Contacts of the helix formed by residues 463 - 481 (chain A) in PDB entry 4Z4H
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 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A GLN* 3.7 15.5 - - - +
460A ARG* 4.1 11.0 - - - +
462A CYS* 1.3 72.2 - - - +
464A GLU* 1.3 60.8 + - - +
465A VAL* 3.6 11.4 + - - +
466A HIS* 2.6 46.7 + - + +
467A LEU* 3.0 25.8 + - - +
494A TYR* 3.0 9.3 + - - -
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Residues in contact with GLU 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A GLN* 3.0 26.4 + - - +
463A THR* 1.3 75.3 - - - +
465A VAL* 1.3 58.2 + - + +
467A LEU* 3.5 8.6 + - + +
468A LYS* 3.0 27.5 + - - +
494A TYR* 3.1 22.4 - - + +
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Residues in contact with VAL 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A THR* 3.1 10.7 - - - +
464A GLU* 1.3 77.0 - - + +
466A HIS* 1.3 65.7 + - + +
468A LYS* 3.3 6.0 + - - +
469A SER* 2.9 32.3 + - - -
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Residues in contact with HIS 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ARG 5.8 0.2 - - - -
461A GLN 3.8 16.0 + - - -
462A CYS* 4.0 4.4 - - - -
463A THR* 2.6 49.5 + - + +
465A VAL* 1.3 80.3 - - + +
467A LEU* 1.3 57.2 + - - +
469A SER* 3.4 5.7 + - - -
470A PHE* 2.9 30.7 + - - +
552A VAL* 3.9 17.9 - - + +
553A GLN* 4.1 35.1 + - + +
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Residues in contact with LEU 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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453A ILE* 4.5 13.5 - - + -
455A CYS* 4.3 9.2 - - + -
462A CYS* 4.4 9.4 - - - -
463A THR 3.0 12.9 + - - +
464A GLU* 3.7 9.0 - - - +
465A VAL 3.3 0.2 - - - -
466A HIS* 1.3 74.2 - - - +
468A LYS* 1.3 61.5 + - - +
470A PHE* 3.4 7.3 + - + +
471A THR* 2.9 34.5 + - - -
492A CYS* 4.1 26.2 - - - -
494A TYR* 3.7 33.2 - - + +
521A ILE* 3.9 28.3 - - + -
552A VAL* 4.2 13.5 - - + -
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Residues in contact with LYS 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A GLU 3.0 18.8 + - - +
465A VAL* 3.7 7.2 - - - +
467A LEU* 1.3 76.3 - - - +
469A SER* 1.3 58.1 + - - +
471A THR* 3.3 6.6 + - - -
472A GLU* 3.0 64.4 + - - +
488A GLN* 4.1 30.2 - - - +
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Residues in contact with SER 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A VAL* 2.9 20.9 + - - -
466A HIS* 3.8 6.1 - - - -
468A LYS* 1.3 74.0 - - - +
470A PHE* 1.3 65.3 + - - +
472A GLU* 3.3 16.2 + - - +
473A GLN* 3.1 38.0 + - - +
552A VAL 6.0 0.2 - - - -
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Residues in contact with PHE 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A TRP* 6.0 0.9 - + - -
453A ILE* 5.2 8.1 - - + -
466A HIS 2.9 19.2 + - - +
467A LEU* 3.7 8.3 - - + +
469A SER* 1.3 76.0 - - - +
471A THR* 1.3 63.8 + - - +
473A GLN* 3.5 8.4 + - - +
474A LEU* 3.0 49.6 + - + +
519A VAL* 4.5 16.8 - - + -
521A ILE* 4.7 3.4 - - + -
547A VAL* 4.5 10.5 - - + -
551A ASN 4.2 6.3 - - - -
552A VAL* 3.7 41.0 + - + +
555A THR* 3.6 19.5 - - + -
560A LEU* 3.8 19.3 - - + -
563A LEU* 4.1 21.5 - - + -
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Residues in contact with THR 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A TRP* 3.9 23.8 - - + -
453A ILE* 3.6 22.7 - - - +
467A LEU 2.9 22.2 + - - -
468A LYS* 3.5 8.5 - - + +
469A SER 3.2 0.2 - - - -
470A PHE* 1.3 79.5 - - - +
472A GLU* 1.3 64.6 + - - +
474A LEU* 4.1 3.7 - - - +
475A ARG* 3.1 30.2 + - - +
488A GLN* 3.9 31.2 - - - +
489A PRO* 4.3 3.3 - - + +
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Residues in contact with GLU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LYS* 3.0 46.0 + - - +
469A SER* 3.3 18.5 + - - +
471A THR* 1.3 78.7 - - - +
473A GLN* 1.3 65.2 + - + +
475A ARG* 3.4 6.7 + - - +
476A LYS* 3.1 22.4 + - - +
488A GLN* 6.0 1.6 - - - +
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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
----------------------------------------------------------
469A SER* 3.1 27.4 + - - +
470A PHE* 4.0 2.0 - - - +
472A GLU* 1.3 79.1 - - + +
474A LEU* 1.3 61.3 + - - +
476A LYS* 3.2 10.7 + - + +
477A ILE* 2.9 33.4 + - + +
555A THR* 2.3 40.3 + - - +
560A LEU* 3.7 16.8 - - + -
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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
----------------------------------------------------------
451A TRP* 4.9 15.5 - - + -
470A PHE* 3.0 40.0 + - + +
471A THR* 4.1 3.6 - - - +
473A GLN* 1.3 76.6 - - - +
475A ARG* 1.3 53.7 + - + +
477A ILE* 3.3 1.9 + - - -
478A SER* 2.8 36.4 + - - -
485A ILE* 3.9 20.9 - - + -
519A VAL* 5.2 6.3 - - + -
560A LEU* 4.2 26.1 - - + +
563A LEU* 4.4 12.6 - - + -
564A CYS* 3.8 24.2 - - - -
567A ILE* 4.8 14.6 - - + -
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Residues in contact with ARG 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A TRP* 4.8 0.7 - - + -
471A THR* 3.1 30.2 + - + +
472A GLU* 3.7 5.6 - - - +
474A LEU* 1.3 73.4 - - + +
476A LYS* 1.3 65.2 + - - +
478A SER* 3.0 21.1 + - - -
479A ARG* 3.1 25.1 + - - +
485A ILE* 3.0 37.3 + - + +
486A GLN* 3.1 27.1 + - - +
487A GLY* 3.4 22.8 + - - -
488A GLN* 3.8 23.2 - - - +
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Residues in contact with LYS 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A GLU 3.1 13.8 + - - +
473A GLN* 3.2 14.8 + - + +
475A ARG* 1.3 76.4 - - - +
477A ILE* 1.3 70.3 + - + +
479A ARG* 3.2 21.1 + - - +
480A ASP* 3.2 32.6 + - - +
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Residues in contact with ILE 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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473A GLN* 2.9 19.7 + - + +
474A LEU* 3.8 3.4 - - - +
476A LYS* 1.3 84.8 - - + +
478A SER* 1.3 58.7 + - - +
480A ASP* 3.4 16.9 + - + +
481A THR* 3.0 34.8 + - - +
557A PRO* 4.6 20.9 - - + +
560A LEU* 4.0 27.8 - - + +
561A SER* 3.8 33.4 - - - +
564A CYS* 4.1 6.1 - - - -
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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 LEU 2.8 16.7 + - - -
475A ARG* 3.0 14.0 + - - -
477A ILE* 1.3 77.3 - - - +
479A ARG* 1.3 58.2 + - - +
481A THR* 4.0 8.3 - - - -
482A GLY 3.3 1.9 + - - -
483A MET* 2.9 55.9 + - - -
485A ILE* 3.1 34.3 + - - +
564A CYS* 4.0 3.3 - - - -
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Residues in contact with ARG 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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441A GLN* 3.4 9.2 + - - -
475A ARG* 3.1 24.1 + - - +
476A LYS* 3.2 13.7 + - - +
478A SER* 1.3 76.4 + - - +
480A ASP* 1.3 70.8 + - - +
482A GLY* 3.2 10.7 + - - -
484A PRO* 4.3 21.2 - - + +
485A ILE 5.5 4.5 - - - +
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Residues in contact with ASP 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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440A LYS 3.3 12.4 + - - +
441A GLN* 2.7 23.1 + - - +
476A LYS* 3.2 29.4 + - - +
477A ILE* 3.8 23.4 - - + +
479A ARG* 1.3 80.6 + - - +
481A THR* 1.3 58.2 + - - +
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Residues in contact with THR 481 (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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437A MET* 3.9 20.0 - - - +
440A LYS 4.2 6.1 - - - -
441A GLN* 3.4 3.8 - - - -
442A PHE* 3.1 53.3 + - + -
477A ILE* 3.0 20.4 + - - +
478A SER* 3.8 10.3 - - - +
479A ARG 3.1 0.2 - - - -
480A ASP* 1.3 80.5 - - - +
482A GLY* 1.3 56.6 + - - +
483A MET* 3.9 4.9 - - + +
561A SER* 4.4 10.4 + - - -
564A CYS* 3.8 18.1 - - + +
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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
------------------------------------------------------------
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