Contacts of the strand formed by residues 525 - 530 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B ARG* 4.9 3.1 - - - +
524B VAL* 1.3 71.7 - - - +
526B THR* 1.3 65.2 + - - +
527B SER* 3.5 14.8 - - - +
773B GLN* 4.3 14.8 - - - -
776B LEU* 4.4 14.1 - - + -
777B VAL* 6.3 4.7 - - + -
780B VAL* 3.7 13.9 - - + +
786B VAL* 3.4 27.6 - - + -
788B ALA* 4.7 9.2 - - + -
790B GLU* 4.2 7.4 - - - +
795B VAL* 4.2 18.6 - - + -
798B ALA 5.5 0.7 - - - +
799B SER* 3.3 28.9 - - - +
800B ASP* 2.6 52.5 + - - +
801B TRP 3.4 1.0 + - - -
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Residues in contact with THR 526 (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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520B PHE* 4.6 4.3 - - + -
521B PRO* 3.3 30.9 + - + +
524B VAL 3.7 6.4 + - - -
525B MET* 1.3 81.2 - - - +
527B SER* 1.3 67.5 + - - +
528B VAL* 5.2 1.1 - - + -
786B VAL 3.0 9.5 + - - +
787B ILE* 3.5 15.2 - - - +
788B ALA* 3.2 22.7 + - - +
801B TRP* 3.1 41.1 - - + +
803B LEU* 4.6 13.2 - - + +
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Residues in contact with SER 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B MET* 3.5 12.3 - - - +
526B THR* 1.3 76.7 - - - +
528B VAL* 1.3 62.9 + - - +
529B THR* 3.9 2.9 + - - -
788B ALA 3.3 4.3 - - - -
790B GLU* 3.6 19.2 + - - +
796B VAL* 3.7 24.2 - - - +
799B SER* 3.1 24.7 + - - -
801B TRP 2.8 7.0 + - - +
802B VAL* 3.3 5.3 - - - -
803B LEU 3.0 23.2 + - - -
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Residues in contact with VAL 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B PHE* 4.2 10.8 - - + -
526B THR* 5.2 1.1 - - + -
527B SER* 1.3 77.8 - - - +
529B THR* 1.3 56.5 + - - +
536B LYS* 3.3 22.9 - - + +
539B LEU* 4.6 2.5 - - + -
540B VAL* 3.5 34.3 - - + -
787B ILE* 4.0 15.5 - - + -
788B ALA 2.7 17.5 + - - +
789B VAL* 3.6 4.2 - - - +
790B GLU 3.3 13.9 + - - -
803B LEU* 3.4 14.6 - - + +
805B ILE* 3.7 29.8 - - + -
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Residues in contact with THR 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B HIS* 5.5 0.2 - - - -
527B SER* 4.5 2.5 - - - -
528B VAL* 1.3 76.4 - - - +
530B GLY* 1.3 58.4 + - - +
536B LYS* 3.3 5.4 - - - +
790B GLU 3.6 11.2 - - - +
793B MET* 4.8 4.9 - - + -
796B VAL* 3.5 35.9 - - + -
802B VAL* 3.6 21.2 - - + +
803B LEU 2.9 7.9 + - - +
804B ASP* 2.4 35.8 + - - +
805B ILE* 3.0 20.1 + - - +
833B THR* 3.4 15.1 + - - +
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Residues in contact with GLY 530 (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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413B HIS* 3.4 20.6 + - - +
529B THR* 1.3 79.2 + - - +
531B VAL* 1.3 69.2 + - - +
532B SER 3.7 0.2 + - - -
534B SER* 3.6 7.4 - - - -
536B LYS* 3.1 21.8 - - - +
790B GLU 4.4 2.1 + - - +
791B HIS* 4.6 1.6 + - - -
804B ASP* 3.7 8.2 + - - -
805B ILE 4.0 7.2 - - - -
832B VAL* 6.1 0.2 - - - -
833B THR* 3.8 3.6 - - - +
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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
------------------------------------------------------------
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