Contacts of the helix formed by residues 525 - 534 (chain A) in PDB entry 4EY6
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 ARG 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A LYS 3.3 24.4 + - - -
333A ASP* 5.2 3.4 + - - +
334A GLU 5.6 1.4 - - - +
400A ASP* 2.8 37.0 + - - +
403A GLY* 5.7 0.6 - - - -
404A ASP* 2.8 31.5 + - - -
408A VAL* 4.0 25.3 - - + +
523A GLY 3.0 8.7 + - - -
524A LEU* 1.3 74.2 - - - +
526A ALA* 1.3 60.1 + - - +
527A GLN 3.3 2.9 - - - -
528A ALA* 3.2 10.9 + - + -
529A CYS* 2.9 29.0 + - - -
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Residues in contact with ALA 526 (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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508A GLN* 3.5 24.7 - - - +
523A GLY* 4.2 4.1 - - - -
524A LEU 3.2 4.1 - - - +
525A ARG* 1.3 74.5 - - - +
527A GLN* 1.3 63.0 + - + +
529A CYS* 4.7 0.9 - - - -
530A ALA* 3.0 22.0 + - - +
606A EDO 3.3 21.8 - - - -
385B TRP* 3.9 10.8 - - + +
386B LEU* 4.0 23.3 - - + -
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Residues in contact with GLN 527 (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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381A HIS* 3.5 20.2 - - + +
525A ARG 3.3 0.8 - - - -
526A ALA* 1.3 79.3 - - + +
528A ALA* 1.3 63.8 + - - +
530A ALA* 3.6 9.2 + - - +
531A PHE 3.6 4.9 + - - -
380B LEU* 4.9 3.1 + - - +
383B THR 3.4 22.2 + - - -
384B ASP* 3.3 13.3 - - - +
385B TRP* 2.9 35.8 + - - +
386B LEU* 3.9 5.9 + - + +
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Residues in contact with ALA 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A HIS* 3.4 17.2 + - - +
382A TYR* 3.4 24.5 - - + +
404A ASP* 3.7 14.8 - - + +
525A ARG* 3.2 13.6 + - + +
527A GLN* 1.3 79.7 - - - +
529A CYS* 1.3 59.8 + - - +
531A PHE* 3.1 17.5 + - - +
532A TRP* 3.1 20.5 + - - -
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Residues in contact with CYS 529 (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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408A VAL* 4.2 6.3 - - - -
409A CYS* 2.0 55.6 - - - -
412A ALA* 4.3 5.8 - - + -
524A LEU 3.5 15.9 - - - +
525A ARG* 2.9 22.2 + - - +
526A ALA* 4.3 3.4 - - - +
528A ALA* 1.3 74.7 - - - +
530A ALA* 1.3 61.0 + - - +
532A TRP 4.3 0.2 - - - +
533A ASN* 2.8 47.7 + - - +
606A EDO 3.9 7.6 - - - +
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Residues in contact with ALA 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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526A ALA 3.0 13.1 + - - +
527A GLN 3.6 3.6 - - - +
529A CYS* 1.3 75.8 - - - +
531A PHE* 1.3 59.3 + - - +
534A ARG* 2.8 38.2 + - - +
535A PHE 3.2 2.8 + - - -
606A EDO 3.5 11.5 + - - -
380B LEU* 3.6 8.4 - - + +
385B TRP* 3.4 48.2 - - + +
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Residues in contact with PHE 531 (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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377A ALA* 3.8 24.5 - - + -
378A VAL* 3.9 28.3 - - + -
381A HIS* 4.1 26.0 - + + +
382A TYR* 4.7 7.9 - + - -
527A GLN 3.6 2.0 + - - +
528A ALA 3.1 9.4 + - - +
530A ALA* 1.3 82.1 - - - +
532A TRP* 1.3 106.3 + + - +
535A PHE* 3.3 9.3 + + - -
536A LEU* 2.8 55.1 + - + +
380B LEU* 3.7 28.2 - - + +
381B HIS* 5.8 1.8 - + - -
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Residues in contact with TRP 532 (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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367A VAL* 4.0 18.6 - - + -
378A VAL* 3.8 19.5 - - + -
382A TYR* 2.9 35.6 + + - -
401A VAL* 4.1 12.1 - - + -
404A ASP* 3.7 4.5 - - + +
405A HIS* 3.2 52.9 - + + +
409A CYS* 3.7 31.9 - - + -
528A ALA 3.1 25.5 + - - +
529A CYS 4.3 0.2 - - - +
531A PHE* 1.3 91.6 - + - +
533A ASN* 1.3 62.1 + - - +
536A LEU* 3.5 36.9 - - + +
537A PRO* 3.2 21.5 - - - +
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Residues in contact with ASN 533 (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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409A CYS* 3.0 35.8 + - - +
410A PRO* 4.5 1.9 - - - +
412A ALA* 4.5 1.4 - - - +
413A GLN* 3.7 45.4 + - - +
529A CYS* 2.8 36.6 + - - +
532A TRP* 1.3 80.1 - - - +
534A ARG* 1.3 63.3 + - + +
537A PRO* 3.7 13.1 - - - +
606A EDO 4.8 5.7 + - - +
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Residues in contact with ARG 534 (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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530A ALA* 2.8 23.7 + - + +
533A ASN* 1.3 79.1 - - + +
535A PHE* 1.3 64.5 + - + +
537A PRO* 3.8 5.7 - - - +
538A LYS* 3.6 29.3 + - - +
606A EDO 2.8 46.7 + - - +
380B LEU* 5.3 2.0 - - + -
385B TRP* 3.6 37.1 - - + -
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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