Contacts of the strand formed by residues 508 - 514 (chain A) in PDB entry 3OJX
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 LEU 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A LEU* 3.7 42.9 - - + +
284A ALA 3.4 4.0 - - - -
285A ALA* 3.5 35.9 - - + +
493A TRP* 4.1 0.3 - - - -
497A LYS* 2.9 26.0 + - - +
506A ARG* 3.0 19.6 + - + +
507A ALA* 1.3 72.1 - - - +
509A VAL* 1.3 61.3 + - - +
510A PRO* 3.7 8.1 - - - +
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Residues in contact with VAL 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE 3.4 0.2 - - - +
283A LEU* 4.1 1.1 - - - -
284A ALA 2.8 33.0 + - - +
286A VAL* 3.9 21.3 - - + -
303A LEU* 5.6 0.2 - - + -
305A LEU* 4.3 18.2 - - + -
322A VAL* 3.6 29.4 - - + -
493A TRP* 3.4 26.5 - - + -
494A LEU* 4.1 17.0 - - + -
497A LYS* 4.2 9.4 - - + -
508A LEU* 1.3 75.0 - - - +
510A PRO* 1.3 67.9 - - - +
511A MET* 3.3 6.1 + - - +
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Residues in contact with PRO 510 (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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269A TYR* 3.5 41.7 - - + +
281A PRO* 4.2 9.6 - - + -
282A PHE 3.7 6.3 - - - +
283A LEU* 4.1 15.3 - - + -
322A VAL* 3.2 6.4 - - - +
323A TYR* 3.2 36.4 + - + +
493A TRP* 3.5 22.2 - - + -
508A LEU 3.7 5.2 - - - +
509A VAL* 1.3 81.9 - - - +
511A MET* 1.3 59.5 + - - +
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Residues in contact with MET 511 (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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276A PHE* 5.1 0.2 - - - +
281A PRO* 4.0 2.9 - - - +
282A PHE* 2.9 44.4 + - - +
284A ALA* 4.2 7.6 - - + -
305A LEU* 4.2 11.7 - - + -
307A ILE* 3.5 28.9 - - + -
312A ILE* 4.1 19.4 - - + +
320A VAL* 3.8 26.2 - - + -
321A ALA 3.0 16.4 - - - +
322A VAL* 4.0 6.7 - - + -
323A TYR* 5.5 0.2 - - - -
469A VAL* 4.1 13.2 - - + -
509A VAL 3.5 9.6 - - - +
510A PRO* 1.3 74.3 - - - +
512A PHE* 1.3 68.8 + - - +
513A VAL* 4.7 8.1 - - + -
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Residues in contact with PHE 512 (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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276A PHE 4.5 4.7 - - - +
277A ASP* 3.6 26.0 - - + +
278A ALA* 3.8 34.8 - - + -
281A PRO* 4.7 0.7 - - + -
312A ILE* 5.1 3.4 - - - -
320A VAL* 3.7 3.5 - - - +
321A ALA* 3.0 53.4 + - + +
323A TYR* 3.7 34.3 - + - -
453A ALA* 4.4 6.1 - - + -
455A TYR* 4.0 11.4 - + - -
511A MET* 1.3 84.0 - - - +
513A VAL* 1.3 66.3 + - - +
514A CYS* 3.5 30.1 - - - -
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Residues in contact with VAL 513 (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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276A PHE 5.3 2.0 + - - -
277A ASP* 6.1 0.2 - - - -
312A ILE* 3.6 32.0 - - + +
313A ARG 4.0 12.6 - - - +
314A TYR* 4.3 19.1 - - + -
318A ASP* 4.4 5.4 - - + -
319A HIS 3.7 11.0 - - - +
320A VAL* 5.1 0.9 - - - -
458A ILE* 4.4 7.9 - - + -
469A VAL* 5.1 2.7 - - + -
511A MET* 4.7 11.4 - - + -
512A PHE* 1.3 82.0 - - - +
514A CYS* 1.3 78.0 + - - +
515A LYS* 4.3 13.7 + - + +
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Residues in contact with CYS 514 (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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147A CYS* 3.1 43.5 - - - -
150A GLN* 5.3 1.3 - - - +
318A ASP* 3.8 0.7 - - - +
319A HIS* 3.0 37.3 + - + +
321A ALA* 5.1 1.1 - - + -
455A TYR* 3.7 13.5 - - + -
512A PHE* 3.5 32.7 + - - -
513A VAL* 1.3 78.6 - - - +
515A LYS* 1.3 66.0 + - - +
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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