Contacts of the helix formed by residues 525 - 534 (chain B) in PDB entry 2W8D
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 ASP 525 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521B ALA* 3.5 0.9 - - - -
522B GLY 2.8 33.8 + - - +
524B VAL* 1.3 79.9 - - - +
526B VAL* 1.3 61.2 + - - +
527B ALA 3.3 0.9 - - - -
528B PRO* 3.1 15.5 - - - +
529B THR* 2.9 18.8 + - - -
545B GLY* 3.4 1.6 - - - -
546B SER 3.0 36.2 + - - +
548B ILE* 3.7 15.5 - - + -
553B HIS* 3.4 8.6 - - - -
554B ARG* 3.0 34.2 + - - -
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Residues in contact with VAL 526 (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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249B TYR* 3.7 14.4 - - - +
288B PHE* 3.7 26.0 - - + -
304B MSE 3.6 40.2 - - + -
467B VAL* 3.9 18.6 - - + -
505B LEU* 4.1 12.1 - - + -
507B ILE* 5.3 1.1 - - + -
523B ASP 3.4 13.4 + - - +
525B ASP* 1.3 77.1 - - - +
527B ALA* 1.3 57.9 + - - +
529B THR* 3.0 10.1 + - - -
530B ILE* 2.8 34.1 + - + +
548B ILE* 5.1 2.2 - - - -
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Residues in contact with ALA 527 (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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249B TYR* 4.5 5.8 - - - -
303B MSE 4.3 3.1 + - - +
304B MSE 3.3 25.5 + - - +
307B SER* 4.0 18.6 - - - +
328B VAL* 4.0 16.3 - - + +
523B ASP 4.7 1.0 + - - -
524B VAL 4.4 1.2 + - - -
526B VAL* 1.3 78.9 - - - +
528B PRO* 1.4 70.4 - - + +
530B ILE* 3.2 2.1 + - - +
531B LEU* 3.0 30.1 + - - +
543B MSE 4.6 3.4 - - + -
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Residues in contact with PRO 528 (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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307B SER* 3.8 7.2 - - - +
524B VAL 3.4 10.3 - - - +
525B ASP 3.1 17.5 - - - +
527B ALA* 1.4 95.2 - - + +
529B THR* 1.3 59.0 + - - +
532B HIS* 3.0 32.3 + - + -
538B THR* 4.3 25.8 - - + +
543B MSE 4.6 6.0 - - + -
545B GLY 3.7 21.5 - - - +
546B SER* 4.5 0.2 - - - -
547B ASP* 3.5 26.0 - - + +
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Residues in contact with THR 529 (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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285B PHE* 5.3 0.2 - - + -
507B ILE* 4.2 22.9 - - + -
525B ASP 2.9 16.0 + - - -
526B VAL* 3.0 12.0 + - - -
528B PRO* 1.3 78.5 - - - +
530B ILE* 1.3 64.9 + - - +
532B HIS* 3.4 2.3 + - - +
533B LEU* 3.1 26.7 + - + +
547B ASP* 3.7 16.6 - - - +
548B ILE* 3.0 31.5 + - + +
549B LEU* 4.1 23.9 - - + +
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Residues in contact with ILE 530 (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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247B VAL* 4.0 30.7 - - + -
249B TYR* 3.6 21.5 - - + +
328B VAL* 6.1 1.3 - - + -
403B TYR* 5.7 2.7 - - + -
465B ILE* 4.6 7.6 - - + -
467B VAL* 3.6 28.5 - - + -
507B ILE* 3.9 26.0 - - + -
526B VAL* 2.8 25.7 + - + +
527B ALA 4.0 2.9 - - - +
529B THR* 1.3 72.9 - - + +
531B LEU* 1.3 69.0 + - + +
533B LEU* 3.0 16.7 + - + +
534B LEU* 2.9 28.9 + - + +
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Residues in contact with LEU 531 (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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328B VAL* 4.0 30.3 - - + -
331B ILE* 4.3 11.4 - - + -
332B LEU* 4.1 22.7 - - + -
527B ALA 3.0 17.9 + - - +
528B PRO 3.9 0.9 - - - +
530B ILE* 1.3 79.6 - - + +
532B HIS* 1.3 61.2 + - - +
534B LEU* 3.0 24.6 - - + +
536B VAL* 3.1 33.3 + - + +
538B THR* 3.6 32.1 - - + -
543B MSE 4.0 21.8 - - + -
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Residues in contact with HIS 532 (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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231B TYR* 3.4 17.7 + + - -
232B ASP 4.1 9.2 - - - -
234B PRO* 3.5 19.4 - - + +
238B TYR 4.8 0.4 - - - -
239B PHE* 3.3 23.1 - + + -
240B GLY 2.9 16.1 + - - -
528B PRO* 3.0 20.8 + - + +
529B THR 4.0 2.9 - - - +
530B ILE 3.2 0.2 - - - -
531B LEU* 1.3 75.9 - - - +
533B LEU* 1.3 54.6 + - - +
534B LEU 2.5 17.2 - - - +
536B VAL 3.5 15.7 - - - -
538B THR* 2.6 32.3 + - + -
547B ASP* 2.6 42.4 + - + +
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Residues in contact with LEU 533 (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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238B TYR* 4.1 19.7 - - + +
240B GLY* 3.3 7.3 - - - -
242B ALA* 3.0 31.0 + - + +
283B PHE* 4.6 4.0 - - + -
465B ILE* 4.2 12.1 - - + -
507B ILE* 4.1 27.1 - - + -
509B ALA* 4.3 18.2 - - + -
512B VAL* 4.5 19.7 - - + -
529B THR* 3.1 26.5 + - + +
530B ILE* 3.0 19.6 + - + +
532B HIS* 1.3 69.8 - - - +
534B LEU* 1.3 65.7 + - - +
549B LEU* 4.5 19.5 - - + -
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Residues in contact with LEU 534 (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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240B GLY* 3.4 6.4 - - - -
242B ALA 3.5 18.6 - - - +
243B GLU* 3.8 3.4 - - - +
245B LYS 3.4 13.2 - - - +
247B VAL* 4.0 14.6 - - + -
332B LEU* 3.7 35.0 - - + -
337B TYR* 3.4 24.5 - - + +
465B ILE* 3.7 13.0 - - + -
530B ILE* 2.9 21.9 + - + +
531B LEU* 3.0 13.3 - - + +
532B HIS 2.5 26.0 - - - +
533B LEU* 1.3 76.0 - - - +
535B GLY* 1.3 65.6 + - - +
536B VAL* 3.2 7.2 - - + -
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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