Contacts of the strand formed by residues 888 - 894 (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 LEU 888 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815A ILE* 3.6 42.8 - - + -
816A TYR 5.0 3.8 - - - +
817A PRO* 5.7 0.3 - - - +
835A PHE* 4.9 4.5 - - + -
845A LYS* 4.5 1.6 + - - -
876A LEU* 3.5 32.3 - - + +
877A CYS* 5.3 0.9 - - - -
879A LEU* 4.4 20.4 - - + -
880A GLY 5.4 3.0 + - - +
881A HIS* 3.3 25.5 - - + -
886A ILE 4.6 3.8 - - - +
887A ASN* 1.3 75.4 - - - +
889A LEU* 1.3 62.4 + - - +
890A GLY 3.6 0.4 - - - -
900A LEU* 4.2 10.8 - - + -
901A ALA 3.7 4.5 - - - +
902A ILE* 3.8 22.4 - - + -
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Residues in contact with LEU 889 (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* 3.1 25.1 - - - +
819A LEU* 4.4 4.0 - - - +
843A ILE* 4.3 8.0 - - + +
845A LYS* 3.2 34.2 + - + +
850A MET* 3.8 28.0 - - + -
851A ASP 4.5 0.4 - - - +
852A ALA* 4.0 13.0 - - + -
881A HIS* 5.8 0.9 - - + -
887A ASN* 4.0 4.5 - - + +
888A LEU* 1.3 77.9 - - - +
890A GLY* 1.3 57.4 + - - +
901A ALA* 2.8 19.4 + - + +
902A ILE 3.5 30.5 - - - +
903A GLU* 3.8 21.3 - - + +
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Residues in contact with GLY 890 (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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815A ILE* 4.4 4.5 - - - -
816A TYR 3.9 5.9 + - - -
817A PRO* 3.1 21.1 - - - -
819A LEU* 3.7 12.6 - - - -
888A LEU* 3.6 2.8 - - - +
889A LEU* 1.3 80.1 - - - +
891A ALA* 1.3 62.4 + - - +
900A LEU* 3.7 4.3 - - - +
901A ALA* 2.8 24.1 + - - +
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Residues in contact with ALA 891 (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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815A ILE* 3.8 27.8 + - + +
817A PRO 3.1 6.7 + - - -
818A VAL* 3.6 9.7 - - - +
819A LEU* 3.0 24.4 + - - +
890A GLY* 1.3 75.2 - - - +
892A CYS* 1.3 61.3 - - - +
893A GLU 4.3 0.2 - - - -
898A LEU* 3.8 20.0 - - + -
899A TYR 3.3 10.1 - - - +
900A LEU* 4.2 8.1 - - + -
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Residues in contact with CYS 892 (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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818A VAL* 5.7 1.3 - - - -
819A LEU* 3.3 26.5 - - + +
821A TRP* 3.6 42.2 - - - -
824A ILE* 4.1 17.7 - - + -
891A ALA* 1.3 75.0 - - - +
893A GLU* 1.3 71.6 + - - +
898A LEU* 4.2 2.7 - - - -
899A TYR* 2.7 47.0 + - + +
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Residues in contact with GLU 893 (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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818A VAL* 6.3 0.2 - - - +
821A TRP* 5.7 0.2 - - - +
859A GLU* 2.5 43.8 - - - +
892A CYS* 1.3 76.3 - - - +
894A HIS* 1.3 76.1 + - - +
895A ARG 4.2 0.8 + - - +
896A GLY* 3.3 18.7 + - - -
897A TYR 3.4 6.9 - - - +
898A LEU* 4.4 9.7 - - + +
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Residues in contact with HIS 894 (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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821A TRP* 3.4 75.9 + + + -
892A CYS* 4.5 1.1 - - - -
893A GLU* 1.3 80.0 + - - +
895A ARG* 1.3 99.7 + - + +
896A GLY 3.3 1.8 - - - -
897A TYR* 2.9 23.7 + - - +
899A TYR* 3.6 19.6 + - + -
828B ASP* 3.8 7.5 + - - -
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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