Contacts of the strand formed by residues 884 - 891 (chain A) in PDB entry 1SIW
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 HIS 884 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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849A THR* 3.3 6.4 - - - -
850A LEU* 2.8 59.0 + - + +
851A PRO 3.9 11.2 - - - -
852A ILE* 4.3 7.2 - - - -
853A GLN* 4.8 3.4 + - + +
856A SER* 5.3 1.2 + - - -
858A ALA* 3.8 25.9 - - + +
878A PRO* 4.2 3.6 + - - -
879A GLY* 3.4 29.5 - - - +
883A PRO* 1.3 74.2 - - - +
885A ILE* 1.3 59.7 + - - +
886A MET* 3.8 28.6 - - + +
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Residues in contact with ILE 885 (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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680A VAL* 3.6 35.0 - - + +
683A THR* 3.9 25.8 - - + -
684A VAL* 4.4 11.7 - - + -
687A LEU* 4.6 18.8 - - + -
694A PHE* 6.2 0.4 - - + -
847A ILE* 4.0 19.7 - - + -
848A VAL 3.8 2.7 - - - +
849A THR* 4.5 15.0 - - + -
876A LEU* 5.8 2.9 - - + -
878A PRO* 3.5 23.2 - - + +
882A ALA* 5.9 0.4 - - + -
883A PRO* 3.4 22.4 - - + +
884A HIS* 1.3 74.8 - - - +
886A MET* 1.3 65.9 + - - +
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Residues in contact with MET 886 (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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601A PRO* 3.9 34.8 - - + -
846A ASP 3.5 0.2 - - - +
847A ILE* 3.3 6.8 - - - +
848A VAL* 2.7 49.4 + - + +
850A LEU* 4.1 20.2 - - + -
884A HIS* 3.9 34.1 - - + +
885A ILE* 1.3 79.1 - - - +
887A VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 887 (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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600A ARG 4.7 3.6 - - - +
679A PRO* 3.9 28.0 - - + -
680A VAL* 4.1 16.8 - - + -
845A THR* 3.6 28.7 - - + -
846A ASP 3.4 3.6 - - - +
847A ILE* 4.7 4.9 - - + +
886A MET* 1.3 76.9 - - - +
888A VAL* 1.3 67.0 + - - +
889A GLU* 4.0 13.2 - - + +
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Residues in contact with VAL 888 (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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599A GLN* 4.2 14.4 - - + -
600A ARG 3.6 22.9 - - - +
601A PRO* 4.0 20.0 - - + +
846A ASP* 2.7 46.0 + - - +
848A VAL* 4.0 17.3 - - + -
887A VAL* 1.3 77.4 - - - +
889A GLU* 1.3 72.1 + - - +
890A ARG* 3.4 37.5 - - + +
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Residues in contact with GLU 889 (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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599A GLN* 3.8 19.6 - - - +
843A LYS 5.3 1.0 - - - +
844A GLU 3.1 9.2 - - - +
845A THR* 3.0 36.5 + - - +
887A VAL* 4.0 9.9 - - + +
888A VAL* 1.3 75.2 - - - +
890A ARG* 1.3 62.5 + - - +
891A ASP 4.3 0.2 + - - -
898A ARG* 4.5 4.8 + - - -
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Residues in contact with ARG 890 (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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207A SER 3.5 11.5 + - - -
208A LEU 3.6 15.0 + - - +
209A ILE 4.1 2.0 - - - -
210A GLY* 3.6 13.7 - - - -
599A GLN* 3.0 33.6 - - - +
601A PRO 4.9 6.9 + - - -
602A ALA* 6.0 1.4 - - - +
603A ARG* 3.4 16.4 - - - +
666A LEU* 5.1 0.9 - - - -
842A GLY 3.3 2.4 - - - +
843A LYS* 3.3 3.4 - - - -
844A GLU* 2.8 40.5 + - + +
846A ASP* 2.9 31.9 + - + +
848A VAL* 3.7 15.6 - - - +
888A VAL* 3.4 19.7 - - + +
889A GLU* 1.3 77.3 - - - +
891A ASP* 1.3 59.8 + - - +
892A TYR* 3.2 40.4 + - + +
898A ARG* 5.5 0.2 - - - -
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Residues in contact with ASP 891 (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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599A GLN* 4.7 1.4 + - - -
842A GLY 4.0 2.7 - - - -
843A LYS* 3.4 38.0 + - + +
889A GLU 4.3 0.4 + - - -
890A ARG* 1.3 71.1 - - - +
892A TYR* 1.3 57.0 + - - +
893A PRO* 3.5 12.1 - - - +
894A ALA* 2.9 44.1 + - + +
895A THR* 3.4 5.4 + - - -
898A ARG* 3.5 35.4 + - - +
938A PRO* 5.6 2.9 - - - +
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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