Contacts of the strand formed by residues 837 - 845 (chain A) in PDB entry 1FVR
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 GLN 837 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829A VAL* 3.6 12.5 - - + +
830A ILE* 3.2 10.1 + - - +
831A GLY* 3.6 22.0 - - - +
835A PHE 3.7 3.5 + - - +
836A GLY* 1.3 71.5 - - - -
838A VAL* 1.3 64.0 + - - +
855A LYS* 4.2 12.3 + - - +
856A ARG 5.5 0.7 + - - -
856B ARG* 2.9 31.3 + - - +
897B TYR* 4.5 10.3 + - - -
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Residues in contact with VAL 838 (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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829A VAL* 3.4 5.6 - - - +
830A ILE* 2.6 58.1 + - + +
832A GLU* 3.8 28.0 - - + +
835A PHE* 3.8 28.3 - - + +
836A GLY 4.0 0.9 - - - +
837A GLN* 1.3 80.4 - - - +
839A LEU* 1.3 63.9 + - - +
840A LYS 3.7 0.2 + - - -
853A ALA* 4.0 5.8 - - + -
854A ILE 3.5 19.1 - - - +
855A LYS* 4.0 15.0 - - + -
902A ILE* 4.6 4.5 - - + -
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Residues in contact with LEU 839 (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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826A PHE* 3.8 43.3 - - + -
828A ASP 3.3 5.8 - - - +
829A VAL* 3.7 26.9 - - + -
838A VAL* 1.3 73.2 - - - +
840A LYS* 1.3 64.1 + - - +
841A ALA* 3.2 1.2 + - - +
853A ALA* 3.2 3.9 - - - -
854A ILE* 2.7 49.5 + - + +
856A ARG* 5.0 7.6 - - + -
899A TYR* 4.7 9.0 - - + -
826B PHE* 6.2 0.4 - - + -
829B VAL* 3.8 21.8 - - + -
839B LEU* 3.9 17.9 - - + -
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Residues in contact with LYS 840 (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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826A PHE* 3.9 0.9 - - - -
827A GLN* 2.8 52.8 + - + +
828A ASP* 2.8 35.4 + - + +
830A ILE* 4.3 23.3 - - + +
838A VAL 3.7 3.2 + - - -
839A LEU* 1.3 71.7 - - - +
841A ALA* 1.3 61.9 + - - +
851A ASP* 4.8 8.7 + - + +
852A ALA 3.8 6.5 - - - +
853A ALA* 4.4 2.2 - - - +
904A TYR* 3.3 47.2 - - + +
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Residues in contact with ALA 841 (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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824A ILE* 4.4 0.7 - - + -
825A LYS 3.1 19.3 - - - +
826A PHE* 4.1 7.2 - - + -
827A GLN* 3.3 15.7 + - - +
839A LEU 3.2 7.4 + - - +
840A LYS* 1.3 76.6 - - - +
842A ARG* 1.3 62.8 + - - +
843A ILE* 4.9 1.6 - - + -
851A ASP* 3.6 4.2 - - - +
852A ALA* 2.8 37.4 + - - +
854A ILE* 4.1 24.2 - - + -
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Residues in contact with ARG 842 (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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823A ASP 3.5 0.5 - - - +
824A ILE* 4.4 0.2 - - - +
825A LYS* 2.9 41.8 + - + +
827A GLN* 3.2 32.1 - - - +
841A ALA* 1.3 74.9 - - - +
843A ILE* 1.3 64.8 + - - +
849A ARG* 3.4 39.7 + - - +
850A MET* 3.2 33.9 - - - +
851A ASP* 2.9 25.5 + - - +
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Residues in contact with ILE 843 (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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819A LEU* 4.2 21.5 - - + -
823A ASP* 3.7 6.1 - - + +
824A ILE* 4.2 20.0 - - + -
841A ALA* 4.9 0.2 - - + -
842A ARG* 1.3 80.8 - - - +
844A LYS* 1.3 63.0 + - - +
845A LYS* 4.8 4.5 - - + -
848A LEU 3.6 0.3 - - - +
849A ARG* 3.3 9.3 - - - -
850A MET* 2.9 49.1 + - + +
852A ALA* 3.9 26.5 - - + -
854A ILE* 4.3 17.3 - - + -
889A LEU* 4.3 15.9 - - + +
901A ALA* 4.0 17.5 - - + -
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Residues in contact with LYS 844 (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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819A LEU* 3.9 18.9 - - - +
823A ASP* 3.8 35.4 + - + +
843A ILE* 1.3 73.7 - - - +
845A LYS* 1.3 66.1 + - - +
847A GLY* 4.0 31.2 - - - +
848A LEU 3.4 10.5 - - - +
849A ARG* 3.4 23.3 - - - +
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Residues in contact with LYS 845 (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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817A PRO* 4.3 18.3 - - + +
819A LEU* 5.4 1.3 - - + -
843A ILE* 4.0 5.8 + - + -
844A LYS* 1.3 76.5 - - - +
846A ASP* 1.3 93.2 + - - +
847A GLY 3.1 0.9 - - - -
848A LEU* 2.8 26.6 + - - +
850A MET* 4.0 29.8 - - + +
881A HIS* 5.8 2.8 - - - -
888A LEU 4.5 2.2 + - - -
889A LEU* 3.2 55.2 + - + +
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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