Contacts of the helix formed by residues 582 - 589 (chain A) in PDB entry 4WGK
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 THR 582 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASN* 2.6 29.3 + - - +
544A MET* 3.8 7.2 - - + -
545A SER* 3.2 26.8 + - - +
548A ARG* 3.6 19.5 - - - -
581A THR* 1.3 76.4 - - - +
583A TYR* 1.3 59.2 + - - +
584A GLU* 3.5 1.4 + - - -
585A GLU* 3.1 27.1 + - - +
586A TYR* 2.9 28.0 + - - +
600A PRO 4.9 0.2 - - - -
603A LEU* 3.6 17.0 - - + -
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Residues in contact with TYR 583 (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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548A ARG* 4.4 4.6 - - - +
581A THR 3.9 0.4 + - - -
582A THR* 1.3 72.3 - - - +
584A GLU* 1.3 80.7 + - + +
586A TYR* 3.4 7.7 + - - +
587A GLN* 3.1 54.3 + - + +
600A PRO* 3.7 35.0 + - + +
601A HIS* 3.9 26.2 - + - -
603A LEU* 5.0 3.2 - - - +
604A SER* 5.6 4.9 - - - +
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Residues in contact with GLU 584 (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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264A GLN* 3.3 46.6 - - + +
265A ASN* 3.7 4.7 - - - +
266A PRO* 3.6 18.1 - - + +
548A ARG* 3.0 39.8 + - - -
582A THR* 3.5 2.4 + - - -
583A TYR* 1.3 86.6 + - + +
585A GLU* 1.3 64.9 + - - +
587A GLN* 3.3 24.6 + - - +
588A ALA 4.1 0.2 + - - -
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Residues in contact with GLU 585 (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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261A SER* 3.2 38.7 - - - +
262A TYR* 4.2 7.3 - - - -
264A GLN* 4.7 0.4 - - - -
265A ASN* 2.8 22.8 + - - +
352A ASP* 4.9 3.5 - - - +
542A THR* 2.8 32.4 + - - +
544A MET* 3.5 14.9 + - - +
581A THR* 3.6 11.2 - - + +
582A THR* 3.1 28.6 + - - +
584A GLU* 1.3 74.0 - - - +
586A TYR* 1.3 65.5 + - - +
588A ALA* 3.2 17.5 + - - +
593A ALA* 3.5 12.0 - - - +
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Residues in contact with TYR 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A HIS* 2.5 37.2 + - - -
500A LYS 3.8 6.1 - - - -
501A PRO* 3.9 5.3 - - + +
502A LYS* 3.2 16.2 - - + +
581A THR* 3.7 4.4 + - - +
582A THR 2.9 13.1 + - - +
583A TYR* 3.4 13.7 - - - +
584A GLU 3.2 0.2 - - - -
585A GLU* 1.3 77.3 - - - +
587A GLN* 1.3 70.5 + - - +
589A GLN* 2.7 41.4 + - - +
593A ALA* 3.6 30.5 - - - -
596A THR* 3.8 21.3 - - + -
599A GLY 3.5 14.6 - - - -
600A PRO* 3.5 39.4 - - + +
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Residues in contact with GLN 587 (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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264A GLN* 5.6 4.3 - - + +
474A THR* 3.6 17.7 - - - +
500A LYS 5.1 0.4 + - - -
501A PRO* 3.3 33.0 - - - +
583A TYR* 3.1 59.1 + - + +
584A GLU* 3.4 15.0 - - - +
585A GLU 3.1 0.4 - - - -
586A TYR* 1.3 90.8 - - - +
588A ALA* 1.3 60.4 + - - +
589A GLN* 3.4 0.9 + - - +
600A PRO* 4.5 0.8 - - - +
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Residues in contact with ALA 588 (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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260A TYR 5.5 0.4 - - - +
261A SER* 3.4 32.5 - - - +
264A GLN* 4.5 13.2 - - + +
472A GLY* 3.2 19.9 - - - +
474A THR* 4.1 3.5 - - - +
584A GLU 4.1 0.6 + - - -
585A GLU 3.2 7.1 + - - +
587A GLN* 1.3 76.0 - - - +
589A GLN* 1.3 71.4 + - - +
590A ARG* 4.6 2.8 - - + +
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Residues in contact with GLN 589 (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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453A GLY* 4.5 0.3 - - - -
455A SER* 3.0 25.5 + - - -
472A GLY 3.0 4.6 + - - -
473A LYS 3.3 24.7 - - - +
474A THR* 4.0 3.8 - - + -
501A PRO 4.1 6.3 - - - +
502A LYS* 3.3 48.9 - - - +
503A PRO* 4.0 3.6 - - - +
585A GLU 3.8 2.6 + - - -
586A TYR* 2.7 34.8 + - - +
587A GLN 3.2 7.6 - - - +
588A ALA* 1.3 81.2 - - - +
590A ARG* 1.3 60.7 + - - +
593A ALA* 3.6 19.8 + - - -
594A ALA* 3.4 18.7 - - - +
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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