Contacts of the strand formed by residues 468 - 474 (chain A) in PDB entry 3OJW
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 SER 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A THR* 4.8 2.1 + - - -
304A GLU* 3.8 11.8 + - - +
305A LEU 3.2 12.4 + - - -
306A ASP* 5.1 1.1 - - - -
307A ILE* 3.8 1.6 - - - +
314A TYR* 2.9 23.4 + - - -
460A SER* 3.4 4.3 + - - -
465A HIS* 3.0 17.7 + - - +
466A PRO 3.5 1.0 - - - -
467A ASN* 1.3 82.1 - - - +
469A VAL* 1.3 64.2 + - - +
470A HIS* 3.3 25.3 + - - -
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Residues in contact with VAL 469 (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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304A GLU* 3.7 0.7 - - - -
305A LEU* 2.9 42.5 + - + +
307A ILE* 3.7 31.6 - - + -
314A TYR* 3.8 17.7 - - + -
320A VAL* 4.0 22.2 - - + -
458A ILE* 3.6 33.9 - - + -
460A SER* 3.9 2.5 - - - -
468A SER* 1.3 75.5 - - - +
470A HIS* 1.3 65.9 + - - +
471A ILE* 4.1 1.4 + - + +
511A MET* 4.6 7.9 - - + -
513A VAL* 5.1 3.4 - - + -
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Residues in contact with HIS 470 (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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302A HIS* 3.7 18.0 + + - +
303A LEU 3.2 5.6 - - - +
304A GLU* 3.4 36.0 + - + +
458A ILE* 3.4 8.8 - - - -
459A ALA* 2.8 35.6 + - + +
460A SER* 3.3 24.7 + - - -
465A HIS* 4.0 33.9 - + - -
468A SER* 3.3 29.9 + - - -
469A VAL* 1.3 74.3 - - - +
471A ILE* 1.3 64.3 + - - +
545A GLN* 4.6 5.5 + - - -
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Residues in contact with ILE 471 (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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302A HIS* 3.3 9.0 - - - -
303A LEU* 2.9 47.0 + - + +
305A LEU* 4.0 23.6 - - + -
320A VAL* 3.9 29.4 - - + -
322A VAL* 4.8 7.6 - - + -
456A TYR* 3.9 39.0 - - + -
457A SER 4.6 4.0 - - - -
459A ALA* 4.8 0.2 - - - -
469A VAL* 4.6 5.6 - - + +
470A HIS* 1.3 78.6 - - - +
472A THR* 1.3 72.0 + - - +
473A ALA* 4.3 5.4 - - + -
494A LEU* 4.9 14.1 - - + -
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Residues in contact with THR 472 (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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292A LEU* 4.0 13.9 - - + -
300A LEU* 6.3 0.4 - - + -
301A MET 3.5 4.3 - - - -
457A SER 4.8 4.2 + - - -
459A ALA* 3.7 14.0 - - - +
471A ILE* 1.3 74.2 - - - +
473A ALA* 1.3 64.4 + - - +
535A THR* 4.3 28.4 - - + +
537A ILE* 4.9 0.4 - - + -
538A ALA* 3.7 15.8 - - + +
574A LEU* 4.5 5.2 - - + -
575A TYR* 2.6 36.1 + - + +
752A FAD 2.8 26.4 + - - +
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Residues in contact with ALA 473 (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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300A LEU* 3.5 1.3 - - - -
301A MET* 2.8 59.1 + - + +
303A LEU* 5.8 0.2 - - + -
456A TYR* 3.9 18.2 - - + -
471A ILE* 4.2 6.7 - - + +
472A THR* 1.3 77.0 - - - +
474A VAL* 1.3 62.4 + - - +
491A THR* 4.6 1.6 - - + -
494A LEU* 5.4 1.3 - - + -
535A THR* 4.4 7.4 - - - -
752A FAD 3.2 19.5 - - + +
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Residues in contact with VAL 474 (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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298A ARG* 4.0 26.2 - - + +
299A HIS 3.6 5.4 - - - +
300A LEU* 3.7 28.9 - - + +
301A MET* 4.7 0.2 - - - -
473A ALA* 1.3 72.5 - - - +
475A ALA* 1.3 74.4 + - - +
476A VAL* 3.4 11.7 + - + +
491A THR* 3.4 15.0 - - - +
535A THR* 4.1 13.0 - - + +
632A ASP* 5.9 2.9 - - - +
752A FAD 3.4 12.1 + - - +
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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