Contacts of the helix formed by residues 499 - 508 (chain A) in PDB entry 6WPJ
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 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A GLN* 5.8 0.2 - - - -
478A GLU* 3.5 39.8 - - - +
497A THR* 3.1 15.3 + - - +
498A ASP* 1.3 73.4 - - - +
500A GLN* 1.3 62.0 + - - +
501A TYR* 3.7 8.5 + - - +
502A ALA* 3.2 21.9 + - - +
503A LEU* 3.1 20.4 + - - +
535A TRP* 3.8 2.9 - - - +
722T A 6.2 3.4 - - - -
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Residues in contact with GLN 500 (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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498A ASP 3.8 0.8 + - - -
499A SER* 1.3 69.0 - - - +
501A TYR* 1.3 62.1 + - - +
503A LEU* 3.9 9.5 - - + +
504A GLY* 2.9 26.7 + - - -
535A TRP* 3.8 18.1 - - - +
420B PRO* 4.6 17.1 - - + +
422B LEU* 3.9 32.5 - - + +
721T G 3.5 36.3 + - - +
722T A 2.9 30.5 + - - +
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Residues in contact with TYR 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A HIS* 4.7 1.2 + - - -
475A GLN* 3.5 54.2 - - + +
479A LEU* 4.1 19.8 - - + +
499A SER* 3.8 8.7 - - - +
500A GLN* 1.3 82.6 - - - +
502A ALA* 1.3 74.3 + - + +
504A GLY* 3.3 0.7 + - - -
505A ILE* 3.1 40.0 + - + +
809P C 3.3 34.5 + - - -
810P T 3.0 26.3 + - - -
722T A 6.3 2.9 - - - -
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Residues in contact with ALA 502 (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* 4.6 5.8 - - + -
479A LEU* 3.8 20.4 - - + +
482A ILE* 3.6 27.8 - - + -
497A THR* 4.8 0.4 - - - +
499A SER* 3.2 21.4 + - - +
501A TYR* 1.3 86.3 - - + +
503A LEU* 1.3 56.7 + - - +
505A ILE* 3.4 3.0 + - - +
506A ILE* 3.0 35.9 + - - +
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Residues in contact with LEU 503 (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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497A THR* 4.6 12.5 - - + +
499A SER 3.1 16.3 + - - +
500A GLN* 3.9 5.8 - - + +
502A ALA* 1.3 78.1 - - - +
504A GLY* 1.3 58.4 + - - +
506A ILE* 4.3 0.2 - - - +
507A GLN* 2.8 60.5 + - - +
533A LEU* 3.7 41.7 - - + +
534A ALA 4.8 2.2 - - - +
535A TRP* 4.2 24.2 - - + -
421B PRO* 4.9 10.3 - - + -
422B LEU* 4.3 20.9 - - + -
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Residues in contact with GLY 504 (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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406A TRP* 3.6 25.4 - - - -
500A GLN 2.9 18.0 + - - -
501A TYR 3.8 0.9 - - - -
503A LEU* 1.3 75.3 - - - +
505A ILE* 1.3 67.6 + - - +
507A GLN* 4.6 3.1 - - - -
508A ALA* 3.7 4.5 + - - +
420B PRO* 6.1 0.9 - - - -
421B PRO* 4.9 10.5 - - - -
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Residues in contact with ILE 505 (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 HIS* 3.3 44.4 - - + +
479A LEU* 4.9 10.8 - - + -
501A TYR* 3.1 41.0 + - + +
502A ALA* 3.8 7.0 - - - +
503A LEU 3.3 0.2 - - - -
504A GLY* 1.3 80.1 - - - +
506A ILE* 1.3 74.0 + - + +
507A GLN 3.0 0.5 + - - -
508A ALA* 3.1 11.3 + - - +
510A PRO* 3.5 16.8 - - + +
518A VAL* 4.3 20.9 - - + -
810P T 3.4 13.9 - - - +
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Residues in contact with ILE 506 (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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427A TYR* 4.1 4.1 + - - -
429A LEU* 3.9 18.0 - - + +
479A LEU* 4.6 9.2 - - + -
482A ILE* 3.6 47.1 - - + -
502A ALA 3.0 20.0 + - - +
505A ILE* 1.3 81.5 - - + +
507A GLN* 1.3 62.0 + - - +
509A GLN* 3.3 14.3 + - - -
510A PRO* 4.0 6.1 - - + +
518A VAL* 6.2 1.6 - - + -
521A ILE* 4.4 19.1 - - + -
525A LEU* 4.1 21.3 - - + -
531A VAL* 6.3 0.7 - - + -
533A LEU* 3.8 24.7 - - + -
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Residues in contact with GLN 507 (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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401A TRP* 5.6 0.2 - - - -
404A GLU 5.5 4.3 - - - +
405A TYR* 6.0 0.2 - - - -
406A TRP* 3.5 25.6 - - + -
429A LEU* 3.9 21.6 - - + +
503A LEU* 2.8 49.7 + - - +
504A GLY* 4.2 1.8 - - - +
506A ILE* 1.3 77.7 - - - +
508A ALA* 1.3 56.9 + - - +
509A GLN* 3.1 18.2 + - - +
533A LEU* 5.0 4.4 + - - +
421B PRO* 4.3 14.7 - - + +
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Residues in contact with ALA 508 (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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363A ASN* 3.3 13.7 + - - -
366A LYS* 4.2 20.9 - - - +
401A TRP* 3.4 12.3 - - - -
405A TYR* 4.4 9.4 - - + -
406A TRP* 3.8 22.4 - - + -
504A GLY 3.7 3.9 + - - +
505A ILE* 3.1 12.0 + - - +
507A GLN* 1.3 75.2 - - - +
509A GLN* 1.3 70.9 + - - +
510A PRO* 3.5 3.0 - - + +
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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