Contacts of the helix formed by residues 488 - 496 (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 GLY 488 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A VAL* 2.7 32.5 + - - +
487A LYS* 1.3 71.1 - - - +
489A VAL* 1.3 64.7 + - - -
491A THR* 3.9 0.7 - - - -
492A SER* 2.7 25.1 + - - -
752A FAD 3.2 30.3 - - - -
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Residues in contact with VAL 489 (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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324A PRO* 3.8 23.3 - - + -
325A ALA 4.2 12.2 - - - +
326A ASN* 3.4 28.5 - - - +
327A ASP 6.3 0.2 - - - +
378A THR* 3.2 36.6 - - + +
451A LEU* 4.5 7.2 - - + -
454A ARG* 3.8 10.1 - - - +
487A LYS 4.2 1.1 - - - +
488A GLY* 1.3 72.8 - - - +
490A ALA* 1.3 64.5 + - - +
492A SER* 4.0 1.8 - - - -
493A TRP* 3.2 21.7 + - - +
752A FAD 2.8 21.5 + - - +
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Residues in contact with ALA 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 4.6 7.6 - - + -
324A PRO* 3.6 21.5 - - + -
454A ARG* 3.5 26.2 - - + -
456A TYR* 3.5 11.9 - - + +
489A VAL* 1.3 71.5 - - - +
491A THR* 1.3 53.9 + - - +
493A TRP* 3.1 2.6 + - + +
494A LEU* 2.7 41.4 + - + +
752A FAD 2.7 19.8 + - - +
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Residues in contact with THR 491 (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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301A MET* 3.4 16.9 - - + +
456A TYR* 3.6 11.2 - - + +
473A ALA* 4.6 1.8 - - + -
474A VAL 3.4 17.5 - - - +
475A ALA* 3.7 17.4 - - - +
476A VAL* 3.0 20.8 + - - +
488A GLY* 3.9 2.4 - - - -
490A ALA* 1.3 72.7 - - - +
492A SER* 1.3 58.1 + - - +
494A LEU* 4.3 2.5 - - + -
495A ARG* 2.9 29.6 + - - +
752A FAD 2.7 52.2 + - - +
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Residues in contact with SER 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ASP* 6.1 2.9 - - - -
475A ALA* 5.9 1.7 - - - +
476A VAL 4.3 2.4 + - - -
487A LYS* 3.5 37.6 - - - +
488A GLY 2.7 24.3 + - - -
489A VAL* 4.0 2.5 - - - -
490A ALA 3.2 0.6 - - - -
491A THR* 1.3 78.7 + - - +
493A TRP* 1.3 61.9 + - - +
495A ARG* 3.5 7.7 + - - +
496A ALA* 3.4 21.1 + - - +
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Residues in contact with TRP 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 4.0 15.3 - - + -
323A TYR 3.3 21.3 - - - -
324A PRO* 3.6 24.2 - - + -
325A ALA* 3.7 37.7 - - + +
373A TYR* 5.8 0.6 - + - -
489A VAL 3.2 16.2 + - - +
490A ALA* 3.4 11.2 - - - +
492A SER* 1.3 79.2 - - - +
494A LEU* 1.3 88.5 + - + +
496A ALA* 3.4 11.9 + - - +
497A LYS* 3.4 47.9 + - - +
509A VAL* 3.7 13.7 - - + -
510A PRO* 3.6 24.0 - - + -
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Residues in contact with LEU 494 (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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289A ASN* 3.0 14.4 + - - -
301A MET* 4.2 12.8 - - + -
303A LEU* 3.8 20.6 - - + +
305A LEU* 5.6 1.1 - - + -
322A VAL* 4.7 7.4 - - + -
456A TYR* 4.1 35.9 - - + +
471A ILE* 4.9 16.4 - - + -
473A ALA* 5.4 0.7 - - + -
490A ALA 2.7 24.1 + - - +
491A THR* 4.0 6.5 - - - +
493A TRP* 1.3 97.1 - - + +
495A ARG* 1.3 65.0 + - - +
497A LYS* 3.0 18.4 + - - +
509A VAL* 4.1 20.9 - - + -
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Residues in contact with ARG 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ASN* 3.6 12.9 + - - +
299A HIS* 3.2 62.3 + - + +
301A MET* 3.8 13.2 - - + -
475A ALA* 4.4 11.3 - - - +
477A GLU* 4.7 12.1 + - - -
487A LYS* 6.4 0.2 - - - +
491A THR 2.9 18.8 + - - +
492A SER* 3.7 7.9 - - - +
493A TRP 3.3 0.2 - - - -
494A LEU* 1.3 78.0 - - - +
496A ALA* 1.3 58.7 + - - +
497A LYS 3.5 0.5 + - - +
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Residues in contact with ALA 496 (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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492A SER 3.4 13.9 + - - +
493A TRP* 3.4 7.4 + - + +
494A LEU 3.2 1.0 - - - -
495A ARG* 1.3 76.3 - - - +
497A LYS* 1.3 59.0 + - - +
498A GLU* 3.0 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