Contacts of the helix formed by residues 460 - 474 (chain A) in PDB entry 6WCZ
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 ASN 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A ASN* 3.2 34.3 + - - +
459A MET* 1.3 74.0 - - - +
461A GLN* 1.3 80.6 + - - +
462A LEU 3.1 0.2 - - - -
463A SER* 2.8 28.6 + - - +
464A ILE* 3.9 4.5 - - - +
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Residues in contact with GLN 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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424A VAL* 3.5 30.5 - - + +
425A THR* 3.4 27.7 - - + +
426A GLU* 5.6 0.2 + - - -
456A ILE* 3.8 11.0 - - + -
457A SER 4.7 0.4 - - - +
458A ASN* 3.1 24.8 + - + +
460A ASN* 1.3 98.2 + - - +
462A LEU* 1.3 52.9 + - - +
463A SER 3.2 0.4 - - - -
464A ILE* 3.4 18.2 - - - +
465A ALA* 2.6 41.3 + - - +
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Residues in contact with LEU 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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324A MET* 5.6 2.9 - - + -
327A THR* 4.3 24.0 - - + +
330A ARG* 5.0 13.9 - - + -
333A ILE* 4.7 12.4 - - + +
456A ILE* 3.7 26.5 - - + -
459A MET* 3.1 55.7 + - + +
460A ASN 3.1 1.2 - - - -
461A GLN* 1.3 78.3 - - - +
463A SER* 1.3 57.0 + - - +
465A ALA* 3.8 4.3 - - - +
466A TRP* 2.9 31.2 + - - +
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Residues in contact with SER 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A MET 4.4 0.4 + - - -
460A ASN* 2.8 19.7 + - - -
462A LEU* 1.3 78.2 - - - +
464A ILE* 1.3 75.6 + - - +
466A TRP* 3.1 4.9 + - - +
467A ALA* 2.9 28.7 + - - +
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Residues in contact with ILE 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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425A THR* 3.4 25.4 - - - +
426A GLU* 5.0 4.3 - - - +
460A ASN 3.9 6.5 - - - +
461A GLN* 3.4 34.5 - - - +
463A SER* 1.3 86.9 + - - +
465A ALA* 1.3 57.7 + - - +
467A ALA* 3.9 8.4 - - + +
468A SER* 2.4 39.4 + - - +
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Residues in contact with ALA 465 (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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333A ILE* 3.7 24.7 - - + -
425A THR* 3.7 23.1 - - + -
454A VAL* 4.4 5.0 - - + +
456A ILE* 4.5 2.5 - - + -
461A GLN 2.6 26.0 + - - +
462A LEU* 3.8 1.3 - - - +
464A ILE* 1.3 78.6 - - - +
466A TRP* 1.3 57.5 + - - +
468A SER* 3.2 6.2 - - - -
469A VAL* 2.8 31.3 + - - +
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Residues in contact with TRP 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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247A ILE* 3.1 57.2 - - + -
330A ARG* 3.3 38.6 - - - -
331A PRO* 3.7 27.8 - - + -
333A ILE* 4.5 8.3 - - + -
462A LEU 2.9 18.5 + - - +
463A SER* 3.8 3.1 - - - +
465A ALA* 1.3 74.3 - - - +
467A ALA* 1.3 62.4 + - - +
469A VAL* 2.9 35.1 + - + +
470A LEU* 3.0 36.6 + - + +
503A GLN* 3.8 16.6 - - + +
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Residues in contact with ALA 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 SER 2.9 17.1 + - - +
464A ILE* 4.2 9.9 - - + +
466A TRP* 1.3 73.2 - - - +
468A SER* 1.3 53.6 + - - +
470A LEU* 4.2 6.8 - - - +
471A TRP* 2.6 42.2 + - + +
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Residues in contact with SER 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A THR* 4.3 18.8 + - - -
426A GLU* 4.8 2.4 + - - -
454A VAL* 5.8 2.7 - - - -
464A ILE* 2.4 26.5 + - - +
465A ALA* 3.2 10.2 - - - -
466A TRP 3.2 0.2 - - - -
467A ALA* 1.3 76.6 - - - +
469A VAL* 1.3 57.5 + - - +
471A TRP* 3.0 10.3 + - - +
472A PHE* 2.9 35.5 + - - +
484A PHE* 6.2 2.2 - - - -
485A PHE* 4.7 16.5 - - - -
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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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247A ILE* 4.7 6.5 - - + -
332A LEU* 4.1 29.6 - - + +
333A ILE* 4.7 7.4 - - + -
454A VAL* 5.3 6.1 - - + -
465A ALA 2.8 17.5 + - - +
466A TRP* 2.9 47.7 + - + +
468A SER* 1.3 75.9 - - - +
470A LEU* 1.3 57.9 + - - +
472A PHE* 3.3 11.0 - - + -
473A ASN* 2.8 49.8 + - - +
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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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247A ILE* 5.2 7.2 - - + -
466A TRP* 3.0 61.3 + - + +
467A ALA* 4.2 5.8 - - - +
469A VAL* 1.3 77.5 - - + +
471A TRP* 1.3 57.5 + - - +
472A PHE 3.0 7.0 + - - -
473A ASN* 4.3 4.5 - - - +
474A LEU* 3.0 28.8 + - + +
475A LEU* 4.2 1.7 + - - +
496A LEU* 4.0 35.0 - - + +
499A ALA* 4.1 26.0 - - + -
500A LEU* 5.1 6.7 - - + +
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Residues in contact with TRP 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ALA* 2.6 28.3 + - + +
468A SER* 3.0 12.3 + - - +
470A LEU* 1.3 73.7 - - - +
472A PHE* 1.3 57.2 + - + +
475A LEU* 3.3 27.8 - - + +
485A PHE* 4.8 19.4 - + - -
488A PRO* 3.8 31.3 - - + +
489A PRO 4.7 4.9 + - - -
490A LYS* 3.6 51.6 - - + -
491A ALA* 4.1 22.9 - - + -
493A TRP* 5.8 1.1 - - - -
496A LEU* 5.7 2.9 - - + -
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Residues in contact with PHE 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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332A LEU* 3.8 13.7 - - + -
451A LEU* 5.5 0.9 - - + -
452A PRO* 3.5 39.0 - - + -
454A VAL* 6.2 3.6 - - + -
468A SER* 2.9 25.8 + - - +
469A VAL* 3.3 23.1 - - + -
471A TRP* 1.3 77.7 - - + +
473A ASN* 1.3 91.8 + - - +
474A LEU 3.1 2.9 - - - -
475A LEU 2.7 24.1 + - - +
476A SER* 2.9 34.0 + - - +
479A LEU* 4.5 10.2 - - + +
484A PHE* 5.9 15.7 - + + -
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Residues in contact with ASN 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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243A GLN 5.2 5.4 - - - +
244A LYS* 4.1 26.0 - - - +
247A ILE* 5.3 9.7 - - + +
332A LEU* 3.6 9.4 - - - +
451A LEU* 5.1 6.9 - - - +
469A VAL* 2.8 43.3 + - + +
470A LEU* 3.0 3.1 + - - +
472A PHE* 1.3 105.8 - - - +
474A LEU* 1.3 57.5 + - - +
476A SER 6.0 0.2 - - - -
479A LEU* 4.4 11.5 - - - +
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Residues in contact with LEU 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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244A LYS* 5.4 9.4 - - - +
470A LEU* 3.0 13.3 + - + +
472A PHE 3.6 0.4 - - - -
473A ASN* 1.3 77.4 - - - +
475A LEU* 1.3 71.7 + - + +
476A SER 3.6 3.0 + - - -
477A PRO* 5.8 0.5 - - - +
492A PRO* 4.6 9.9 - - + +
494A SER* 6.0 1.3 - - - +
495A LEU* 3.7 39.7 - - + +
496A LEU* 3.7 35.2 - - + +
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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