Contacts of the helix formed by residues 535 - 541 (chain B) 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 GLY 535 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512B ASN* 4.1 1.8 - - - -
513B LEU* 4.3 10.1 - - - +
533B GLY 3.3 0.4 - - - -
534B SER* 1.3 81.1 + - - +
536B LYS* 1.3 64.2 + - - +
538B THR* 2.7 23.1 + - - -
539B LEU* 3.0 15.2 + - - +
805B ILE* 4.4 6.5 - - - +
901B ADP 3.2 23.6 + - - -
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Residues in contact with LYS 536 (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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528B VAL* 3.5 22.2 - - + +
529B THR* 3.2 41.7 - - - +
530B GLY 2.8 21.2 + - - -
531B VAL 3.0 10.5 + - - -
532B SER* 4.2 3.4 - - - +
534B SER* 3.6 8.1 - - - +
535B GLY* 1.3 75.1 - - - +
537B SER* 1.3 60.0 + - - +
539B LEU* 3.3 2.3 + - - +
540B VAL* 3.0 34.0 + - - +
789B VAL* 4.2 14.1 - - + -
790B GLU 4.4 4.3 - - - -
791B HIS* 3.9 30.8 + - - -
805B ILE* 4.5 6.3 - - + -
901B ADP 2.8 29.1 + - - +
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Residues in contact with SER 537 (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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536B LYS* 1.3 73.5 - - - +
538B THR* 1.3 57.9 + - - +
541B SER* 2.7 46.8 + - - +
542B GLN* 3.0 15.6 + - - +
758B ASP* 3.9 13.0 - - - -
789B VAL* 4.8 3.7 - - - +
901B ADP 2.6 42.1 + - - -
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Residues in contact with THR 538 (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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510B ARG* 4.2 10.4 - - - -
511B ASN* 2.9 39.0 - - + +
512B ASN* 4.8 0.5 - - - +
513B LEU* 4.3 12.0 - - - +
535B GLY* 2.7 26.9 + - - -
537B SER* 1.3 74.6 - - - +
539B LEU* 1.3 50.5 + - - -
542B GLN* 3.2 23.5 - - - +
543B ALA* 2.7 36.4 + - - +
901B ADP 2.7 34.5 + - + +
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Residues in contact with LEU 539 (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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505B LEU* 4.2 16.0 - - + +
508B VAL* 4.5 7.0 - - + -
513B LEU* 4.2 13.6 - - + +
516B LEU* 4.2 22.0 - - + -
518B VAL* 4.2 20.0 - - + -
520B PHE* 3.9 22.7 - - + -
528B VAL* 4.3 2.7 - - + -
535B GLY 3.0 17.1 + - - +
536B LYS 3.6 3.1 - - - +
538B THR* 1.3 76.5 + - - +
540B VAL* 1.3 68.4 + - + +
543B ALA* 3.7 4.0 - - - +
544B LEU* 2.9 27.4 + - - +
803B LEU* 4.5 3.4 - - + -
805B ILE* 3.4 28.5 - - + -
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Residues in contact with VAL 540 (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 6.7 - - + -
528B VAL* 3.7 36.3 - - + -
536B LYS 3.0 16.5 + - - +
539B LEU* 1.3 86.3 - - + +
541B SER* 1.3 66.9 + - - +
542B GLN 3.2 1.3 - - - -
544B LEU* 3.4 13.2 - - + +
545B VAL* 3.3 27.2 + - - +
756B VAL* 4.4 15.5 - - + -
757B LEU 5.3 0.4 - - - +
787B ILE* 4.1 22.0 - - + +
789B VAL* 4.2 20.6 - - + +
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Residues in contact with SER 541 (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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537B SER* 2.7 26.3 + - - -
540B VAL* 1.3 76.0 - - - +
542B GLN* 1.3 60.8 + - - +
545B VAL* 3.2 25.1 - - - +
546B ASP* 5.1 0.7 - - - +
588B ARG* 3.3 27.9 + - - +
756B VAL* 4.9 2.6 - - - +
758B ASP* 3.3 28.4 + - - +
789B VAL* 4.1 6.1 - - - +
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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