 2.9 32.5 + - - +
1004A GLN 3.4 5.2 - - - -
1005A PHE* 3.5 29.7 - - + -
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Residues in contact with VAL 991 (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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972A LEU* 4.4 8.5 - - + -
976A ARG* 3.9 36.1 - - + -
977A LEU 3.5 4.9 - - - +
978A VAL* 3.8 12.8 - - + -
990A GLU* 1.3 75.0 - - - +
992A MET* 1.3 60.1 + - - +
993A THR* 4.2 2.9 + - - +
1002A GLU 4.6 0.2 - - - -
1003A ASN* 3.6 3.5 - - - -
1004A GLN* 2.9 47.1 + - - +
1006A LEU* 3.5 39.0 - - + -
1040A LEU* 4.1 11.0 - - + -
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Residues in contact with MET 992 (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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944A ILE* 5.0 2.0 - - + -
961A LEU* 3.2 52.7 - - + +
962A LYS* 4.1 18.4 - - + +
976A ARG* 3.2 8.1 - - - +
977A LEU* 2.8 69.8 + - + +
990A GLU 3.9 1.0 - - - -
991A VAL* 1.3 73.1 - - - +
993A THR* 1.3 63.2 + - - +
994A PHE* 3.6 15.4 - - + -
1000A GLY* 5.2 8.5 - - - -
1002A GLU 3.3 13.2 - - - +
1003A ASN* 3.7 11.3 + - + +
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Residues in contact with THR 993 (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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974A LYS 4.2 11.2 - - - +
975A ARG* 3.5 10.5 - - + +
976A ARG* 3.7 14.4 - - + +
991A VAL* 4.8 3.3 + - - +
992A MET* 1.3 77.3 + - - +
994A PHE* 1.3 73.8 + - - +
1000A GLY* 3.9 2.0 - - - -
1001A LYS* 2.9 38.2 + - + +
1002A GLU* 3.1 26.9 + - - +
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Residues in contact with PHE 994 (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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925A VAL* 4.2 18.4 - - + -
928A VAL* 4.4 12.1 - - + -
931A LEU* 3.9 24.0 - - + -
933A CYS* 5.0 2.7 - - - -
946A ALA* 4.6 0.7 - - + -
961A LEU* 3.6 27.8 - - + -
975A ARG* 2.9 48.5 + - + +
977A LEU* 4.0 23.1 - - + -
992A MET* 3.6 23.6 - - + -
993A THR* 1.3 83.5 - - - +
995A ALA* 1.3 67.3 + - - +
998A GLY* 3.3 25.1 - - - +
999A GLY 3.4 6.5 - - - -
1000A GLY* 4.7 2.5 - - - -
1001A LYS* 4.4 1.1 - - - +
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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