Contacts of the strand formed by residues 805 - 809 (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 PHE 805 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A TYR* 3.6 27.8 - + + -
78A PRO* 3.6 45.3 - - + -
80A THR* 5.4 1.8 - - + -
87A HIS* 3.5 37.0 - + - -
798A ASN 3.9 6.8 - - - +
799A THR* 3.9 10.3 - - - +
800A SER 4.5 0.7 + - - -
803A HIS* 3.2 40.4 + + + +
804A PRO* 1.3 93.5 - - + +
806A ILE* 1.3 61.0 + - - +
807A HIS* 3.9 4.1 - - + -
1003A PRO* 4.3 13.9 - - + -
1004A ARG 3.3 4.5 - - - +
1005A LYS* 4.0 22.2 - - + -
1006A ILE* 5.0 0.7 - - - -
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Residues in contact with ILE 806 (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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196A MET* 4.4 3.4 - - + -
585A PRO* 5.3 2.9 - - + -
797A MET* 3.7 42.2 - - + -
798A ASN 3.6 7.9 - - - +
799A THR* 3.3 21.5 - - + -
804A PRO 4.0 0.2 + - - -
805A PHE* 1.3 73.5 - - - +
807A HIS* 1.3 63.9 + - - +
956A LEU* 4.7 7.6 - - + -
962A THR* 4.8 7.0 - - + -
994A ILE* 4.0 21.8 - - + -
999A ILE* 3.6 26.9 - - + +
1003A PRO* 3.7 0.7 - - - +
1004A ARG 2.9 33.1 + - - +
1006A ILE* 4.2 9.2 - - + -
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Residues in contact with HIS 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A THR* 3.6 36.2 - - + +
56A SER* 2.7 35.4 + - - -
57A CYS 3.6 17.0 - - - -
58A SER* 3.7 15.0 + - - -
77A TYR* 5.1 4.0 - + - -
797A MET* 3.6 1.7 - - - -
798A ASN* 2.9 39.0 + - - +
803A HIS* 4.1 5.6 - + - -
805A PHE* 3.9 14.1 - - + -
806A ILE* 1.3 76.0 - - - +
808A PRO* 1.3 71.9 + - + +
999A ILE* 3.8 6.7 - - - -
1003A PRO* 4.0 20.2 - - + -
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Residues in contact with PRO 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 4.0 10.8 - - + +
47A SER* 3.4 19.3 + - - -
48A THR* 3.5 13.1 - - - +
796A ASP 3.3 13.0 - - - +
797A MET* 4.3 0.2 - - - -
807A HIS* 1.3 92.5 + - + +
809A LEU* 1.3 59.8 + - - +
810A SER* 4.3 3.8 - - - +
996A PHE* 3.7 24.9 - - + -
999A ILE* 3.3 25.6 - - + +
1000A GLN* 3.6 31.0 - - + +
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Residues in contact with LEU 809 (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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47A SER* 3.3 7.0 - - - +
48A THR* 3.3 35.4 - - + +
49A HIS 4.7 0.9 - - - +
50A GLY 4.5 4.5 - - - +
194A MET 3.6 19.7 - - - +
195A SER* 4.6 5.6 - - - -
791A TRP* 3.8 35.7 - - + +
794A LYS* 3.3 26.2 - - - +
795A ASP* 3.2 4.5 - - - +
796A ASP* 2.8 49.2 + - + +
797A MET 4.2 0.9 - - - +
798A ASN* 4.2 7.6 - - + -
808A PRO* 1.3 75.7 - - - +
810A SER* 1.3 63.6 + - - +
996A PHE* 3.9 1.2 - - - -
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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