Contacts of the strand formed by residues 671 - 675 (chain C) in PDB entry 2FH2
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 VAL 671 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645C CYS* 2.8 37.6 + - + +
670C ASP* 1.3 78.3 - - - +
672C MET* 1.3 67.0 + - - +
682C VAL* 3.4 28.7 - - + -
683C TRP 3.3 14.6 - - - +
684C VAL* 4.5 7.0 - - + -
688C SER* 3.9 14.6 - - - +
692C GLU* 4.0 10.6 + - + +
693C LYS* 3.8 29.6 - - + +
696C ALA* 3.6 20.0 - - + -
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Residues in contact with MET 672 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C LEU* 3.9 28.5 - - + -
643C PHE 3.1 20.2 - - - +
644C ALA* 3.6 30.5 - - + +
657C VAL* 4.1 4.9 - - + -
665C ASP 3.4 24.7 - - - +
666C LEU* 3.9 13.7 - - + -
667C ALA* 4.0 10.1 - - - +
670C ASP* 4.5 8.3 - - - -
671C VAL* 1.3 77.9 - - - +
673C LEU* 1.3 63.3 + - - +
682C VAL* 3.6 3.8 - - - -
683C TRP* 2.8 61.7 + - + +
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Residues in contact with LEU 673 (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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641C ARG 3.7 1.2 - - - +
642C LEU* 3.3 7.5 - - - +
643C PHE* 2.8 49.5 + - + -
645C CYS* 4.0 16.6 - - - -
654C ILE* 5.7 0.7 - - + -
672C MET* 1.3 79.8 - - - +
674C LEU* 1.3 59.5 + - - +
675C ASP* 3.9 1.1 - - + +
680C VAL* 4.5 8.5 - - + -
681C PHE 3.3 3.8 - - - +
682C VAL* 4.0 21.3 - - + -
696C ALA* 3.6 37.2 - - + +
699C SER* 4.1 17.3 - - - -
700C ALA* 4.1 12.6 - - + +
703C TYR* 4.2 20.9 - - + -
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Residues in contact with LEU 674 (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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640C PRO* 4.1 12.1 - - + -
641C ARG 3.2 17.3 - - - +
642C LEU* 4.4 11.4 - - + -
661C LEU* 3.8 24.7 - - + -
672C MET 4.2 0.6 - - - -
673C LEU* 1.3 71.3 - - - +
675C ASP* 1.3 61.3 + - - +
676C THR* 3.6 24.0 + - + -
679C GLN 3.7 1.0 - - - +
680C VAL* 3.4 3.6 - - - -
681C PHE* 2.9 50.2 + - + +
729C PHE* 4.0 31.1 - - + +
732C TRP* 4.0 19.7 - - + -
733C PHE* 4.7 7.0 - - + -
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Residues in contact with ASP 675 (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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639C PRO 4.6 0.7 - - - +
640C PRO* 3.2 3.5 - - - +
641C ARG* 3.0 54.4 + - + +
643C PHE* 4.5 13.9 - - + -
673C LEU* 3.9 1.4 - - + -
674C LEU* 1.3 70.6 - - - +
676C THR* 1.3 58.2 + - - +
677C TRP* 3.0 25.2 + - - -
679C GLN 3.9 2.2 - - - -
680C VAL* 3.9 17.7 - - + +
703C TYR* 4.2 11.7 - - + +
711C ARG* 3.2 35.3 + - - -
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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