Contacts of the helix formed by residues 460 - 474 (chain A) in PDB entry 2WWA
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 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456A GLY 3.4 16.7 + - - -
457A ILE* 3.6 6.0 - - - -
458A ALA 3.3 0.4 - - - -
459A GLY* 1.4 78.0 - - - +
461A PHE* 1.4 56.6 + - - +
462A SER 3.5 0.2 - - - -
463A LEU* 3.9 12.2 - - - +
464A LEU* 3.5 18.0 + - - +
53B ALA* 4.5 15.5 - - - +
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Residues in contact with PHE 461 (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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261A CYS* 3.5 33.0 - - - -
264A GLN* 3.7 11.0 - - + +
265A SER* 5.0 6.3 - - - -
267A ARG* 4.2 13.2 - - - -
457A ILE 3.4 17.4 + - - +
458A ALA* 3.9 1.7 - - - -
460A GLY* 1.4 75.2 - - - +
462A SER* 1.4 63.5 + - - +
463A LEU 3.3 0.9 - - - -
464A LEU* 3.6 32.2 - - + +
465A GLU* 3.1 46.3 + - + +
46B GLU* 4.8 12.6 - - + -
49B LYS* 4.2 5.8 - - + -
50B ILE* 3.6 36.1 - - + -
53B ALA* 4.5 5.4 - - + -
54B VAL* 6.3 0.4 - - + -
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Residues in contact with SER 462 (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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264A GLN* 3.4 19.0 + - - +
287A LYS* 3.5 18.4 + - - +
290A TYR* 3.2 37.5 - - - -
458A ALA 3.4 16.0 + - - -
459A GLY* 4.1 8.7 - - - -
460A GLY 3.5 0.2 - - - -
461A PHE* 1.4 75.4 - - - +
463A LEU* 1.4 61.8 + - - +
465A GLU* 3.4 6.0 + - - -
466A VAL* 3.4 22.5 + - - +
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Residues in contact with LEU 463 (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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178A SER* 5.6 11.7 - - - +
459A GLY 3.6 17.7 + - - +
460A GLY* 3.9 10.8 - - - +
462A SER* 1.4 77.8 - - - +
464A LEU* 1.4 60.3 + - - +
466A VAL* 3.4 7.3 + - + +
467A ILE* 3.2 43.4 + - + +
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Residues in contact with LEU 464 (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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460A GLY 3.5 14.1 + - - +
461A PHE* 3.6 39.3 - - + +
462A SER 3.3 0.4 - - - -
463A LEU* 1.4 77.9 - - - +
465A GLU* 1.4 59.0 + - + +
467A ILE* 3.4 16.8 - - + +
468A THR* 3.0 49.7 + - + +
49B LYS* 3.6 31.4 - - + +
52B LYS* 5.6 8.1 - - + -
53B ALA* 3.9 13.0 - - + -
56B ILE* 6.4 2.7 - - + -
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Residues in contact with GLU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A GLN* 3.1 31.0 + - - +
267A ARG* 3.0 42.9 + - - +
287A LYS* 3.1 32.7 + - - +
461A PHE* 3.1 21.1 + - + +
462A SER 3.6 1.3 - - - +
463A LEU 3.4 0.2 - - - -
464A LEU* 1.4 79.3 - - + +
466A VAL* 1.4 63.1 + - - +
468A THR* 3.2 16.3 + - - -
469A ILE* 3.3 28.2 - - + +
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Residues in contact with VAL 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LYS* 3.8 19.7 - - - +
462A SER* 3.4 16.0 + - - +
463A LEU* 3.9 8.7 - - + +
464A LEU 3.4 0.8 - - - -
465A GLU* 1.4 77.1 - - - +
467A ILE* 1.4 67.0 + - + +
469A ILE* 3.5 5.5 + - - +
470A GLU* 3.2 33.6 + - + +
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Residues in contact with ILE 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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463A LEU* 3.2 34.7 + - + +
464A LEU* 3.4 25.6 - - + +
466A VAL* 1.4 78.4 - - + +
468A THR* 1.4 64.3 + - + +
470A GLU* 3.4 6.5 + - + +
471A TYR* 3.0 65.0 + - + +
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Residues in contact with THR 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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464A LEU* 3.0 43.3 + - + +
465A GLU* 3.2 13.3 + - - -
467A ILE* 1.4 78.6 - - + +
469A ILE* 1.4 58.5 + - - +
471A TYR* 3.3 14.4 + - + +
472A GLN* 3.1 48.6 + - - +
49B LYS* 5.5 9.3 - - + +
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Residues in contact with ILE 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 GLU* 3.3 26.3 + - + +
466A VAL* 3.9 6.1 - - - +
468A THR* 1.4 74.6 + - - +
470A GLU* 1.4 68.4 + - - +
472A GLN* 4.4 4.5 - - + +
473A GLN* 3.1 53.7 + - + +
474A SER* 3.7 4.6 + - - +
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Residues in contact with GLU 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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466A VAL* 3.2 26.6 + - + +
467A ILE* 3.6 11.0 - - - +
468A THR 3.3 0.2 - - - -
469A ILE* 1.4 78.0 - - + +
471A TYR* 1.4 63.4 + - + +
474A SER* 3.3 29.7 + - - -
475A GLY 2.9 26.4 + - - +
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Residues in contact with TYR 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 ILE* 3.0 60.1 + - + +
468A THR* 3.3 14.3 + - + +
470A GLU* 1.4 79.9 - - + +
472A GLN* 1.4 58.8 + - + +
473A GLN 3.6 0.2 - - - -
475A GLY 3.3 14.7 - - - +
476A GLY* 5.1 2.0 - - - -
477A GLN* 3.1 30.6 - - + +
478A SER* 2.9 20.3 + - - -
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Residues in contact with GLN 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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468A THR* 3.1 39.1 + - - +
469A ILE* 4.3 3.3 - - - +
471A TYR* 1.4 78.6 - - + +
473A GLN* 1.4 75.8 + - + +
477A GLN 5.1 0.2 - - - +
478A SER* 3.9 5.4 - - - +
479A ALA* 3.7 36.7 - - + +
480A LEU* 3.7 24.8 + - - +
484A LEU* 5.5 0.3 - - - +
49B LYS* 5.9 2.8 - - - +
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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
----------------------------------------------------------
469A ILE* 3.1 40.6 + - + +
471A TYR 3.6 0.2 - - - -
472A GLN* 1.4 92.0 - - + +
474A SER* 1.4 65.4 + - - +
475A GLY 3.5 0.9 - - - +
480A LEU* 5.2 6.5 - - - +
484A LEU* 5.6 16.4 - - + +
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Residues in contact with SER 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ILE* 3.7 4.9 + - - +
470A GLU* 3.3 43.2 + - - -
473A GLN* 1.4 79.6 - - - +
475A GLY* 1.4 57.6 + - - +
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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