Contacts of the strand formed by residues 785 - 789 (chain A) in PDB entry 2VF7
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 THR 785 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A PRO 4.4 3.0 + - - -
522A LEU* 3.8 26.1 - - + +
523A GLY* 3.1 28.5 - - - +
524A VAL 3.6 10.1 - - - -
583A ILE* 5.6 4.0 - - + -
752A GLY 6.2 1.3 - - - -
753A THR 3.1 11.2 + - - +
754A VAL* 3.3 21.9 - - + +
755A TYR* 2.6 35.9 + - - +
783A GLY 5.0 2.0 - - - +
784A ASN* 1.3 74.7 - - - +
786A VAL* 1.3 55.5 + - - +
787A ILE* 4.4 9.0 - - - +
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Residues in contact with VAL 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A VAL 3.5 6.4 + - - +
525A MET* 3.4 33.0 - - + -
526A THR 2.9 25.1 + - - -
755A TYR* 3.2 14.1 - - + +
757A LEU* 3.7 25.8 - - + -
776A LEU* 4.3 10.8 - - + +
779A LEU* 3.8 20.2 - - + -
780A VAL* 3.4 29.4 - - + -
785A THR* 1.3 72.8 - - - +
787A ILE* 1.3 66.6 + - - +
788A ALA* 4.4 1.8 - - + -
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Residues in contact with ILE 787 (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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503A LEU* 5.8 2.7 - - + -
520A PHE* 3.9 34.5 - - + -
521A PRO 5.6 2.7 - - - +
522A LEU* 6.4 1.3 - - + -
524A VAL 5.9 0.2 - - - +
526A THR* 3.5 12.8 - - - +
528A VAL* 4.0 20.2 - - + -
540A VAL* 3.9 22.0 - - + +
544A LEU* 3.7 23.6 - - + -
754A VAL* 4.1 17.9 - - + -
755A TYR 2.8 7.9 + - - +
756A VAL* 3.3 7.5 - - + +
757A LEU* 2.8 25.8 + - - +
785A THR* 4.4 9.4 - - - +
786A VAL* 1.3 76.6 - - - +
788A ALA* 1.3 62.0 + - - +
789A VAL 4.3 0.2 + - - -
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Residues in contact with ALA 788 (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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525A MET* 4.1 18.8 - - + -
526A THR 3.0 11.0 + - - +
527A SER* 3.4 4.2 - - - -
528A VAL* 3.0 24.0 + - - -
757A LEU* 3.0 13.2 - - + +
760A PRO* 4.1 24.7 - - + -
776A LEU* 5.9 0.2 - - + -
786A VAL* 4.1 4.0 - - + -
787A ILE* 1.3 75.4 - - - +
789A VAL* 1.3 62.3 + - - +
790A GLU* 3.4 6.3 + - + +
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Residues in contact with VAL 789 (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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528A VAL* 3.7 13.4 - - + +
536A LYS* 4.3 27.6 - - + +
537A SER* 4.8 8.3 - - - +
540A VAL* 3.9 25.9 - - + +
541A SER* 4.1 11.9 - - - +
757A LEU 2.8 14.0 + - - +
758A ASP* 3.4 26.9 - - - +
759A GLU* 2.8 32.2 + - - -
760A PRO* 4.1 0.5 - - - +
787A ILE 4.2 0.6 - - - -
788A ALA* 1.3 70.0 - - - +
790A GLU* 1.3 59.9 + - - +
791A HIS* 4.1 14.6 - - + +
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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