Contacts of the helix formed by residues 582 - 589 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ASN* 2.7 25.3 + - - +
544B MET* 3.8 7.0 - - + -
545B SER* 3.2 28.7 + - - +
548B ARG* 3.6 12.6 - - - -
581B THR* 1.3 77.4 - - - +
583B TYR* 1.3 54.7 + - - +
584B GLU* 3.4 9.8 + - - -
585B GLU* 3.0 27.8 + - - +
586B TYR* 2.8 33.7 + - - +
600B PRO 4.9 0.4 - - - -
603B LEU* 3.7 15.9 - - + -
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Residues in contact with TYR 583 (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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439B LEU* 5.9 1.1 - - + -
548B ARG* 4.5 3.6 - - - +
581B THR 4.0 0.2 + - - -
582B THR* 1.3 73.8 - - - +
584B GLU* 1.3 78.4 + - + +
586B TYR* 3.3 7.6 + - - +
587B GLN* 3.0 51.7 + - + +
600B PRO* 3.7 35.4 + - + +
601B HIS* 3.6 32.1 - + - +
603B LEU* 5.0 2.4 - - - +
604B SER* 5.8 4.3 - - - +
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Residues in contact with GLU 584 (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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264B GLN* 3.4 41.9 - - + +
265B ASN* 3.7 6.7 - - - +
266B PRO* 3.7 17.0 - - + +
548B ARG* 3.1 41.7 + - - -
582B THR* 3.4 4.7 + - - -
583B TYR* 1.3 86.6 + - + +
585B GLU* 1.3 64.6 + - - +
587B GLN* 3.4 22.4 + - - +
588B ALA 4.1 2.1 + - - -
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Residues in contact with GLU 585 (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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261B SER* 3.3 39.5 + - - +
262B TYR* 4.2 7.7 - - - -
264B GLN* 4.8 0.2 - - - -
265B ASN* 2.8 22.7 + - - +
352B ASP* 4.9 3.7 - - - +
542B THR* 2.9 31.9 + - - +
544B MET* 3.5 14.4 + - - +
581B THR* 3.6 11.3 - - + +
582B THR* 3.0 29.4 + - - +
584B GLU* 1.3 74.4 - - - +
586B TYR* 1.3 65.6 + - - +
588B ALA* 3.2 17.5 + - - +
593B ALA* 3.6 11.8 - - - +
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Residues in contact with TYR 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B HIS* 2.5 36.2 + - - -
500B LYS 3.8 5.6 - - - -
501B PRO* 3.8 11.2 - - + +
502B LYS* 3.2 17.8 + - - -
581B THR* 3.7 6.2 + - - +
582B THR 2.8 16.7 + - - +
583B TYR* 3.4 10.1 - - - +
584B GLU 3.2 0.2 - - - -
585B GLU* 1.3 77.0 - - - +
587B GLN* 1.3 64.8 + - - +
589B GLN* 2.8 42.2 + - - +
593B ALA* 3.5 31.0 - - - -
596B THR* 3.8 20.9 - - + -
599B GLY 3.5 14.1 - - - -
600B PRO* 3.5 38.7 - - + +
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Residues in contact with GLN 587 (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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264B GLN* 6.0 1.8 - - + +
474B THR* 3.6 17.3 - - - +
501B PRO* 3.3 33.9 - - + +
583B TYR* 3.0 59.3 + - + +
584B GLU* 3.5 15.0 - - - +
585B GLU 3.1 0.4 - - - -
586B TYR* 1.3 89.6 - - - +
588B ALA* 1.3 60.5 + - - +
589B GLN* 3.4 0.7 + - - +
600B PRO* 4.5 0.8 - - - +
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Residues in contact with ALA 588 (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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261B SER* 3.5 31.2 - - - +
264B GLN* 4.7 11.9 - - + -
472B GLY* 3.2 19.6 - - - +
474B THR* 4.0 4.6 - - - +
584B GLU 4.1 0.2 + - - -
585B GLU 3.2 8.1 + - - +
586B TYR 3.2 0.6 - - - -
587B GLN* 1.3 76.5 - - - +
589B GLN* 1.3 69.7 + - - +
590B ARG* 3.3 3.6 + - + +
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Residues in contact with GLN 589 (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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453B GLY* 4.5 0.5 - - - -
454B TYR 5.4 0.2 + - - -
455B SER* 3.0 13.7 + - - -
472B GLY* 3.0 15.4 + - - -
473B LYS 3.4 20.9 - - - +
474B THR* 3.9 6.1 - - + -
501B PRO 4.1 7.6 - - - +
502B LYS* 3.3 48.3 - - - +
503B PRO* 4.0 3.5 - - - +
586B TYR* 2.8 34.2 + - - +
587B GLN 3.2 7.8 - - - +
588B ALA* 1.3 80.4 - - - +
590B ARG* 1.3 62.6 + - - +
593B ALA* 3.6 23.0 + - - +
594B ALA* 3.5 18.6 - - - +
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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