Contacts of the helix formed by residues 535 - 541 (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 GLY 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A ASN* 3.6 12.3 - - - -
513A LEU* 4.6 5.5 - - - +
533A GLY 3.2 0.6 - - - -
534A SER* 1.3 80.4 + - - +
536A LYS* 1.3 70.7 + - - +
537A SER 3.1 3.5 + - - -
538A THR* 3.5 3.9 + - - -
539A LEU* 3.3 20.4 + - - +
805A ILE* 3.9 8.6 - - - +
1844A ADP 2.9 20.0 + - - -
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Residues in contact with LYS 536 (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* 3.4 38.8 - - + +
529A THR* 4.0 10.1 - - - +
530A GLY 2.6 29.9 + - - +
531A VAL 2.7 20.3 + - - -
532A SER* 4.7 2.0 - - - +
534A SER* 2.7 12.9 + - - +
535A GLY* 1.3 78.3 - - - +
537A SER* 1.3 58.8 + - - +
539A LEU* 3.1 4.6 + - - +
540A VAL* 2.8 30.3 + - - +
789A VAL* 3.8 27.6 - - + -
790A GLU 4.8 0.7 - - - +
791A HIS* 3.5 25.8 - - + +
805A ILE* 4.2 3.5 - - + +
1844A ADP 2.8 22.3 + - - +
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Residues in contact with SER 537 (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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535A GLY 3.2 0.2 - - - -
536A LYS* 1.3 77.8 - - - +
538A THR* 1.3 57.9 + - - +
541A SER* 2.8 16.4 + - - +
542A GLN* 2.8 35.6 + - - -
758A ASP* 3.8 21.3 - - - -
789A VAL* 4.7 2.7 - - - -
1844A ADP 2.2 50.7 + - - -
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Residues in contact with THR 538 (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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510A ARG* 3.7 15.7 + - - +
511A ASN* 3.1 31.4 - - + +
512A ASN* 5.1 0.7 - - - +
513A LEU* 3.6 19.5 - - - +
535A GLY* 4.2 1.7 + - - +
536A LYS 3.3 0.2 - - - -
537A SER* 1.3 78.7 - - - +
539A LEU* 1.3 59.2 + - - +
542A GLN* 3.4 18.4 - - - +
543A ALA* 2.9 28.9 + - - +
1844A ADP 2.5 46.6 + - + +
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Residues in contact with LEU 539 (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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505A LEU* 3.9 20.5 - - + +
508A VAL* 4.5 2.0 - - + -
513A LEU* 3.7 16.2 - - + -
516A LEU* 4.2 19.7 - - + -
518A VAL* 4.2 16.8 - - + -
520A PHE* 4.4 11.2 - - + -
528A VAL* 4.4 4.9 - - + -
535A GLY 3.3 10.7 + - - +
536A LYS 3.1 7.6 + - - +
538A THR* 1.3 80.7 + - - +
540A VAL* 1.3 73.1 + - + +
543A ALA* 3.5 4.5 - - - +
544A LEU* 2.9 29.0 + - - +
803A LEU* 4.9 7.0 - - + -
805A ILE* 4.1 30.1 - - + -
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Residues in contact with VAL 540 (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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520A PHE* 4.3 9.9 - - + -
528A VAL* 3.6 29.8 - - + -
536A LYS 2.8 19.4 + - - +
539A LEU* 1.3 86.2 - - + +
541A SER* 1.3 64.1 + - - +
542A GLN 3.5 0.2 - - - -
544A LEU* 3.5 18.1 - - + +
545A VAL* 3.8 2.1 - - - +
756A VAL* 3.6 27.1 - - + +
757A LEU 5.4 1.6 - - - +
787A ILE* 4.2 18.2 - - + +
789A VAL* 3.7 21.3 - - + +
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Residues in contact with SER 541 (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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537A SER* 2.8 19.5 + - - -
540A VAL* 1.3 83.0 - - - +
542A GLN* 1.3 64.6 + - - +
545A VAL* 3.4 25.5 - - - +
546A ASP* 4.5 0.5 - - - +
588A ARG* 4.1 11.7 + - - -
756A VAL* 4.9 2.6 - - - +
758A ASP* 3.4 38.8 + - - +
789A VAL* 4.6 0.9 - - - +
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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