Contacts of the strand formed by residues 657 - 664 (chain C) in PDB entry 3FCS
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 ALA 657 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653C LEU* 3.9 12.1 - - + +
654C PRO* 3.2 43.5 + - + +
655C GLN 4.7 0.2 - - - +
656C GLY* 1.3 78.3 - - - +
658C HIS* 1.3 66.4 + - - +
683C ARG* 3.7 15.1 + - - -
705C VAL* 3.7 20.6 - - + -
706C SER 3.6 5.4 - - - -
707C VAL* 4.0 5.5 - - + +
719C PHE* 3.9 4.9 - - + -
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Residues in contact with HIS 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397C GLU* 4.7 9.0 - - - -
653C LEU* 4.2 4.9 - - - -
655C GLN 4.8 5.2 + - - -
656C GLY* 3.3 28.6 + - - -
657C ALA* 1.3 73.3 + - - +
659C TYR* 1.3 66.3 + - - +
660C MET 3.5 0.2 + - - -
676C GLN* 4.6 1.6 - - - +
683C ARG* 3.1 40.8 + - - -
705C VAL* 3.3 8.3 - - - -
706C SER* 3.0 47.1 + - - +
708C GLY* 4.8 3.8 - - - -
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Residues in contact with TYR 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653C LEU* 4.0 4.4 - - - +
658C HIS* 1.3 72.9 - - - +
660C MET* 1.3 70.8 + - - +
661C ARG* 3.6 24.2 - - - +
662C ALA* 3.4 23.5 + - + +
671C ARG* 6.0 1.4 - - - +
672C LEU 4.9 2.8 + - - -
674C CYS* 3.3 37.4 - - + +
676C GLN* 3.7 29.0 + - + +
685C VAL* 3.6 36.6 - - + -
703C MET* 3.8 19.3 - - + -
704C LEU 4.3 2.0 - - - -
705C VAL* 4.8 3.6 - - - -
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Residues in contact with MET 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630C VAL* 3.7 26.5 - - + -
658C HIS* 5.7 0.2 - - + -
659C TYR* 1.3 86.6 - - - +
661C ARG* 1.3 65.9 + - + +
704C LEU* 3.2 24.7 + - + +
705C VAL 3.7 4.9 - - - -
706C SER* 3.4 43.3 - - - +
529D VAL* 5.2 6.4 - - - +
557D TYR* 4.4 16.5 + - - +
2N NAG 3.8 39.9 - - - +
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Residues in contact with ARG 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659C TYR* 3.6 10.2 - - - +
660C MET* 1.3 84.7 - - + +
662C ALA* 1.3 68.6 + - - +
663C LEU* 3.5 34.9 - - - +
671C ARG* 5.2 8.1 - - - +
703C MET* 3.4 4.9 - - - +
704C LEU* 2.8 58.5 + - + +
529D VAL* 5.8 2.5 - - + -
556D TYR* 4.1 38.4 - - + +
557D TYR* 5.3 4.0 - - - +
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Residues in contact with ALA 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659C TYR* 3.4 21.4 + - + +
661C ARG* 1.3 78.9 - - - +
663C LEU* 1.3 77.5 + - - +
671C ARG* 3.3 17.8 - - - +
672C LEU* 4.6 11.9 - - + +
674C CYS* 3.7 21.3 - - - -
687C CYS* 4.6 1.6 - - - -
701C ILE* 5.0 1.8 - - + -
702C ALA 3.4 8.1 - - - +
703C MET* 4.2 9.2 - - + -
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Residues in contact with LEU 663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661C ARG* 3.5 36.1 - - - +
662C ALA* 1.3 83.5 - - - +
664C SER* 1.3 63.5 + - - +
670C GLU* 3.8 12.6 - - + +
671C ARG* 4.1 20.0 - - + +
672C LEU* 4.4 3.6 - - - +
701C ILE* 3.4 10.0 - - - +
702C ALA* 2.8 41.6 + - + +
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Residues in contact with SER 664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663C LEU* 1.3 78.0 - - - +
665C ASN* 1.3 60.4 + - - +
666C VAL* 3.5 7.5 + - - +
669C PHE* 2.9 24.1 + - - +
670C GLU* 3.0 21.1 + - - +
672C LEU* 3.9 22.7 - - - +
699C ILE* 4.0 15.9 - - - +
700C GLY 3.2 13.7 - - - -
702C ALA 4.9 0.2 - - - +
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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