Contacts of the helix formed by residues 423 - 437 (chain A) in PDB entry 5VOT
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 423 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404A PRO 3.3 8.5 - - - -
405A TYR 3.2 11.4 - - - -
407A MET* 4.5 0.9 - - - -
422A GLU* 1.3 76.8 - - - +
424A TYR* 1.3 66.1 - - - +
425A CYS 3.5 0.2 - - - -
426A VAL* 3.3 16.0 - - - +
427A ASP* 3.3 5.7 + - - +
766A TRP* 3.2 34.0 - - - -
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Residues in contact with TYR 424 (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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404A PRO 3.0 17.1 + - - +
405A TYR* 3.0 10.7 + + - -
423A GLY* 1.3 70.3 - - - -
425A CYS* 1.3 75.8 + - - +
427A ASP* 2.9 16.1 + - - +
428A LEU* 2.9 26.4 + - + +
495A PHE* 4.0 33.7 - + - -
496A MET* 4.5 7.3 - - + +
759A LEU* 4.0 25.1 + - - +
762A LEU* 3.6 29.4 - - + -
763A LYS* 3.8 9.8 - - - +
766A TRP* 3.4 33.1 - + + +
767A TRP* 3.8 29.2 - + + -
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Residues in contact with CYS 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A THR* 5.7 0.2 - - - -
405A TYR* 3.1 44.8 + - - +
406A VAL* 4.0 11.0 - - + -
424A TYR* 1.3 83.4 - - - +
426A VAL* 1.3 57.4 + - - +
428A LEU* 3.8 10.7 - - - +
429A ALA* 2.9 32.6 + - - +
442A LEU* 6.1 0.4 - - - -
476A ILE* 3.8 19.7 - - + +
477A ALA* 3.9 25.1 - - - -
478A PRO* 4.0 0.7 - - - -
495A PHE* 6.0 3.6 - - - -
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Residues in contact with VAL 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A TYR 4.6 2.2 - - - +
406A VAL* 4.9 7.9 - - + -
418A ASN 5.6 0.7 - - - +
421A TYR* 4.2 15.9 - - + +
422A GLU* 3.4 41.5 - - - +
423A GLY* 3.3 11.0 - - - +
424A TYR 3.0 0.4 + - - -
425A CYS* 1.3 77.3 - - - +
427A ASP* 1.3 64.1 + - - +
429A ALA* 3.8 3.4 - - - +
430A ALA* 2.9 31.7 + - + +
440A TYR* 5.6 0.2 + - - -
442A LEU* 4.4 21.8 - - + -
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Residues in contact with ASP 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLY 3.7 5.2 - - - +
424A TYR 2.9 6.9 + - - +
426A VAL* 1.3 81.5 - - - +
428A LEU* 1.3 64.2 + - - +
430A ALA* 3.2 9.0 + - - +
431A GLU* 2.9 28.5 + - + +
762A LEU* 4.6 19.5 - - + +
765A LYS* 4.0 16.9 + - - +
766A TRP* 2.9 36.2 + - - +
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Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A TYR* 2.9 35.8 + - + +
425A CYS* 3.8 8.3 - - - +
427A ASP* 1.3 75.6 - - - +
429A ALA* 1.3 63.9 + - - +
431A GLU* 2.9 9.1 + - - +
432A ILE* 2.9 39.0 + - + +
476A ILE* 3.9 19.3 - - + -
495A PHE* 4.7 19.1 - - + -
734A ILE* 4.2 14.6 - - + -
750A VAL* 5.9 6.1 - - + -
753A LEU* 4.4 19.3 - - + -
759A LEU* 4.6 14.6 - - + -
762A LEU* 5.0 8.1 - - + +
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Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A VAL* 4.9 11.4 - - + -
425A CYS 2.9 22.6 + - - +
426A VAL* 3.8 4.3 - - - +
428A LEU* 1.3 73.8 - - - +
430A ALA* 1.3 57.9 + - - +
432A ILE* 3.1 3.8 + - - +
433A ALA* 2.9 30.2 + - - +
438A PHE* 5.5 0.7 - - - -
440A TYR* 5.1 8.1 - - + -
442A LEU* 5.0 9.2 - - + -
476A ILE* 3.6 33.8 - - + +
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Residues in contact with ALA 430 (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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426A VAL* 2.9 21.3 + - + +
427A ASP* 3.4 9.6 - - - +
429A ALA* 1.3 76.7 - - - +
431A GLU* 1.3 59.9 + - + +
433A ALA* 3.3 5.4 + - - +
434A LYS* 2.9 27.3 + - - +
440A TYR* 4.4 19.0 + - - +
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Residues in contact with GLU 431 (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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427A ASP* 2.9 21.1 + - + +
428A LEU* 2.9 8.0 + - - +
430A ALA* 1.3 78.0 - - + +
432A ILE* 1.3 57.2 + - - +
434A LYS* 3.1 13.5 + - - +
435A HIS* 2.9 52.0 + - + -
753A LEU* 3.8 28.7 - - + +
758A LEU* 4.6 19.3 - - + +
762A LEU* 5.4 4.3 - - + -
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Residues in contact with ILE 432 (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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428A LEU* 2.9 34.2 + - + +
429A ALA* 3.1 10.7 + - - +
431A GLU* 1.3 78.4 - - - +
433A ALA* 1.3 57.7 + - - +
435A HIS* 3.3 3.5 + - - -
436A CYS* 2.9 44.2 + - + +
438A PHE* 5.0 7.4 - - + -
474A ILE* 5.6 2.2 - - + -
476A ILE* 4.6 14.1 - - + -
734A ILE* 5.8 3.1 - - + -
746A VAL* 3.9 26.2 - - + +
749A ALA* 4.1 21.5 - - + -
750A VAL* 4.4 20.0 - - + +
753A LEU* 5.0 6.1 - - + -
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Residues in contact with ALA 433 (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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429A ALA 2.9 13.8 + - - +
430A ALA 3.7 3.4 - - - +
432A ILE* 1.3 78.0 - - - +
434A LYS* 1.3 55.0 + - - +
437A GLY* 2.5 34.3 + - - -
438A PHE* 3.4 29.0 + - + +
440A TYR* 3.6 36.6 - - + -
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Residues in contact with LYS 434 (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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430A ALA 2.9 15.2 + - - +
431A GLU* 3.1 19.5 + - - +
433A ALA* 1.3 79.6 - - - +
435A HIS* 1.3 93.3 + - + +
436A CYS 3.3 0.2 + - - -
437A GLY* 3.7 6.4 + - - -
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Residues in contact with HIS 435 (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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431A GLU* 2.9 49.2 + - + +
432A ILE* 3.3 2.2 + - + +
434A LYS* 1.3 103.0 + - + +
436A CYS* 1.3 61.7 + - - +
749A ALA* 4.0 27.6 - - + -
752A LYS* 3.4 41.2 + - + +
753A LEU* 4.4 16.7 - - + +
756A GLN* 4.8 5.8 + - - -
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Residues in contact with CYS 436 (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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432A ILE* 2.9 24.9 + - - +
435A HIS* 1.3 87.0 - - - +
437A GLY* 1.3 65.9 + - - +
438A PHE* 3.3 21.8 - - + +
742A LEU* 5.3 11.6 - - + +
745A ALA* 4.7 10.5 - - - -
746A VAL* 4.0 35.9 - - - -
749A ALA* 5.1 2.0 - - - -
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Residues in contact with GLY 437 (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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433A ALA 2.5 19.1 + - - -
434A LYS 3.7 6.4 + - - -
436A CYS* 1.3 77.1 - - - +
438A PHE* 1.3 59.6 + - - +
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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