Contacts of the strand formed by residues 863 - 868 (chain A) in PDB entry 3VFQ
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 ASN 863 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859A LEU* 3.6 14.5 - - + +
860A LEU* 2.7 41.1 + - - +
861A PRO 4.7 0.7 - - - -
862A GLY* 1.3 80.6 - - - +
864A ALA* 1.3 66.9 + - - +
880A ALA* 3.5 1.4 - - - -
881A VAL* 2.9 27.3 + - + +
899A ARG* 5.5 1.2 + - - -
900A ALA* 4.1 6.0 - - - +
903A LEU* 4.0 4.5 - - - +
1100A GLY 4.6 1.4 - - - +
1102A THR* 2.4 44.4 + - - +
1105A LEU* 3.9 12.1 - - - +
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Residues in contact with ALA 864 (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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859A LEU* 4.5 3.8 - - - -
863A ASN* 1.3 81.3 + - - +
865A THR* 1.3 61.3 + - - +
878A ILE* 4.8 0.2 - - + -
879A HIS 3.1 11.4 - - - +
880A ALA* 4.3 1.1 - - - -
900A ALA 4.2 0.4 - - - +
903A LEU* 3.8 24.9 - - + +
904A SER* 3.8 24.0 - - - +
907A LEU* 3.6 20.1 - - + +
1100A GLY 5.0 5.0 + - - +
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Residues in contact with THR 865 (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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827A LEU* 4.1 23.1 - - + -
852A ILE* 4.3 12.7 - - + +
856A GLU* 4.2 17.2 + - - -
859A LEU* 3.8 24.7 - - + +
864A ALA* 1.3 73.7 - - - +
866A ILE* 1.3 72.4 + - - +
878A ILE* 3.4 5.9 - - - +
879A HIS* 2.6 49.4 + - + +
907A LEU* 3.7 7.6 - - - -
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Residues in contact with ILE 866 (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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852A ILE* 3.8 11.1 - - - +
865A THR* 1.3 88.2 + - - +
867A SER* 1.3 61.4 + - - +
876A HIS* 4.0 30.3 - - + +
877A VAL 3.4 8.3 - - - +
878A ILE* 3.3 29.8 - - + -
879A HIS* 4.7 0.4 - - - -
907A LEU* 4.3 17.9 - - + +
911A TYR* 3.7 47.6 - - + +
913A TYR* 5.0 4.3 - - + -
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Residues in contact with SER 867 (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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845A LEU* 4.1 1.1 - - - +
848A ASP* 3.4 16.8 - - - -
849A CYS* 3.9 9.8 - - - -
852A ILE* 3.5 14.8 - - - -
866A ILE* 1.3 72.7 - - - +
868A LYS* 1.3 67.7 + - - +
876A HIS* 3.1 14.5 - - - +
877A VAL* 2.9 31.7 + - - +
879A HIS* 2.6 34.9 + - - -
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Residues in contact with LYS 868 (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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844A GLU* 4.8 19.5 - - + +
845A LEU* 3.3 24.0 - - - +
848A ASP* 2.8 46.1 + - + +
851A GLN* 6.4 0.4 - - - -
867A SER* 1.3 78.2 + - - +
869A ALA* 1.3 60.4 + - - +
870A GLY 3.6 4.9 - - - +
875A HIS 3.8 7.4 - - - +
876A HIS* 4.5 5.1 - - + -
877A VAL 4.5 0.7 + - - -
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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