Contacts of the helix formed by residues 472 - 480 (chain A) in PDB entry 4KZI
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 ARG 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A PHE* 5.4 5.1 - - - -
460A GLY* 2.7 23.4 + - - +
462A LEU* 3.9 10.7 - - - +
471A HIS* 1.3 83.3 + - + +
473A LEU* 1.3 90.4 + - - +
475A CYS* 2.9 20.4 + - - +
476A ALA* 3.1 13.1 + - + +
483A ILE* 4.2 5.8 - - + +
484A ASP* 3.2 32.3 + - - +
487A LEU* 3.9 23.6 - - + -
491A ARG* 6.2 1.1 - - - +
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Residues in contact with LEU 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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389A GLU 4.8 1.1 - - - +
390A LEU* 4.2 17.5 - - + -
391A VAL* 3.7 37.8 - - + +
393A PRO* 3.8 13.8 - - + +
395A PHE* 4.1 26.5 - - + -
471A HIS* 3.1 26.7 - - + +
472A ARG* 1.3 105.3 - - - +
474A GLN* 1.3 59.7 + - - +
475A CYS 3.5 0.2 + - - -
476A ALA* 3.7 15.9 + - + +
477A ARG* 4.8 1.9 + - - +
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Residues in contact with GLN 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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386A LYS* 2.9 25.6 + - - +
387A PHE* 3.6 1.0 - - - -
388A GLN* 3.0 42.7 + - - +
391A VAL* 4.1 21.2 - - + +
402A ASP* 5.5 2.6 - - - +
405A GLN* 4.4 12.5 - - - +
470A LEU* 3.6 20.7 - - + +
471A HIS* 2.8 33.5 + - + +
473A LEU* 1.3 76.2 - - - +
475A CYS* 1.3 60.1 + - - +
477A ARG* 4.7 5.5 + - - +
478A GLY 5.3 1.6 + - - -
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Residues in contact with CYS 475 (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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405A GLN* 5.7 0.9 - - - -
462A LEU* 4.1 19.5 - - - -
464A PHE* 4.2 13.5 - - - -
470A LEU* 3.9 26.0 - - - -
471A HIS 3.6 12.3 - - - -
472A ARG 2.9 9.6 + - - +
474A GLN* 1.3 77.0 - - - +
476A ALA* 1.3 64.6 + - - +
477A ARG 3.2 3.3 + - - -
478A GLY 3.4 2.5 + - - +
479A PHE* 3.0 38.3 + - + +
483A ILE* 3.9 19.5 - - + -
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Residues in contact with ALA 476 (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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393A PRO* 5.1 2.2 - - + -
395A PHE* 4.2 27.1 - - + -
472A ARG* 3.1 9.8 + - + +
473A LEU* 3.7 17.3 - - + +
474A GLN 3.4 1.4 - - - -
475A CYS* 1.3 78.3 - - - +
477A ARG* 1.3 60.2 + - + +
480A GLY* 3.0 36.1 + - - +
483A ILE* 4.7 3.4 - - + -
484A ASP* 6.1 2.0 - - - +
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Residues in contact with ARG 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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393A PRO* 3.9 25.4 - - + -
394A HIS* 2.9 30.3 + - - +
395A PHE* 5.7 1.6 - - + -
397A LYS* 2.8 61.2 - - - +
398A GLU* 3.4 17.5 - - - +
399A ASP* 3.3 37.0 + - - +
402A ASP* 2.7 31.5 + - - +
473A LEU 4.8 1.7 + - - +
474A GLN 4.7 4.2 + - - +
475A CYS 3.3 0.4 - - - -
476A ALA* 1.3 81.1 - - + +
478A GLY* 1.3 57.0 + - - +
572A ARG* 2.8 22.5 + - - -
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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
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398A GLU* 5.1 1.1 - - - -
402A ASP* 3.8 28.5 - - - +
403A VAL* 5.1 2.0 - - - -
406A PHE* 3.8 12.6 - - - -
474A GLN 5.3 1.0 + - - -
475A CYS 3.4 4.6 + - - -
477A ARG* 1.3 78.9 - - - +
479A PHE* 1.3 53.7 + - - +
572A ARG* 2.7 29.3 + - - -
576A LEU* 3.8 12.0 - - - +
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Residues in contact with PHE 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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405A GLN* 5.9 1.3 - - - -
406A PHE* 3.7 37.7 - + - -
409A LEU* 4.1 27.8 - - + -
410A LEU* 5.1 0.9 - - + -
447A PHE* 4.2 16.4 - + - -
464A PHE* 4.2 21.1 - + - -
475A CYS* 3.0 33.2 + - + +
478A GLY* 1.3 78.8 - - - +
480A GLY* 1.3 63.3 + - - +
482A TRP* 3.4 35.4 - + - +
483A ILE* 3.9 35.4 - - + +
486A ILE* 5.3 0.2 - - + -
572A ARG* 3.4 17.4 - - - +
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Residues in contact with GLY 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 ALA* 3.0 25.0 + - - +
478A GLY 3.5 2.0 - - - -
479A PHE* 1.3 75.7 - - - +
481A ASP* 1.3 66.7 + - - -
482A TRP 2.9 5.2 + - - -
483A ILE* 3.3 18.0 + - - +
484A ASP* 4.9 1.1 - - - +
572A ARG* 3.6 17.3 - - - +
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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