Contacts of the strand formed by residues 888 - 894 (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 LEU 888 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815B ILE* 3.9 40.2 - - + -
816B TYR 5.0 3.3 - - - +
835B PHE* 4.6 7.4 - - + -
845B LYS* 4.1 2.9 + - - -
876B LEU* 3.7 32.5 - - + +
877B CYS* 5.3 0.4 - - - -
879B LEU* 4.4 16.6 - - + -
880B GLY 5.3 3.0 + - - +
881B HIS* 3.4 24.4 + - + +
886B ILE 4.5 7.4 - - - +
887B ASN* 1.3 75.3 - - - +
889B LEU* 1.3 62.8 + - - +
890B GLY 3.5 0.6 + - - -
900B LEU* 4.3 11.9 - - + -
901B ALA 3.7 4.9 - - - +
902B ILE* 3.8 23.1 - - + -
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Residues in contact with LEU 889 (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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817B PRO* 3.4 11.8 - - - +
819B LEU* 4.2 5.5 - - - +
843B ILE* 4.0 12.5 - - + +
845B LYS* 3.4 39.0 + - + +
850B MET* 4.1 21.1 - - + -
851B ASP 4.3 2.5 - - - +
852B ALA* 3.8 19.3 - - + -
881B HIS* 5.8 0.7 - - + +
887B ASN* 4.1 9.9 - - + +
888B LEU* 1.3 79.7 - - - +
890B GLY* 1.3 57.6 + - - +
901B ALA* 2.8 14.8 + - + +
902B ILE 3.7 27.8 - - - +
903B GLU* 4.0 17.5 - - + +
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Residues in contact with GLY 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815B ILE* 4.2 7.2 - - - +
816B TYR 3.9 12.8 + - - -
817B PRO 3.2 15.0 - - - -
819B LEU* 3.8 10.3 - - - -
888B LEU* 3.5 3.0 + - - +
889B LEU* 1.3 79.5 - - - +
891B ALA* 1.3 62.8 + - - +
900B LEU* 3.8 3.6 - - - +
901B ALA 2.8 24.4 + - - +
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Residues in contact with ALA 891 (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* 3.9 25.1 + - + +
817B PRO 3.2 6.3 + - - -
818B VAL* 3.7 7.8 - - - +
819B LEU* 2.8 28.8 + - - +
890B GLY* 1.3 77.2 - - - +
892B CYS* 1.3 63.1 + - - +
898B LEU* 3.8 21.1 - - + -
899B TYR 3.4 9.6 - - - +
900B LEU* 4.1 9.6 - - + -
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Residues in contact with CYS 892 (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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818B VAL* 5.6 2.0 - - - -
819B LEU* 3.5 27.8 - - + +
821B TRP* 3.6 41.3 - - - -
824B ILE* 4.3 9.9 - - + -
891B ALA* 1.3 78.4 - - - +
893B GLU* 1.3 71.7 + - - +
898B LEU* 4.0 2.9 - - - -
899B TYR* 2.7 45.9 + - + +
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Residues in contact with GLU 893 (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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859B GLU* 3.0 30.1 - - - +
892B CYS* 1.3 78.2 - - - +
894B HIS* 1.3 64.3 - - - +
897B TYR 3.5 6.1 - - - +
898B LEU* 3.7 20.9 - - + -
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Residues in contact with HIS 894 (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* 3.7 14.0 + - - -
821B TRP* 3.4 74.7 + + + -
892B CYS* 3.7 1.8 + - - -
893B GLU* 1.3 76.9 - - - +
895B ARG* 1.3 84.1 + - + +
896B GLY 3.3 1.5 - - - +
897B TYR* 2.8 22.6 + - - +
899B TYR* 3.6 19.9 + - + -
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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