Contacts of the helix formed by residues 464 - 478 (chain A) in PDB entry 4A8W
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 ALA 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A THR* 3.3 33.4 - - - +
419A ALA* 4.0 8.1 - - + -
421A HIS* 3.8 0.6 - - + -
445A GLU* 2.9 24.1 + - + +
446A ILE* 3.8 17.7 - - + -
459A TRP* 3.4 5.9 - - + -
463A ARG* 1.3 76.8 - - - +
465A LEU* 1.4 59.4 + - - +
466A VAL 3.4 0.4 - - - -
467A GLY 3.1 3.3 + - - -
468A GLY 2.9 23.9 + - - -
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Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A SER* 3.8 30.5 - - - -
319A LEU* 4.0 7.6 - - + -
445A GLU* 4.3 0.8 + - - -
459A TRP* 3.7 26.4 - - + -
460A THR 3.6 11.6 + - - +
461A LYS* 4.0 24.9 - - + +
462A GLY 3.4 15.5 + - - +
463A ARG 3.4 1.6 - - - -
464A ALA* 1.4 76.4 - - - +
466A VAL* 1.3 63.4 + - - +
468A GLY* 3.1 11.1 + - - -
469A HIS* 3.2 41.6 + - + +
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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
----------------------------------------------------------
462A GLY 4.6 1.4 + - - +
463A ARG* 3.7 17.3 - - - +
465A LEU* 1.3 76.6 - - - +
467A GLY* 1.3 64.3 + - - +
469A HIS* 3.3 11.9 + - + +
470A ARG* 3.3 39.6 + - + +
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Residues in contact with GLY 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A HIS 3.7 8.0 - - - +
418A THR* 3.4 18.2 - - - +
463A ARG 4.7 0.2 + - - -
464A ALA 3.1 7.8 + - - -
466A VAL* 1.3 80.2 - - - +
468A GLY* 1.3 59.7 + - - +
470A ARG* 3.1 29.1 + - - +
471A LEU* 2.9 26.0 + - - +
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Residues in contact with GLY 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 3.4 15.4 - - - +
321A VAL* 4.7 2.4 - - - +
418A THR* 3.4 3.9 - - - +
459A TRP* 3.6 33.8 - - - -
464A ALA 2.9 10.3 + - - -
465A LEU 3.1 6.0 + - - -
467A GLY* 1.3 76.7 - - - +
469A HIS* 1.4 54.0 + - - +
471A LEU* 3.4 3.3 + - - +
472A PHE* 3.1 22.9 + - - +
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Residues in contact with HIS 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A SER 5.1 4.3 + - - -
319A LEU* 3.8 27.8 - - + +
465A LEU* 3.2 48.4 + - + +
466A VAL* 3.6 10.3 - - + +
467A GLY 3.2 0.4 - - - -
468A GLY* 1.4 70.9 - - - +
470A ARG* 1.4 59.2 + - + +
472A PHE* 3.5 7.7 + - - +
473A GLU* 3.0 27.5 + - - +
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Residues in contact with ARG 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A HIS 3.7 20.5 + - - +
418A THR* 5.3 1.0 - - - +
466A VAL* 3.3 33.2 + - + +
467A GLY* 3.1 19.8 + - - +
469A HIS* 1.4 71.3 - - - +
471A LEU* 1.3 60.6 + - - +
473A GLU* 3.2 8.3 + - - +
474A MET* 2.8 29.8 + - - +
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Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL* 5.8 1.3 - - + -
413A MET* 4.2 27.4 - - + +
414A GLN* 4.9 1.3 - - + +
417A HIS* 4.1 12.0 + - + +
418A THR* 4.1 10.5 - - + -
457A LEU* 5.2 3.1 - - + -
459A TRP* 3.9 29.8 - - + -
467A GLY 2.9 13.1 + - - +
468A GLY 3.6 7.6 - - - +
470A ARG* 1.3 73.8 - - - +
472A PHE* 1.3 58.4 + - - +
474A MET* 3.1 34.8 + - + +
475A LEU* 2.9 40.8 + - + +
482A PRO* 3.8 17.0 - - + -
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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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72A TYR* 3.5 50.9 - + + -
74A ARG* 4.0 31.0 - - + -
319A LEU* 3.7 25.1 - - + -
320A CYS 4.5 10.5 - - - -
321A VAL* 3.8 28.3 - - + -
322A ALA 5.6 2.0 - - - -
468A GLY 3.1 14.3 + - - +
469A HIS* 3.7 13.7 - - - +
471A LEU* 1.3 75.1 - - - +
473A GLU* 1.3 56.3 + - - +
475A LEU* 3.2 11.8 + - + +
476A LYS* 2.9 26.9 + - + +
490A TYR* 4.8 10.8 - + + -
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Residues in contact with GLU 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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72A TYR* 2.6 30.5 + - - -
469A HIS 3.0 15.3 + - - +
470A ARG* 3.2 12.3 + - - +
472A PHE* 1.3 76.6 - - - +
474A MET* 1.4 55.9 + - - +
476A LYS* 3.2 26.0 + - - +
477A GLU* 2.9 53.0 + - - +
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Residues in contact with MET 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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417A HIS* 3.5 34.1 - - + +
470A ARG 2.8 15.7 + - - +
471A LEU* 3.4 36.8 - - + +
473A GLU* 1.4 73.1 - - - +
475A LEU* 1.3 61.6 + - + +
477A GLU* 3.4 11.6 + - - +
478A GLY* 3.1 19.6 + - - -
479A LYS 4.5 2.1 + - - -
480A VAL* 3.9 37.9 - - + +
482A PRO* 3.7 12.3 - - + -
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Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL* 3.6 31.2 - - + -
323A THR* 4.7 9.9 - - + -
413A MET* 5.5 1.6 - - - -
457A LEU* 6.3 0.2 - - + -
471A LEU* 2.9 31.1 + - + +
472A PHE* 3.2 9.2 + - + +
474A MET* 1.3 74.5 - - - +
476A LYS* 1.4 63.1 + - - +
478A GLY* 3.1 16.0 + - - -
480A VAL 5.8 0.9 - - - +
482A PRO* 3.7 32.1 - - + -
488A ILE* 4.1 3.1 - - + +
489A SER* 3.8 29.0 - - - +
490A TYR* 3.4 31.6 + - + -
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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
----------------------------------------------------------
71A GLU* 3.6 33.3 + - + +
72A TYR* 3.4 43.7 - - + -
472A PHE* 2.9 14.0 + - + +
473A GLU* 3.5 27.1 - - - +
475A LEU* 1.4 75.6 - - - +
477A GLU* 1.3 63.8 + - - +
478A GLY* 3.3 1.0 + - - -
490A TYR* 3.8 21.7 + - + +
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Residues in contact with GLU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A GLU* 2.9 44.7 + - - +
474A MET* 3.7 9.1 - - - +
475A LEU 3.3 0.2 - - - -
476A LYS* 1.3 78.4 - - + +
478A GLY* 1.3 63.5 + - - +
479A LYS* 3.3 27.0 + - + +
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Residues in contact with GLY 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A MET 3.1 11.5 + - - -
475A LEU* 3.1 14.3 + - - -
476A LYS 4.3 1.1 - - - -
477A GLU* 1.3 76.7 - - - +
479A LYS* 1.3 59.8 + - - +
480A VAL 3.7 4.5 - - - -
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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