Contacts of the helix formed by residues 444 - 458 (chain A) in PDB entry 4R8A
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 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A ASP* 1.3 76.0 + - - +
445A SER* 1.3 64.0 + - - +
446A TYR* 3.1 8.9 + - - -
447A ARG* 3.5 20.6 + - - +
448A ASP* 4.4 2.3 + - - +
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Residues in contact with SER 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG* 3.2 51.5 + - - +
443A ASP* 3.1 20.1 + - - -
444A GLY* 1.3 74.9 - - - +
446A TYR* 1.3 50.2 + - - +
447A ARG 3.3 0.4 - - - -
448A ASP* 3.2 8.7 + - - +
449A ALA* 2.7 35.8 + - - +
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Residues in contact with TYR 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LEU* 4.4 11.0 - - + -
440A ARG* 3.0 21.5 + - - +
441A LEU* 3.5 30.1 - - + +
443A ASP 3.8 15.7 - - - -
444A GLY* 3.1 5.0 + - - -
445A SER* 1.3 75.5 - - - +
447A ARG* 1.3 117.8 + - + +
449A ALA* 3.7 7.1 - - - +
450A ILE* 3.1 33.5 + - + +
479A LEU* 3.9 16.6 + - + -
482A LEU 4.0 9.9 + - - -
484A ALA* 3.8 23.4 + - + +
487A LEU* 3.7 22.4 - - + -
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Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLY* 3.5 11.2 + - - +
445A SER 3.3 0.8 + - - -
446A TYR* 1.3 134.5 + - + +
448A ASP* 1.3 60.9 + - + +
451A ARG* 3.4 39.9 + - - +
479A LEU* 3.5 40.5 + - + +
480A ASP* 3.7 14.1 + - - +
482A LEU 5.5 0.6 + - - -
484A ALA* 5.6 1.0 - - - +
516A ARG* 3.5 26.7 - - - +
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Residues in contact with ASP 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLY 4.4 1.7 + - - +
445A SER* 3.2 9.9 + - - +
447A ARG* 1.3 77.6 - - - +
449A ALA* 1.3 63.1 + - - +
450A ILE 3.3 0.4 - - - -
451A ARG* 3.3 20.5 + - - +
452A CYS* 3.2 37.0 + - - -
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LEU* 4.5 7.9 - - + -
440A ARG* 3.4 33.6 - - - +
445A SER 2.7 22.5 + - - +
446A TYR* 3.3 7.8 + - - +
448A ASP* 1.3 73.2 - - - +
450A ILE* 1.3 61.1 + - - +
452A CYS* 3.4 5.4 + - - +
453A ARG* 3.2 39.5 + - - +
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Residues in contact with ILE 450 (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 LEU* 3.9 15.0 - - + +
396A LEU* 3.6 26.2 - - + -
397A LEU* 3.4 48.2 - - + +
446A TYR* 3.1 21.6 + - + +
447A ARG 4.0 4.7 - - - +
449A ALA* 1.3 74.8 - - - +
451A ARG* 1.3 65.4 + - - +
452A CYS 3.1 0.2 + - - -
453A ARG* 3.1 5.5 + - - +
454A TYR* 2.9 22.3 + - - +
475A LEU* 3.8 22.9 - - + -
479A LEU* 4.4 13.7 - - + -
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Residues in contact with ARG 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ARG* 3.4 37.9 + - - +
448A ASP* 3.3 25.9 + - - +
450A ILE* 1.3 79.6 - - - +
452A CYS* 1.3 62.3 + - - +
454A TYR* 3.8 6.2 - - - +
455A ARG* 3.5 41.7 + - - +
475A LEU* 4.9 4.7 - - + -
476A GLU* 3.4 43.3 + - - +
479A LEU* 3.9 19.2 - - + +
480A ASP* 4.2 14.8 + - - -
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Residues in contact with CYS 452 (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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448A ASP* 3.2 30.3 + - - -
449A ALA* 3.7 8.7 - - - +
450A ILE 3.1 0.8 - - - -
451A ARG* 1.3 78.5 - - - +
453A ARG* 1.3 68.4 + - - +
454A TYR 3.2 0.2 - - - -
455A ARG* 3.3 4.9 + - - +
456A ASP* 2.9 43.3 + - - +
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Residues in contact with ARG 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LEU* 3.2 43.6 + - + +
397A LEU* 5.3 0.8 + - - -
399A TRP* 4.0 15.1 - - + +
400A GLU* 2.6 42.4 + - - +
440A ARG* 5.5 6.7 - - - +
449A ALA* 3.2 28.9 + - + +
450A ILE 3.1 6.0 + - - +
452A CYS* 1.3 85.9 - - - +
454A TYR* 1.3 58.0 + - - +
456A ASP* 4.5 8.0 + - - -
457A LYS* 2.6 50.0 + - + +
467A TRP* 4.3 0.3 - - - -
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Residues in contact with TYR 454 (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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396A LEU* 4.1 6.0 - - + +
450A ILE 2.9 16.4 + - - +
451A ARG 3.8 6.1 - - - +
453A ARG* 1.3 78.5 - - - +
455A ARG* 1.3 74.3 + - + +
458A PHE* 3.2 58.0 + + - +
467A TRP* 3.9 21.0 + + - -
470A LEU* 2.8 47.1 + - + -
471A GLY* 3.8 1.4 - - - -
472A GLU* 3.7 31.7 + - + +
475A LEU* 3.7 27.4 - - + -
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Residues in contact with ARG 455 (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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451A ARG* 3.5 35.2 + - - +
452A CYS* 3.3 6.1 + - - +
453A ARG 3.2 0.2 - - - -
454A TYR* 1.3 97.1 - - + +
456A ASP* 1.3 70.5 + - - +
458A PHE* 4.2 7.6 + - - +
472A GLU* 3.3 23.7 + - - +
475A LEU* 5.3 1.0 - - - +
476A GLU* 4.5 13.7 + - - -
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Residues in contact with ASP 456 (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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199A ARG* 5.4 5.0 + - - -
452A CYS* 2.9 31.1 + - - +
453A ARG* 3.9 6.7 + - - +
455A ARG* 1.3 84.1 - - - +
457A LYS* 1.3 74.8 + - + +
458A PHE 3.3 3.1 + - - +
460A LEU* 5.2 1.2 - - - +
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Residues in contact with LYS 457 (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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201A GLU* 2.5 39.1 + - - +
399A TRP* 3.3 45.8 - - + +
453A ARG* 2.6 33.9 + - + +
456A ASP* 1.3 83.1 - - + +
458A PHE* 1.3 64.5 + - - +
460A LEU* 3.1 26.3 + - + +
467A TRP* 3.0 18.0 - - + -
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Residues in contact with PHE 458 (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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199A ARG* 3.0 21.3 + - - -
454A TYR* 3.2 54.1 + + - +
455A ARG* 4.2 7.9 - - - +
456A ASP 3.3 4.2 - - - +
457A LYS* 1.3 77.7 - - - +
459A GLY* 1.3 65.6 + - - +
460A LEU 3.4 0.2 + - - -
467A TRP* 3.4 47.1 - + + -
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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
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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