Contacts of the helix formed by residues 508 - 527 (chain A) in PDB entry 1CEZ
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 PRO 508 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A VAL* 3.8 41.1 - - + -
351A ASP* 5.2 8.7 - - + +
438A ASP* 2.8 20.4 - - + +
502A TRP* 3.6 29.5 - - + +
503A ALA* 4.0 9.0 - - - +
505A GLN 3.3 8.7 - - - +
506A ASP 3.2 11.4 - - - +
507A SER* 1.3 83.0 - - - -
509A PHE* 1.3 57.7 + - + +
511A PHE* 2.9 5.9 + - + +
512A LEU 2.8 24.9 + - - -
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Residues in contact with PHE 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A VAL* 4.0 19.7 - - + +
337A VAL* 4.7 1.3 - - + -
338A ALA* 4.3 20.0 - - + -
341A ILE* 3.9 23.3 - - + -
342A THR* 5.0 1.8 - - + -
349A VAL* 4.0 15.0 - - + -
352A ILE* 4.0 24.9 - - + -
438A ASP* 2.8 28.2 + - - +
439A MET* 3.5 45.3 - - + +
442A GLY* 4.1 10.9 - - - -
502A TRP* 3.9 20.4 - + - -
508A PRO* 1.3 77.5 - - + +
510A CYS* 1.3 56.2 + - - +
512A LEU* 3.3 7.6 + - + +
513A ALA* 3.0 26.3 + - - +
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Residues in contact with CYS 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ASP* 3.0 35.9 + - - +
441A LYS* 3.8 30.7 - - - -
442A GLY* 3.9 4.9 - - - -
463A HIS* 4.7 6.6 - - + -
467A CYS* 3.7 22.0 - - - -
507A SER* 3.9 7.2 - - - +
509A PHE* 1.3 77.4 - - - +
511A PHE* 1.3 62.1 + - - +
513A ALA* 3.4 7.4 + - - +
514A PHE* 3.1 21.8 + - - +
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Residues in contact with PHE 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A GLY 3.5 26.9 - - - -
467A CYS* 3.8 12.1 - - + +
468A ALA* 3.9 17.9 - - + -
481A PHE* 4.8 5.2 - + - -
482A ILE* 6.0 0.4 - - + -
489A ILE* 4.6 3.1 - - + -
501A TRP* 3.6 38.1 - + - -
502A TRP* 3.8 12.3 - - + -
505A GLN* 3.6 27.4 - - + -
507A SER 2.8 18.9 + - - +
508A PRO* 2.9 5.6 + - + +
510A CYS* 1.3 76.0 - - - +
512A LEU* 1.3 63.8 + - - +
514A PHE* 3.2 20.6 + + - +
515A CYS* 3.0 51.7 + - - -
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Residues in contact with LEU 512 (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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334A VAL* 4.7 11.2 - - + -
337A VAL* 3.9 39.0 - - + -
492A CYS 4.4 5.6 - - - +
496A PRO* 4.1 12.3 - - + -
502A TRP* 3.7 36.6 - - + -
508A PRO 2.8 12.8 + - - +
509A PHE* 3.6 10.1 - - + +
510A CYS 3.2 0.2 - - - -
511A PHE* 1.3 74.7 - - - +
513A ALA* 1.3 66.4 + - - +
515A CYS* 2.9 24.3 + - + +
516A PHE* 3.1 39.6 + - + -
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Residues in contact with ALA 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASN* 4.1 6.8 + - - +
334A VAL* 3.8 21.5 - - + +
442A GLY* 4.3 7.9 - - - +
444A LEU 6.0 0.2 - - - +
509A PHE 3.0 13.3 + - - +
510A CYS* 3.6 11.0 - - - +
511A PHE 3.3 0.2 - - - -
512A LEU* 1.3 78.8 - - - +
514A PHE* 1.3 61.9 + - - +
516A PHE* 3.3 7.6 + - - +
517A GLU* 3.2 22.9 + - - +
532A LEU* 4.0 24.3 - - + +
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Residues in contact with PHE 514 (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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460A LEU* 3.3 33.9 - - + -
461A LYS* 4.0 6.3 - - - -
463A HIS* 4.6 5.2 - - - +
464A GLY* 3.2 33.4 - - - -
467A CYS* 5.1 0.2 - - - -
482A ILE* 3.9 9.0 - - + -
489A ILE* 3.7 35.9 - - + -
510A CYS 3.1 13.7 + - - +
511A PHE* 3.4 24.2 - + - +
513A ALA* 1.3 77.6 - - - +
515A CYS* 1.3 63.7 + - - +
517A GLU* 3.3 2.6 + - - +
518A TYR* 2.8 57.7 + + + +
532A LEU* 3.8 17.0 - - + +
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Residues in contact with CYS 515 (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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489A ILE* 3.9 32.4 - - - +
492A CYS* 4.3 10.5 - - - -
493A ALA* 3.3 21.1 - - + +
502A TRP* 4.7 0.7 - - - -
511A PHE* 3.0 50.1 + - - -
512A LEU* 2.9 16.9 + - + +
514A PHE* 1.3 86.4 - - - +
516A PHE* 1.3 59.6 + - - +
518A TYR* 3.9 1.4 - - - +
519A ALA* 3.1 17.0 + - - +
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Residues in contact with PHE 516 (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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331A ASN* 4.8 2.9 - - - +
333A LYS* 3.3 71.6 + - + +
334A VAL* 3.9 10.8 - - + -
337A VAL* 4.6 0.2 - - + -
492A CYS 4.4 1.1 - - - -
493A ALA* 3.2 39.9 - - + -
496A PRO* 4.2 16.2 - - + -
512A LEU* 3.1 47.7 + - + -
513A ALA* 3.3 5.4 + - - +
515A CYS* 1.3 73.0 - - - +
517A GLU* 1.3 71.3 + - - +
519A ALA* 3.3 3.7 + - - +
520A GLY* 3.0 18.9 + - - -
528A TYR* 4.7 1.7 + - - -
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Residues in contact with GLU 517 (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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331A ASN* 5.3 4.9 + - - -
333A LYS* 4.6 7.1 + - - -
445A THR* 6.0 0.7 - - - -
460A LEU* 4.3 9.2 - - + -
513A ALA 3.2 10.3 + - - +
514A PHE 3.5 9.0 - - - +
516A PHE* 1.3 84.6 - - - +
518A TYR* 1.3 63.0 + - - +
520A GLY* 3.0 11.3 + - - -
521A VAL* 3.1 15.9 + - - +
528A TYR* 3.2 27.9 + - - -
529A ASN 4.5 0.9 - - - +
530A CYS* 3.2 39.6 - - - -
531A SER* 4.2 3.3 + - - -
532A LEU* 3.7 28.8 + - + +
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Residues in contact with TYR 518 (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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457A TYR* 3.9 17.0 + + - -
460A LEU* 4.1 10.0 - - + +
461A LYS* 4.3 10.3 - - + +
482A ILE* 3.4 28.5 + - + +
483A GLU* 4.9 4.5 - - - +
486A HIS* 2.8 39.6 - + - +
489A ILE* 3.6 24.7 - - + -
490A MET* 3.7 14.1 - - - -
514A PHE* 2.8 46.7 + + + +
515A CYS 3.9 3.8 - - - +
517A GLU* 1.3 72.2 - - - +
519A ALA* 1.3 63.3 + - - +
521A VAL* 3.3 4.0 + - - +
522A GLN* 3.2 37.6 + - - -
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Residues in contact with ALA 519 (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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490A MET* 3.9 25.6 - - + -
493A ALA* 3.6 20.6 - - + -
515A CYS 3.1 18.4 + - - +
516A PHE 3.6 5.2 - - - +
517A GLU 3.2 0.2 - - - -
518A TYR* 1.3 74.6 - - - +
520A GLY* 1.3 64.5 + - - +
522A GLN* 3.3 2.3 + - - +
523A HIS* 2.8 35.2 + - + +
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Residues in contact with GLY 520 (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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516A PHE 3.0 10.7 + - - -
517A GLU 3.0 8.4 + - - -
519A ALA* 1.3 75.5 - - - +
521A VAL* 1.3 64.7 + - - +
523A HIS* 3.0 5.4 + - - -
524A HIS* 2.9 29.8 + - - +
528A TYR* 3.9 24.9 - - - -
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Residues in contact with VAL 521 (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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452A ILE* 4.3 9.6 - - + -
457A TYR* 3.4 43.5 - - + -
460A LEU* 4.1 12.1 - - + -
517A GLU 3.1 14.0 + - - +
518A TYR 3.3 7.4 + - - +
520A GLY* 1.3 75.0 - - - +
522A GLN* 1.3 61.2 + - - +
523A HIS 3.1 0.2 + - - -
525A GLY* 2.7 36.8 + - - +
526A LEU* 4.3 18.8 - - + -
528A TYR* 3.9 23.5 - - + -
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Residues in contact with GLN 522 (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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457A TYR* 2.7 34.4 + - - -
486A HIS* 3.5 15.2 + - + +
490A MET* 3.6 34.1 - - + -
518A TYR* 3.2 36.9 + - + +
519A ALA 3.5 6.3 - - - +
520A GLY 3.2 0.4 - - - -
521A VAL* 1.3 78.3 - - - +
523A HIS* 1.3 61.0 + - + +
525A GLY 4.7 0.9 + - - -
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Residues in contact with HIS 523 (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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490A MET* 4.1 19.7 - - + -
494A LYS* 6.1 1.4 + - - -
519A ALA* 2.8 25.7 + - + +
520A GLY* 3.0 5.6 + - - +
522A GLN* 1.3 82.7 - - + +
524A HIS* 1.3 80.2 + + + +
525A GLY 3.7 0.2 - - - -
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Residues in contact with HIS 524 (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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520A GLY* 2.9 16.0 + - - +
523A HIS* 1.3 95.8 - + + +
525A GLY* 1.3 63.4 + - - +
527A SER* 3.3 16.2 + - - +
528A TYR* 4.0 30.6 - + + +
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Residues in contact with GLY 525 (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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521A VAL* 2.7 25.2 + - - +
522A GLN 4.6 1.0 + - - -
523A HIS 3.7 1.0 - - - -
524A HIS* 1.3 70.7 - - - +
526A LEU* 1.3 60.7 + - - -
527A SER 2.8 12.9 + - - -
528A TYR* 2.9 22.3 + - - +
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Residues in contact with LEU 526 (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 PRO* 4.1 1.7 - - - +
452A ILE* 3.3 8.0 + - + +
453A GLY* 2.8 43.1 + - - +
454A LYS* 3.3 35.0 - - + +
457A TYR* 4.2 26.9 - - + -
521A VAL* 4.3 8.1 - - + -
525A GLY* 1.3 69.9 - - - -
527A SER* 1.3 57.8 + - - +
528A TYR 3.2 1.8 - - - -
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Residues in contact with SER 527 (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 PRO* 3.5 21.9 - - - +
524A HIS* 3.3 18.2 + - - +
525A GLY 2.8 1.4 + - - -
526A LEU* 1.3 77.0 - - - +
528A TYR* 1.3 65.0 + - - +
529A ASN* 3.3 2.8 + - - +
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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