Contacts of the strand formed by residues 843 - 850 (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 LYS 843 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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842A GLY* 1.3 67.5 - - - -
844A GLU* 1.3 63.4 + - - +
845A THR* 5.1 1.6 + - - -
889A GLU* 5.3 0.6 - - - +
890A ARG 3.3 8.1 - - - +
891A ASP* 3.4 32.1 + - + +
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Residues in contact with GLU 844 (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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666A LEU* 4.0 31.1 - - + +
840A HIS 4.5 1.7 - - - +
841A LEU* 3.8 13.9 - - + +
842A GLY* 3.2 21.6 + - - +
843A LYS* 1.3 76.7 - - - +
845A THR* 1.3 63.5 + - - +
889A GLU* 3.1 9.0 - - - +
890A ARG* 2.8 33.0 + - + +
892A TYR* 3.6 37.7 - - + -
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Residues in contact with THR 845 (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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665A PRO 3.8 1.6 - - - +
666A LEU* 3.6 28.0 + - - +
669A ALA* 3.7 29.7 - - + +
679A PRO* 5.6 1.8 - - + -
843A LYS 5.1 0.9 + - - -
844A GLU* 1.3 76.2 + - - +
846A ASP* 1.3 62.8 + - - +
847A ILE* 4.4 4.2 - - + +
887A VAL* 3.6 28.5 - - + -
888A VAL 3.8 0.4 - - - -
889A GLU* 3.0 21.8 + - - +
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Residues in contact with ASP 846 (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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182A PRO* 3.3 10.8 - - - +
603A ARG* 2.9 38.4 + - - -
665A PRO* 3.5 8.4 - - - +
666A LEU* 3.8 13.2 - - + +
845A THR* 1.3 74.6 - - - +
847A ILE* 1.3 83.4 + - - +
848A VAL* 3.8 3.9 + - - -
886A MET 3.5 0.5 - - - +
887A VAL* 3.4 5.2 - - - -
888A VAL* 2.7 46.1 + - + +
890A ARG* 2.9 32.8 + - - +
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Residues in contact with ILE 847 (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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603A ARG* 3.3 7.1 + - - -
660A GLN* 4.1 2.4 - - - +
661A LEU* 4.4 20.6 - - + +
665A PRO* 3.3 18.9 + - + +
668A ILE* 3.9 29.2 - - + -
669A ALA* 4.4 5.6 - - + +
679A PRO* 3.8 28.3 - - + +
680A VAL* 6.4 0.2 - - + -
683A THR* 4.1 10.5 - - + +
845A THR* 4.4 13.7 - - + -
846A ASP* 1.3 93.4 + - - +
848A VAL* 1.3 62.3 + - - +
849A THR* 4.3 1.3 + - + -
885A ILE* 4.0 25.4 - - + -
886A MET 3.3 4.5 - - - +
887A VAL* 4.7 7.2 - - + -
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Residues in contact with VAL 848 (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* 4.4 11.4 - - + +
602A ALA 4.2 11.0 - - - +
603A ARG* 3.5 35.7 - - + +
660A GLN* 3.7 11.9 - - - +
846A ASP* 3.7 4.9 - - - +
847A ILE* 1.3 77.6 - - - +
849A THR* 1.3 74.9 + - - +
884A HIS 3.7 0.2 - - - +
886A MET* 2.7 47.3 + - + +
888A VAL* 4.0 18.4 - - + -
890A ARG* 3.7 19.7 - - - +
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Residues in contact with THR 849 (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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602A ALA 5.3 0.5 - - - +
657A SER* 5.2 7.1 + - - -
660A GLN* 2.9 48.0 + - + +
661A LEU* 4.5 28.3 - - + -
687A LEU* 6.3 0.7 - - + -
694A PHE* 5.0 8.8 - - + -
847A ILE* 5.4 0.9 - - + -
848A VAL* 1.3 82.4 - - - +
850A LEU* 1.3 61.5 + - - +
851A PRO* 4.3 4.3 - - - +
883A PRO* 4.2 15.9 - - + -
884A HIS 3.3 7.9 - - - -
885A ILE* 4.5 19.5 - - + -
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Residues in contact with LEU 850 (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* 3.8 31.9 - - + -
602A ALA 4.4 9.4 - - - +
604A HIS* 6.1 4.9 - - + +
849A THR* 1.3 76.9 - - - +
851A PRO* 1.3 77.5 - - + +
853A GLN* 3.8 30.3 - - + +
883A PRO* 3.8 2.9 - - - -
884A HIS* 2.8 49.9 + - + -
886A MET* 4.1 28.9 - - + -
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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