Contacts of the strand formed by residues 680 - 684 (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 680 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673C LEU* 4.5 12.3 - - + -
674C LEU 3.4 10.3 - - - +
675C ASP* 3.9 25.1 - - + +
679C GLN* 1.3 76.9 - - - +
681C PHE* 1.3 74.3 + - - +
682C VAL* 4.9 0.7 - - + +
700C ALA* 3.9 25.8 - - + +
703C TYR* 5.6 2.0 - - + -
704C ILE* 3.8 30.3 - - + -
711C ARG* 4.4 1.6 - - - +
715C THR* 4.9 0.2 - - + -
716C PRO 3.2 6.9 + - - +
717C ILE* 3.3 14.9 - - + +
718C THR* 3.0 24.6 + - - -
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Residues in contact with PHE 681 (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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672C MET 3.7 0.5 - - - +
673C LEU* 3.3 6.4 - - - -
674C LEU* 2.9 46.7 + - + +
676C THR* 4.5 12.3 - - + -
679C GLN* 3.7 37.5 - - + -
680C VAL* 1.3 76.4 - - - +
682C VAL* 1.3 62.8 + - - +
683C TRP 3.8 0.2 + - - -
718C THR* 3.3 24.0 - - + +
720C VAL* 3.9 13.0 - - + -
726C PRO* 4.4 4.0 - - + -
728C SER* 3.7 29.2 - - - -
729C PHE* 3.6 52.9 - + + -
732C TRP* 5.5 0.2 - - - -
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Residues in contact with VAL 682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671C VAL* 3.4 27.6 - - + -
672C MET 3.6 2.9 - - - -
673C LEU* 4.0 14.1 - - + -
681C PHE* 1.3 73.7 - - - +
683C TRP* 1.3 56.1 + - - +
684C VAL* 3.9 10.0 + - + -
693C LYS* 5.0 5.2 - - + +
696C ALA* 4.2 10.5 - - + +
697C LEU* 3.9 18.6 - - + -
700C ALA* 4.6 6.1 - - + -
717C ILE* 3.8 26.0 - - + -
718C THR 2.9 6.6 + - - +
719C VAL* 3.4 15.0 - - + +
720C VAL* 2.8 29.9 + - - +
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Residues in contact with TRP 683 (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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666C LEU* 3.7 36.5 - - + +
667C ALA 3.4 25.1 - - - -
668C THR* 4.4 0.2 - - - -
670C ASP 4.2 0.4 - - - -
671C VAL* 3.3 4.9 - - - +
672C MET* 2.8 59.0 + - + +
674C LEU 6.1 0.4 - - - +
681C PHE 3.8 1.6 - - - +
682C VAL* 1.3 72.3 - - - +
684C VAL* 1.3 59.3 + - - +
685C GLY* 3.5 16.2 - - - -
720C VAL* 3.4 22.2 - - + -
722C GLN* 3.6 45.3 - - + +
725C GLU* 3.0 21.1 + - + +
729C PHE* 3.4 35.4 - + + -
741C TRP* 3.9 10.3 - + - -
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Residues in contact with VAL 684 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671C VAL* 4.5 8.1 - - + -
682C VAL* 4.2 10.5 - - + +
683C TRP* 1.3 76.7 - - - +
685C GLY* 1.3 64.6 - - - +
686C LYS* 4.7 0.2 - - - -
688C SER* 3.6 17.5 - - - +
693C LYS* 4.1 26.0 - - + -
719C VAL* 3.8 28.9 - - + -
720C VAL 2.9 10.7 + - - +
721C LYS* 3.9 17.8 - - + +
722C GLN* 3.1 21.5 + - - +
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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
------------------------------------------------------------
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