Contacts of the helix formed by residues 477 - 492 (chain A) in PDB entry 4CCZ
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 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473A SER 4.8 0.3 - - - +
474A LEU* 3.0 16.9 + - - +
475A LYS 3.4 2.0 + - - -
476A GLU* 1.3 81.9 + - - +
478A GLU* 1.3 65.2 + - - -
479A ASP 3.5 1.6 - - - -
480A ASP 3.7 0.3 + - - -
481A PHE* 3.3 21.3 + - - +
502A GLU* 3.6 22.6 + - - +
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Residues in contact with GLU 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* 3.9 10.0 - - - +
477A GLY* 1.3 68.7 - - - -
479A ASP* 1.3 69.4 + - - +
481A PHE* 3.1 4.5 + - - +
482A LEU* 2.9 46.3 + - + +
502A GLU* 4.2 4.2 + - - -
518A ARG* 3.8 22.3 + - - +
522A LEU* 3.6 36.3 - - + +
526A LYS* 5.9 1.9 - - - +
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Residues in contact with ASP 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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477A GLY 3.5 0.4 - - - -
478A GLU* 1.3 85.1 - - - +
480A ASP* 1.3 56.9 + - - +
482A LEU* 3.4 13.0 + - - +
483A GLU* 2.9 29.0 + - - +
486A ARG* 5.5 0.5 + - - -
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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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476A GLU* 3.4 42.3 + - + +
477A GLY 3.7 2.1 + - - +
478A GLU 3.2 0.4 - - - -
479A ASP* 1.3 75.2 - - - +
481A PHE* 1.3 65.7 + - - +
483A GLU* 3.3 6.1 + - - +
484A LYS* 2.8 69.5 + - - +
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Residues in contact with PHE 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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472A ILE* 3.4 29.3 - - + +
473A SER* 3.3 33.3 + - - +
474A LEU* 3.4 28.9 - - + -
477A GLY 3.3 5.5 + - - +
478A GLU 3.1 7.6 + - - +
480A ASP* 1.3 80.0 - - - +
482A LEU* 1.3 63.4 + - + +
484A LYS* 3.4 6.2 + - - +
485A ALA* 2.9 30.7 + - - +
497A VAL* 4.1 16.6 - - + -
519A ALA* 4.0 23.6 - - + -
522A LEU* 4.2 20.2 - - + -
523A LEU* 3.8 33.9 - - + -
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Residues in contact with LEU 482 (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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478A GLU* 2.9 44.8 + - + +
479A ASP* 3.7 11.0 - - - +
481A PHE* 1.3 81.7 - - + +
483A GLU* 1.3 55.3 + - - +
485A ALA* 3.7 2.9 - - - +
486A ARG* 2.7 55.9 + - - +
522A LEU* 3.9 30.7 - - + +
526A LYS* 4.7 11.2 - - + -
527A LEU* 3.6 30.5 - - + +
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Residues in contact with GLU 483 (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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479A ASP 2.9 16.9 + - - +
480A ASP* 3.3 7.6 + - - +
482A LEU* 1.3 75.5 - - - +
484A LYS* 1.3 59.2 - - + +
486A ARG* 3.3 18.5 + - - +
487A LYS* 3.0 49.0 + - + +
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Residues in contact with LYS 484 (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 PHE* 3.6 55.8 - - + +
472A ILE* 4.0 18.2 - - + -
473A SER 5.8 2.4 + - - +
476A GLU* 4.0 12.9 + - - +
480A ASP* 2.8 41.2 + - - +
481A PHE* 3.8 5.2 - - - +
483A GLU* 1.3 75.8 - - + +
485A ALA* 1.3 58.6 + - - +
487A LYS* 3.3 2.3 + - + -
488A ILE* 3.0 34.6 + - - +
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Residues in contact with ALA 485 (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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472A ILE* 3.8 15.4 - - + +
481A PHE* 2.9 20.0 + - + +
482A LEU* 3.9 0.7 - - - +
484A LYS* 1.3 75.3 - - - +
486A ARG* 1.3 57.8 + - - +
489A LYS* 3.1 28.8 + - - +
495A MET* 4.2 9.2 - - + -
523A LEU* 3.5 32.1 - - + -
527A LEU* 3.8 12.1 - - + +
529A PHE* 3.8 6.3 - - + -
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Residues in contact with ARG 486 (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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479A ASP 5.5 0.6 + - - -
482A LEU* 2.7 34.4 + - - +
483A GLU* 3.5 26.5 - - + +
484A LYS 3.2 0.2 - - - -
485A ALA* 1.3 77.4 - - - +
487A LYS* 1.3 61.9 + - + +
489A LYS* 3.7 6.4 + - - +
490A LYS* 3.3 21.9 + - + +
526A LYS* 5.8 1.6 - - - +
527A LEU* 3.7 33.8 - - + +
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Residues in contact with LYS 487 (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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207A PHE* 6.6 0.2 - - - -
453A PHE* 3.7 23.7 - - + -
457A GLU* 3.7 28.4 + - - +
483A GLU* 3.0 32.1 + - + +
484A LYS* 3.3 7.4 + - - +
486A ARG* 1.3 76.1 - - + +
488A ILE* 1.3 64.7 + - - +
490A LYS* 3.1 12.1 + - + +
491A TYR* 3.1 35.4 + - + -
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Residues in contact with ILE 488 (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 PHE* 3.9 20.9 - - + -
460A LEU* 4.8 4.9 - - + -
469A VAL* 3.6 32.8 - - + -
472A ILE* 3.9 9.4 - - + -
484A LYS 3.0 21.2 + - - +
485A ALA 4.0 3.6 - - - +
487A LYS* 1.3 75.1 - - - +
489A LYS* 1.3 51.3 + - - +
491A TYR* 3.1 10.0 + - - +
492A GLY 2.7 31.5 + - - -
493A ALA* 3.4 35.5 + - + +
494A ALA 4.2 3.6 - - - +
495A MET* 3.5 30.7 - - + -
529A PHE* 4.6 1.6 - - + -
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Residues in contact with LYS 489 (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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250A HIS* 4.8 5.7 - - - +
485A ALA 3.1 16.4 + - - +
486A ARG* 3.8 8.1 - - + +
488A ILE* 1.3 79.8 - - - +
490A LYS* 1.3 61.4 + - - +
492A GLY* 3.2 14.4 + - - +
493A ALA 5.1 0.9 - - - +
527A LEU* 5.4 7.6 - - + +
528A GLY 5.7 1.1 - - - +
529A PHE* 3.8 31.6 - - + -
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Residues in contact with LYS 490 (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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207A PHE* 3.5 40.5 + - + -
210A GLN* 3.1 38.0 + - + +
211A ASN* 3.1 34.7 + - - +
214A GLU* 5.6 3.3 - - + +
250A HIS* 3.7 14.7 + - - -
486A ARG* 3.3 12.7 + - + +
487A LYS* 3.1 16.1 + - + +
488A ILE 3.1 0.8 - - - -
489A LYS* 1.3 78.1 - - - +
491A TYR* 1.3 63.5 + - - +
492A GLY 3.4 0.2 + - - -
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Residues in contact with TYR 491 (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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169A PHE* 4.0 22.8 - + - -
203A LYS* 4.4 12.0 + - - -
207A PHE* 3.4 34.9 - + - -
250A HIS* 3.6 16.9 + - - -
453A PHE* 5.7 1.6 - + - -
457A GLU* 3.1 46.2 + - + +
460A LEU* 3.5 46.0 - - + -
461A LYS* 3.4 23.4 - - + -
487A LYS* 3.1 33.8 + - + -
488A ILE* 3.6 4.7 - - - +
490A LYS* 1.3 76.5 - - - +
492A GLY* 1.3 60.8 + - - +
493A ALA* 4.7 0.4 - - - +
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Residues in contact with GLY 492 (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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250A HIS* 3.8 25.3 + - - +
466A LYS* 3.3 29.0 - - - +
488A ILE 2.7 12.3 + - - -
489A LYS* 3.2 14.8 + - - -
490A LYS 3.2 2.2 - - - -
491A TYR* 1.3 76.2 - - - +
493A ALA* 1.3 57.8 + - - -
533A ASP* 6.1 0.2 - - - -
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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