Contacts of the strand formed by residues 525 - 530 (chain A) in PDB entry 2VF8
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 MET 525 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A VAL* 1.3 70.7 - - - +
526A THR* 1.3 80.6 + - - +
527A SER* 4.3 3.8 - - - +
773A GLN* 6.3 1.6 - - - -
776A LEU* 4.7 22.9 - - + -
777A VAL* 5.8 1.3 - - - +
780A VAL* 4.1 11.6 - - + +
786A VAL* 3.3 30.1 - - + +
788A ALA* 4.3 13.0 - - + -
795A VAL* 5.0 12.6 - - + +
798A ALA 5.1 2.9 - - - +
799A SER* 3.3 22.7 - - - +
800A ASP* 2.8 31.5 + - - +
801A TRP 3.0 25.3 + - - -
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Residues in contact with THR 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A PHE* 4.2 14.1 - - + +
521A PRO* 3.5 26.4 + - + +
524A VAL 3.8 1.8 + - - -
525A MET* 1.3 82.5 + - - +
527A SER* 1.3 60.3 + - - +
528A VAL* 4.6 0.7 - - + -
785A THR* 5.3 0.2 - - - +
786A VAL 3.2 8.3 + - - +
787A ILE* 4.1 22.3 - - + +
788A ALA* 2.7 31.4 + - - +
799A SER* 3.6 2.2 - - - -
801A TRP* 3.3 13.5 - - + +
803A LEU* 3.5 32.3 - - + -
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Residues in contact with SER 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A MET* 4.3 4.2 - - - +
526A THR* 1.3 75.7 - - - +
528A VAL* 1.3 61.2 + - - +
529A THR* 3.7 0.9 + - - -
788A ALA* 3.3 7.7 - - - +
790A GLU* 4.6 3.6 - - - +
795A VAL* 4.0 3.8 + - - +
796A VAL* 3.3 42.3 + - - +
799A SER* 2.4 29.8 + - - -
801A TRP 3.1 6.7 + - - -
802A VAL* 3.2 4.8 - - - +
803A LEU 3.0 21.5 + - - -
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Residues in contact with VAL 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A PHE* 4.3 9.4 - - + -
526A THR* 4.6 0.7 - - + -
527A SER* 1.3 74.1 - - - +
529A THR* 1.3 58.3 + - - +
536A LYS* 3.4 33.7 - - + +
539A LEU* 4.4 2.5 - - + -
540A VAL* 3.6 27.6 - - + -
787A ILE* 4.1 17.9 - - + -
788A ALA 3.1 9.5 + - - +
789A VAL* 3.7 6.1 - - - -
790A GLU 3.3 18.3 + - - +
803A LEU* 3.5 25.6 - - + +
805A ILE* 3.6 18.8 - - + -
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Residues in contact with THR 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A HIS* 5.7 0.4 - - - -
527A SER* 3.7 1.3 + - - -
528A VAL* 1.3 78.1 - - - +
530A GLY* 1.3 60.4 + - - +
536A LYS* 4.0 6.2 - - - +
790A GLU 3.7 12.3 - - - +
793A MET* 4.7 9.6 - - + -
796A VAL* 3.1 45.1 - - + -
802A VAL* 3.9 14.0 - - + +
803A LEU 3.0 7.7 + - - +
804A ASP* 2.6 30.5 + - - +
805A ILE 3.0 19.6 + - - -
825A VAL* 5.4 0.2 - - - +
833A THR* 3.4 10.7 + - - -
837A LEU* 6.1 0.4 - - + -
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Residues in contact with GLY 530 (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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413A HIS* 3.2 14.5 + - - +
529A THR* 1.3 80.0 - - - +
531A VAL* 1.3 64.4 + - - -
532A SER 3.6 0.3 + - - -
534A SER* 3.3 9.0 - - - -
536A LYS* 2.6 23.6 + - - +
790A GLU 4.9 0.8 + - - -
791A HIS* 4.3 3.7 + - - +
804A ASP* 3.7 2.4 + - - -
805A ILE 4.1 7.0 - - - -
833A THR* 3.8 15.6 - - - +
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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