Contacts of the helix formed by residues 465 - 480 (chain A) in PDB entry 2FBW
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 THR 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463A ILE 3.8 0.4 + - - -
464A ARG* 1.3 72.9 - - - +
466A SER* 1.3 59.1 + - - +
467A GLU 3.2 0.3 + - - -
468A ALA* 3.2 1.6 + - - -
469A ARG* 2.9 41.7 + - - +
506A LEU* 3.9 12.4 - - - +
507A LYS 3.6 4.2 + - - -
508A THR* 3.8 10.9 - - - +
518A ASP* 4.6 8.0 + - - +
521A GLU* 4.0 10.8 - - + +
522A THR* 2.9 49.2 + - - +
525A LEU* 3.9 13.6 - - + +
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Residues in contact with SER 466 (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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464A ARG* 3.3 13.1 + - - +
465A THR* 1.3 80.3 - - - +
467A GLU* 1.3 58.6 + - - +
469A ARG* 3.5 30.6 + - - +
470A LEU* 3.0 29.3 + - - +
53B ASN* 2.7 43.3 + - - +
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Residues in contact with GLU 467 (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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462A THR 4.6 4.0 - - - +
463A ILE* 4.3 17.2 - - + +
464A ARG* 2.9 31.4 + - + +
466A SER* 1.3 80.2 + - - +
468A ALA* 1.3 64.7 + - - +
470A LEU* 3.9 5.4 - - - +
471A ASN* 3.1 21.6 + - + +
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Residues in contact with ALA 468 (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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463A ILE* 4.1 18.1 - - + +
464A ARG 3.2 6.0 + - - +
465A THR 4.0 0.9 - - - +
467A GLU* 1.3 76.3 - - - +
469A ARG* 1.3 66.5 + - - +
471A ASN* 3.2 8.5 + - - +
472A MET* 2.9 23.2 + - - +
499A ILE* 4.2 13.7 - - + +
502A ASP* 6.1 2.2 - - + +
503A LEU* 4.4 12.8 - - + +
506A LEU* 4.7 4.7 - - + -
525A LEU* 4.0 20.0 - - + -
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Residues in contact with ARG 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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465A THR* 2.9 35.7 + - - +
466A SER* 3.5 16.4 + - - +
468A ALA* 1.3 77.7 - - - +
470A LEU* 1.3 61.4 + - - +
472A MET* 3.2 14.6 + - + +
473A GLN* 2.9 47.4 + - - +
521A GLU* 3.7 28.3 + - - +
525A LEU* 3.8 20.8 - - + +
528A LEU* 4.8 11.2 - - + -
53B ASN* 2.9 39.8 + - - +
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Residues in contact with LEU 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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221A PHE* 3.7 24.7 - - + -
466A SER 3.0 19.7 + - - +
467A GLU* 3.9 5.6 - - - +
469A ARG* 1.3 77.4 - - - +
471A ASN* 1.3 63.1 + - - +
473A GLN* 3.2 11.4 + - - +
474A LYS* 2.9 59.9 + - + +
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Residues in contact with ASN 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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467A GLU 3.1 15.4 + - - +
468A ALA* 3.2 11.6 + - - +
470A LEU* 1.3 76.7 - - - +
472A MET* 1.3 60.2 + - - +
474A LYS* 3.6 5.0 + - - +
475A THR* 2.9 35.3 + - - -
495A LYS* 6.1 0.7 - - - -
499A ILE* 3.5 28.6 - - + +
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Residues in contact with MET 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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219A THR* 4.1 12.3 - - - +
468A ALA 2.9 13.8 + - - +
469A ARG* 3.2 19.0 + - + +
471A ASN* 1.3 77.5 - - - +
473A GLN* 1.3 72.1 + - + +
475A THR* 3.3 3.1 + - - -
476A MET* 3.0 22.9 + - + +
496A LEU* 4.1 10.0 - - + +
499A ILE* 3.9 9.8 - - + +
525A LEU* 3.9 11.9 - - + -
528A LEU* 3.7 42.6 - - + +
529A MET* 3.5 45.8 - - - +
532A ALA* 4.3 9.6 - - + -
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Residues in contact with GLN 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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218A ARG* 2.8 33.9 + - - +
219A THR 3.3 16.6 - - - +
220A TYR 3.3 23.3 + - - +
221A PHE* 3.6 19.1 + - + +
469A ARG* 2.9 43.5 + - - +
470A LEU* 3.8 17.8 - - - +
472A MET* 1.3 80.8 - - + +
474A LYS* 1.3 58.6 + - - +
476A MET* 3.5 1.0 + - - +
477A GLN* 3.0 30.0 + - - +
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Residues in contact with LYS 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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221A PHE* 4.1 23.3 - - + -
470A LEU* 2.9 56.1 + - + +
471A ASN* 4.2 4.9 - - - +
473A GLN* 1.3 76.0 - - - +
475A THR* 1.3 63.6 + - - +
477A GLN* 3.4 6.0 + - - +
478A SER* 3.0 31.6 + - - +
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Residues in contact with THR 475 (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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471A ASN* 2.9 30.9 + - - -
472A MET 3.5 4.5 - - - -
474A LYS* 1.3 77.4 - - - +
476A MET* 1.3 59.1 + - - +
478A SER* 3.2 1.1 + - - -
479A HIS* 2.9 50.4 + - + +
492A GLY* 3.9 23.8 - - - +
495A LYS* 3.9 23.5 - - + +
496A LEU* 4.1 17.7 - - + -
499A ILE* 3.9 6.2 - - - +
536A ILE* 5.0 1.6 - - + -
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Residues in contact with MET 476 (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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216A TYR* 6.2 0.2 - - + -
219A THR* 3.5 23.6 - - - +
220A TYR* 3.4 45.9 - - + +
472A MET* 3.0 21.4 + - + +
473A GLN 3.9 0.7 - - - +
475A THR* 1.3 76.4 - - - +
477A GLN* 1.3 63.0 + - - +
479A HIS* 5.3 0.4 - - - -
480A ALA* 3.0 28.4 + - + +
496A LEU* 3.6 29.4 - - + -
532A ALA* 3.8 23.1 - - + +
535A THR* 3.9 24.2 - - + -
536A ILE* 4.4 11.9 - - + -
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Residues in contact with GLN 477 (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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220A TYR* 3.6 17.8 - - - +
221A PHE* 2.9 42.2 + - + -
222A SER* 2.9 28.0 + - - +
252A PHE* 5.0 6.5 - - - -
363A VAL* 4.8 5.7 - - - +
473A GLN 3.0 17.6 + - - +
474A LYS* 3.7 5.6 - - - +
476A MET* 1.3 77.9 - - - +
478A SER* 1.3 61.4 + - - +
481A ALA* 3.5 24.2 - - - +
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Residues in contact with SER 478 (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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474A LYS* 3.0 19.3 + - - +
475A THR* 4.9 0.2 - - - -
477A GLN* 1.3 80.1 - - - +
479A HIS* 1.3 75.4 + - - +
480A ALA 3.8 0.4 - - - -
481A ALA* 5.2 2.8 - - - +
488A ILE* 3.8 10.4 - - - +
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Residues in contact with HIS 479 (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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475A THR* 2.9 37.9 + - + +
478A SER* 1.3 93.2 - - - +
480A ALA* 1.3 57.7 + - - +
481A ALA 3.8 1.8 - - - -
483A PHE 6.0 0.4 - - - -
484A ARG* 4.6 3.1 - - - +
488A ILE* 2.8 42.6 + - + +
489A LEU* 3.3 26.0 - - - +
491A GLU* 3.6 36.6 - - + -
492A GLY* 3.5 16.6 + - - -
495A LYS* 3.6 18.2 + - + +
536A ILE* 4.1 5.1 - - + +
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Residues in contact with ALA 480 (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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220A TYR* 3.0 31.2 + - - +
252A PHE* 3.8 1.2 - - - -
476A MET* 3.0 22.1 + - + +
479A HIS* 1.3 78.8 - - - +
481A ALA* 1.3 60.5 + - - +
484A ARG* 3.2 28.6 + - - +
489A LEU* 4.4 3.4 - - + -
535A THR* 5.4 1.8 - - + -
536A ILE* 4.3 21.5 - - + -
539A ALA* 5.6 1.1 - - + -
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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