Contacts of the helix formed by residues 478 - 493 (chain A) in PDB entry 4WTJ
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 SER 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A GLU* 2.6 34.8 + - - -
371A SER* 3.4 6.8 + - - -
372A VAL* 3.8 18.0 + - - -
383A TYR* 5.4 0.2 + - - -
476A THR 4.8 0.2 - - - -
477A TYR* 1.3 77.4 - - - +
479A HIS* 1.3 66.4 + - - +
480A HIS 3.5 2.3 + - - -
481A GLU* 3.2 15.4 + - - +
482A LEU* 2.9 23.9 + - - +
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Residues in contact with HIS 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 TYR 4.0 0.8 + - - -
478A SER* 1.3 71.8 - - - +
480A HIS* 1.3 73.3 + + - +
482A LEU* 3.9 7.8 - - - +
483A THR* 2.9 49.1 + - - +
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Residues in contact with HIS 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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361A GLU* 3.5 31.9 + - + +
362A LEU* 3.8 27.6 - - + +
478A SER* 3.2 2.2 + - - -
479A HIS* 1.3 88.5 - + - +
481A GLU* 1.3 60.1 + - - +
483A THR* 3.5 4.0 + - - -
484A ARG* 2.9 34.3 + - - +
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Residues in contact with GLU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A GLU* 4.6 1.8 - - - +
369A ASN* 4.9 0.5 + - - -
371A SER* 4.4 5.0 + - - +
383A TYR* 3.6 18.2 + - - +
385A THR* 2.5 36.9 + - - +
386A ARG 4.5 0.9 - - - +
418A THR* 4.8 1.4 - - - -
419A ILE* 4.4 14.2 - - + +
420A TRP* 3.8 14.9 - - - -
477A TYR* 4.6 3.4 - - + -
478A SER* 3.0 23.8 + - - +
480A HIS* 1.3 78.7 - - - +
482A LEU* 1.3 60.3 + - - +
484A ARG* 2.9 30.5 + - - +
485A VAL* 2.9 39.0 + - - +
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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
----------------------------------------------------------
419A ILE* 3.6 31.2 - - + -
477A TYR* 3.5 29.6 - - + +
478A SER 2.9 17.2 + - - +
479A HIS* 4.0 6.3 - - - +
481A GLU* 1.3 75.0 - - - +
483A THR* 1.3 62.1 + - - +
485A VAL* 4.2 2.6 - - - +
486A ALA* 3.1 27.4 + - - +
497A LEU* 4.7 11.6 - - + +
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Residues in contact with THR 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 HIS* 2.9 44.4 + - - +
480A HIS* 3.8 5.4 - - - -
482A LEU* 1.3 75.3 - - - +
484A ARG* 1.3 67.2 + - - +
486A ALA* 3.9 3.6 - - - +
487A SER* 3.0 30.2 + - - -
490A ARG* 5.0 3.3 + - - +
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Residues in contact with ARG 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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364A THR* 5.1 5.7 + - - +
369A ASN* 2.9 31.1 + - - +
385A THR* 3.6 5.1 - - - +
386A ARG* 3.5 15.2 + - - +
387A ASP* 3.6 48.2 - - - +
388A PRO* 4.3 6.0 - - + +
480A HIS* 2.9 21.2 + - - +
481A GLU* 2.9 29.1 + - - +
483A THR* 1.3 78.1 - - - +
485A VAL* 1.3 60.3 + - + +
487A SER* 3.7 4.4 - - - -
488A ALA* 2.9 27.6 + - - +
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Residues in contact with VAL 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PRO* 4.4 12.8 - - + -
419A ILE* 3.8 22.2 - - + -
420A TRP* 3.9 37.0 - - + -
424A VAL* 5.4 0.2 - - + -
481A GLU* 2.9 27.8 + - - +
482A LEU* 4.2 2.9 - - - +
484A ARG* 1.3 75.9 - - + +
486A ALA* 1.3 67.0 + - - +
488A ALA* 3.2 2.4 + - - +
489A LEU* 3.0 41.8 + - + +
497A LEU* 4.2 18.8 - - + -
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Residues in contact with ALA 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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482A LEU 3.1 18.6 + - - +
483A THR* 3.9 4.9 - - - +
485A VAL* 1.3 78.0 - - - +
487A SER* 1.3 57.5 - - - +
489A LEU* 3.5 9.3 + - - +
490A ARG* 3.0 49.1 + - - +
497A LEU* 5.3 7.6 - - + +
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Residues in contact with SER 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A THR* 3.0 22.9 + - - -
484A ARG* 3.7 5.4 - - - -
486A ALA* 1.3 76.9 - - - +
488A ALA* 1.3 64.1 + - - +
490A ARG* 3.3 24.1 + - - +
491A LYS* 3.0 29.7 + - - +
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Residues in contact with ALA 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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387A ASP* 4.3 1.1 - - - +
388A PRO* 3.8 23.3 - - + -
389A THR* 3.8 21.8 - - - +
392A LEU* 4.6 8.3 - - + -
484A ARG 2.9 18.7 + - - +
485A VAL 3.2 4.0 + - - +
487A SER* 1.3 76.0 + - - +
489A LEU* 1.3 62.6 + - - +
491A LYS* 3.3 14.8 + - - +
492A LEU* 3.1 27.4 + - - +
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Residues in contact with LEU 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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388A PRO* 6.4 0.2 - - + -
392A LEU* 4.0 20.4 - - + -
420A TRP* 6.3 0.7 - - + -
424A VAL* 4.1 23.1 - - + -
485A VAL* 3.0 28.8 + - + +
486A ALA* 3.7 6.7 - - - +
488A ALA* 1.3 77.2 - - + +
490A ARG* 1.3 61.7 + - - +
492A LEU 3.4 1.7 + - - -
493A GLY 3.0 3.5 + - - -
494A ALA* 2.9 50.1 + - + +
495A PRO 3.7 22.2 - - - +
496A PRO* 4.5 3.8 - - + -
497A LEU* 3.8 37.5 - - + +
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Residues in contact with ARG 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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33A TYR* 3.5 12.6 + - - -
483A THR* 5.0 3.6 + - - +
486A ALA* 3.0 36.9 + - - +
487A SER* 3.5 31.8 + - - +
489A LEU* 1.3 75.2 - - + +
491A LYS* 1.3 62.4 + - - +
493A GLY* 3.1 12.3 + - - -
494A ALA 4.9 2.9 - - - -
496A PRO* 6.5 1.6 - - + -
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Residues in contact with LYS 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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33A TYR* 3.3 3.1 - - - -
36A LYS* 2.7 46.2 + - - +
146A CYS* 4.5 13.2 - - - -
147A VAL 5.3 3.6 - - - +
387A ASP* 4.7 4.4 + - - -
389A THR* 2.8 45.7 + - - +
487A SER* 3.0 19.6 + - - +
488A ALA* 3.5 12.5 - - - +
489A LEU 3.3 0.2 - - - -
490A ARG* 1.3 77.5 - - - +
492A LEU* 1.3 58.1 + - - +
493A GLY 3.4 0.2 - - - -
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Residues in contact with LEU 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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31A LEU* 3.4 25.6 - - + +
33A TYR* 3.0 35.4 + - - +
36A LYS* 4.5 2.5 - - + -
37A VAL* 4.1 24.7 - - + -
146A CYS* 3.8 29.8 - - + -
389A THR* 3.8 20.4 - - + +
392A LEU* 3.8 32.8 - - + -
393A ALA* 4.5 2.0 - - - +
488A ALA 3.1 18.4 + - - +
489A LEU 4.4 1.8 - - - +
491A LYS* 1.3 78.0 - - - +
493A GLY* 1.3 62.5 + - - +
494A ALA* 3.3 2.2 - - + +
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Residues in contact with GLY 493 (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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31A LEU* 3.7 0.3 - - - -
32A ARG* 3.0 38.5 + - - +
33A TYR* 3.3 30.1 - - - -
489A LEU 3.0 4.7 + - - -
490A ARG* 3.1 8.5 + - - -
492A LEU* 1.3 78.9 - - - +
494A ALA* 1.3 62.8 + - - +
495A PRO* 4.2 1.2 - - - +
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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