Contacts of the strand formed by residues 657 - 664 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653A LEU* 3.9 11.1 - - + +
654A PRO* 3.3 40.6 + - + +
655A GLN 4.5 0.2 - - - +
656A GLY* 1.3 78.5 - - - +
658A HIS* 1.3 67.4 + - - +
683A ARG* 3.7 16.1 + - - -
705A VAL* 3.7 19.7 - - + -
706A SER 3.5 5.6 - - - -
707A VAL* 4.0 5.5 - - + +
719A PHE* 4.0 6.1 - - + -
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Residues in contact with HIS 658 (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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397A GLU* 4.4 11.9 - - - -
653A LEU* 4.3 3.6 - - - -
655A GLN 4.8 4.4 + - - -
656A GLY 3.5 25.4 + - - -
657A ALA* 1.3 73.8 + - - +
659A TYR* 1.3 67.5 + - - +
676A GLN* 4.5 1.8 + - - +
683A ARG* 3.0 40.3 + - - -
705A VAL* 3.4 5.8 - - - -
706A SER* 2.9 47.6 + - - +
708A GLY* 4.9 4.9 - - - -
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Residues in contact with TYR 659 (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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653A LEU* 3.9 6.2 - - - +
658A HIS* 1.3 74.7 - - - +
660A MET* 1.3 72.8 + - - +
661A ARG* 3.6 24.7 - - - -
662A ALA* 3.3 21.1 + - + +
671A ARG* 6.2 0.2 - - - +
672A LEU 5.0 2.3 + - - -
674A CYS* 3.5 28.6 + - + +
676A GLN* 3.7 31.7 + - + +
685A VAL* 3.7 35.7 - - + -
703A MET* 3.8 22.7 - - + -
704A LEU 4.3 2.5 - - - -
705A VAL* 4.6 4.5 - - - -
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Residues in contact with MET 660 (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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630A VAL* 3.7 23.8 - - + -
659A TYR* 1.3 87.9 - - - +
661A ARG* 1.3 66.0 + - + +
704A LEU* 3.2 26.4 + - + +
705A VAL 3.6 9.2 - - - -
706A SER* 3.2 49.1 - - - +
529B VAL* 4.8 10.4 - - - +
557B TYR* 4.6 7.7 + - - -
2I NAG 3.0 48.5 - - + +
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Residues in contact with ARG 661 (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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659A TYR* 3.6 11.3 - - - +
660A MET* 1.3 84.3 - - + +
662A ALA* 1.3 68.7 + - - +
663A LEU* 3.7 33.1 - - - +
671A ARG* 5.5 7.9 - - + +
703A MET* 3.4 5.2 - - - +
704A LEU* 2.9 58.7 + - + +
529B VAL* 5.8 3.6 - - + -
556B TYR* 4.2 36.8 - - + +
557B TYR* 5.4 4.5 - - - +
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Residues in contact with ALA 662 (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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659A TYR* 3.3 20.1 + - + +
661A ARG* 1.3 80.3 - - - +
663A LEU* 1.3 73.8 + - - +
671A ARG* 3.7 18.6 - - - +
672A LEU* 4.1 13.3 + - + +
674A CYS* 3.7 21.8 - - - -
687A CYS* 4.5 2.5 - - - -
701A ILE* 4.9 1.6 - - + -
702A ALA 3.4 8.3 - - - +
703A MET* 4.2 9.2 - - + -
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Residues in contact with LEU 663 (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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661A ARG* 3.7 34.5 - - - +
662A ALA* 1.3 81.5 - - - +
664A SER* 1.3 61.0 + - - +
670A GLU* 3.9 19.1 - - + +
671A ARG* 4.4 12.6 - - + +
672A LEU* 4.4 3.6 - - - +
701A ILE* 3.4 10.0 - - - +
702A ALA* 2.7 44.9 + - + +
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Residues in contact with SER 664 (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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663A LEU* 1.3 79.0 - - - +
665A ASN* 1.3 59.5 + - - +
666A VAL* 3.5 8.1 + - - +
669A PHE* 3.0 22.7 + - - +
670A GLU* 3.1 20.9 + - - +
672A LEU* 3.9 25.2 - - - +
699A ILE* 4.0 12.3 - - - -
700A GLY 3.2 14.4 - - - -
702A 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