Contacts of the strand formed by residues 897 - 902 (chain B) 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 TYR 897 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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837A GLN* 4.5 10.6 + - - -
856B ARG* 3.0 55.3 + - + +
857B MET 3.5 3.4 - - - +
858B LYS* 3.6 34.6 - - + +
859B GLU* 3.9 4.0 + - - -
893B GLU* 3.5 1.0 - - - +
894B HIS 2.8 34.8 + - - +
895B ARG* 3.3 26.0 - - + -
896B GLY* 1.3 82.1 - - - +
898B LEU* 1.3 62.0 + - - +
899B TYR* 3.5 16.3 - - + -
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Residues in contact with LEU 898 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815B ILE* 5.2 9.0 - - + -
855B LYS 3.4 3.8 - - - +
856B ARG* 3.6 1.2 - - - -
857B MET* 2.8 51.2 + - + +
859B GLU* 4.0 7.4 - - - +
869B PHE* 3.7 33.0 - - + -
873B LEU* 4.2 17.5 - - + -
876B LEU* 6.5 0.2 - - + -
891B ALA* 3.8 29.2 - - + -
892B CYS 3.8 4.5 - - - +
893B GLU* 3.7 25.1 - - + +
897B TYR* 1.3 72.3 - - - +
899B TYR* 1.3 61.1 + - - +
900B LEU* 3.5 5.1 + - + +
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Residues in contact with TYR 899 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A ASP* 2.8 23.5 + - - -
829A VAL 4.3 0.8 + - - -
819B LEU* 5.1 1.2 - - - +
821B TRP* 3.6 32.5 - + + -
824B ILE* 5.1 6.4 - - + +
826B PHE* 3.9 16.6 - + - -
839B LEU* 4.6 4.0 - - + -
854B ILE* 3.8 25.1 - - + +
855B LYS 3.8 3.4 - - - -
856B ARG* 3.0 38.1 + - + -
891B ALA* 3.4 4.6 - - - -
892B CYS* 2.7 45.4 + - + +
894B HIS* 3.6 26.0 + - + -
895B ARG* 6.1 0.3 - - - +
897B TYR* 3.5 19.9 - - + +
898B LEU* 1.3 71.1 - - - +
900B LEU* 1.3 61.7 + - - +
901B ALA* 3.6 2.4 + - - +
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Residues in contact with LEU 900 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815B ILE* 3.4 32.3 - - + -
835B PHE* 4.4 10.3 - - + -
853B ALA 3.7 0.2 - - - +
854B ILE* 3.2 4.3 - - - -
855B LYS* 2.7 51.4 + - + +
857B MET* 4.3 13.7 - - - -
876B LEU* 3.6 28.7 - - + -
888B LEU* 4.3 11.9 - - + -
890B GLY 3.8 15.5 - - - +
891B ALA* 4.1 7.4 - - + -
898B LEU* 3.5 5.7 + - + +
899B TYR* 1.3 70.4 - - - +
901B ALA* 1.3 63.4 + - - +
902B ILE* 3.8 20.3 + - + +
983B PHE* 4.9 0.2 - - + -
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Residues in contact with ALA 901 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819B LEU* 3.6 23.6 - - + -
843B ILE* 4.2 10.8 - - + -
852B ALA* 4.9 1.3 - - + -
853B ALA 3.4 7.0 - - - +
854B ILE* 4.2 11.2 - - + -
888B LEU* 3.7 2.1 - - - -
889B LEU* 2.8 35.8 + - + -
890B GLY 2.8 18.9 + - - +
899B TYR 3.6 2.2 + - - +
900B LEU* 1.3 74.7 - - - +
902B ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 902 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832B GLU* 3.5 23.3 - - - +
835B PHE* 3.7 45.8 - - + -
838B VAL* 4.7 7.0 - - + -
852B ALA* 3.5 6.6 - - - +
853B ALA* 2.8 48.3 + - + +
855B LYS* 5.1 1.8 - - + -
886B ILE* 3.8 8.1 - - + -
887B ASN 3.5 7.4 - - - +
888B LEU* 3.8 20.9 - - + -
889B LEU* 3.8 5.4 - - - -
900B LEU* 4.0 14.1 - - + +
901B ALA* 1.3 80.6 - - - +
903B GLU* 1.3 62.2 + - - +
904B TYR 3.5 0.5 + - - -
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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
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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