Contacts of the helix formed by residues 525 - 534 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A ALA* 3.3 2.4 - - - -
522A GLY 2.9 31.6 + - - +
524A VAL* 1.3 78.2 - - - +
526A VAL* 1.3 56.5 + - - +
527A ALA 3.5 0.2 - - - -
528A PRO* 3.5 5.2 - - - +
529A THR* 2.7 31.5 + - - -
545A GLY* 3.4 0.7 - - - -
546A SER 2.9 33.8 + - - +
548A ILE* 3.6 15.0 - - + -
553A HIS* 3.3 8.5 - - - -
554A ARG* 2.8 40.7 + - - -
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Residues in contact with VAL 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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249A TYR* 3.7 23.1 - - + +
288A PHE* 3.7 30.7 - - + -
304A MSE 3.7 25.4 - - + -
467A VAL* 4.0 16.2 - - + -
505A LEU* 4.3 15.5 - - + -
507A ILE* 5.5 1.8 - - + -
523A ASP 3.2 14.1 + - - +
525A ASP* 1.3 76.2 - - - +
527A ALA* 1.3 63.8 + - - +
529A THR* 3.1 7.8 + - - -
530A ILE* 3.0 31.7 + - + +
548A ILE* 5.0 1.6 - - + -
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Residues in contact with ALA 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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249A TYR* 4.3 7.2 - - - -
303A MSE 4.5 2.4 + - - +
304A MSE 3.3 27.7 + - - +
307A SER* 4.4 15.3 - - - +
328A VAL* 3.8 18.8 - - + +
523A ASP 4.8 0.8 + - - -
524A VAL 4.4 1.0 + - - -
526A VAL* 1.3 78.0 - - - +
528A PRO* 1.4 67.1 - - + +
530A ILE* 3.4 2.6 + - - +
531A LEU* 2.9 33.9 + - - +
543A MSE 4.8 3.4 - - + -
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Residues in contact with PRO 528 (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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307A SER* 3.9 7.9 - - - +
524A VAL 3.6 17.0 - - - +
525A ASP 3.5 12.8 - - - +
527A ALA* 1.4 93.0 - - + +
529A THR* 1.3 63.7 + - - -
531A LEU* 3.9 7.4 - - + -
532A HIS* 3.0 31.5 + - + -
538A THR* 4.5 20.0 - - + +
543A MSE 4.4 8.1 - - + -
545A GLY 4.0 20.4 - - - +
547A ASP* 3.9 17.7 - - + +
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Residues in contact with THR 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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285A PHE* 5.1 0.7 - - + -
507A ILE* 4.1 23.6 - - + -
525A ASP 2.7 20.8 + - - -
526A VAL* 3.1 10.0 + - - -
528A PRO* 1.3 78.0 - - - +
530A ILE* 1.3 61.0 + - - +
532A HIS* 3.3 2.8 + - - +
533A LEU* 3.0 31.2 + - + +
547A ASP* 3.5 18.0 - - - +
548A ILE* 3.1 29.9 + - + +
549A LEU* 4.0 23.2 - - + +
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Residues in contact with ILE 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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247A VAL* 4.3 20.6 - - + -
249A TYR* 3.5 23.1 - - + +
328A VAL* 5.8 2.5 - - + -
403A TYR* 5.6 3.4 - - + -
465A ILE* 4.5 7.2 - - + -
467A VAL* 3.6 24.9 - - + -
507A ILE* 3.8 26.5 - - + -
526A VAL* 3.0 18.7 + - + +
527A ALA* 3.6 6.3 - - - +
529A THR* 1.3 74.1 - - - +
531A LEU* 1.3 68.6 + - + +
533A LEU* 3.2 15.4 + - + +
534A LEU* 3.1 37.1 + - + +
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Residues in contact with LEU 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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328A VAL* 3.8 40.2 - - + -
331A ILE* 4.2 13.0 - - + -
332A LEU* 4.1 26.5 - - + -
527A ALA 2.9 20.5 + - - +
528A PRO 4.2 0.4 - - - +
530A ILE* 1.3 76.6 - - + +
532A HIS* 1.3 61.2 + - - +
534A LEU* 3.0 15.1 + - + +
535A GLY 3.2 0.2 + - - -
536A VAL* 3.0 45.7 + - + +
538A THR* 3.8 26.7 - - + -
543A MSE 4.0 14.4 - - + -
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Residues in contact with HIS 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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231A TYR* 3.6 13.5 + + - -
232A ASP 4.1 10.3 - - - -
234A PRO* 3.8 26.1 - - + +
238A TYR 5.3 0.2 - - - -
239A PHE* 3.2 19.8 - + + -
240A GLY 3.0 13.0 + - - -
528A PRO* 3.0 21.5 + - + +
529A THR 3.6 3.8 - - - +
531A LEU* 1.3 76.8 - - - +
533A LEU* 1.3 56.7 + - - +
535A GLY 2.9 17.3 + - - -
536A VAL 3.4 17.0 - - - -
538A THR* 2.6 30.3 + - + -
547A ASP* 2.6 42.7 + - + +
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Residues in contact with LEU 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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238A TYR* 3.9 31.9 - - + +
241A LYS 3.3 8.1 + - - -
242A ALA* 2.9 36.2 + - + -
283A PHE* 4.8 4.3 - - + -
465A ILE* 4.4 6.3 - - + -
507A ILE* 4.1 29.4 - - + -
509A ALA* 4.5 13.5 - - + -
512A VAL* 4.6 21.8 - - + -
529A THR 3.0 19.5 + - - +
530A ILE* 3.2 19.5 + - + +
532A HIS* 1.3 74.9 - - - +
534A LEU* 1.3 57.5 + - - +
535A GLY 3.2 1.4 + - - -
549A LEU* 4.3 17.5 - - + -
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Residues in contact with LEU 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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242A ALA 3.4 19.5 - - - +
243A GLU* 3.5 16.2 - - - +
244A GLY 4.6 0.9 - - - +
245A LYS 3.7 8.5 - - - +
247A VAL* 3.9 19.5 - - + -
332A LEU* 3.9 28.9 - - + -
335A LYS* 2.8 31.4 + - - +
337A TYR* 3.6 20.6 - - - +
465A ILE* 3.5 20.0 - - + -
530A ILE* 3.1 22.2 + - + +
531A LEU* 3.0 14.7 + - + +
533A LEU* 1.3 74.3 - - - +
535A GLY* 1.3 60.6 + - - +
536A VAL* 3.3 3.8 - - + -
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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