Contacts of the helix formed by residues 517 - 534 (chain A) in PDB entry 2OZO
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 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A VAL* 3.6 16.2 - - - +
509A GLU* 5.5 1.0 + - - -
515A LYS* 4.8 17.8 - - - +
516A PHE* 1.3 77.5 - - - +
518A SER* 1.3 57.9 + - - +
519A ARG* 3.2 15.9 + - - +
520A SER* 2.6 43.8 + - - -
521A ASP* 2.9 8.8 + - - +
580A TRP* 5.4 1.7 - - - -
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Residues in contact with SER 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A GLU* 3.2 53.3 + - - +
456A ASN* 5.7 0.9 - - - -
457A PHE 5.0 4.2 + - - -
458A VAL* 3.9 9.9 - - - +
517A SER* 1.3 74.6 - - - +
519A ARG* 1.3 58.6 + - - +
521A ASP* 3.1 15.0 + - - +
522A VAL* 2.9 33.3 + - - +
586A PHE* 3.5 3.2 - - - -
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Residues in contact with ARG 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A GLU* 5.5 0.7 - - - -
517A SER* 2.9 12.1 - - - +
518A SER* 1.3 79.6 - - - +
520A SER* 1.3 58.9 + - - +
522A VAL* 3.3 12.1 + - - +
523A TRP 3.6 0.7 + - - -
580A TRP* 2.9 42.2 + - + +
581A GLU* 3.2 25.3 + - - +
583A ARG* 2.6 52.7 + - - +
584A PRO 3.8 9.0 - - - -
585A ASP* 3.8 28.7 + - - +
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Residues in contact with SER 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A VAL* 5.3 0.9 - - - +
460A ARG* 5.6 1.6 - - - -
506A TYR* 5.8 0.2 - - - -
507A ALA* 4.1 7.0 + - - +
509A GLU* 4.6 4.7 + - - -
510A CYS* 3.0 28.9 - - - -
515A LYS* 4.2 2.7 - - - -
516A PHE* 4.0 12.4 - - - -
517A SER* 2.6 40.8 + - - -
519A ARG* 1.3 72.5 - - - +
521A ASP* 1.3 60.0 + - - +
523A TRP* 3.4 16.5 + - - +
524A SER* 3.7 8.5 + - - -
583A ARG* 3.6 8.9 - - - +
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Residues in contact with ASP 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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449A MET* 3.9 10.5 - - + +
457A PHE 4.8 0.7 - - - +
458A VAL* 3.5 11.6 - - - +
459A HIS* 2.8 34.7 + - - +
460A ARG* 2.9 28.2 + - - -
461A ASN 4.5 0.2 + - - -
462A LEU* 3.8 8.5 + - + +
517A SER 2.9 10.1 + - - +
518A SER* 3.1 12.3 + - - +
520A SER* 1.3 75.2 + - - +
522A VAL* 1.3 54.7 + - - +
523A TRP 2.9 5.2 - - - -
524A SER* 2.8 28.8 + - - -
525A TYR 2.9 9.9 + - - -
586A PHE* 3.6 14.4 - - + -
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Residues in contact with VAL 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A SER 2.9 24.7 + - - +
519A ARG* 3.3 11.6 + - - +
521A ASP* 1.3 74.9 - - - +
523A TRP* 1.3 60.5 + - - +
525A TYR* 3.6 1.8 - - - +
526A GLY 3.2 14.6 + - - -
575A CYS* 3.5 33.9 - - + +
583A ARG* 4.8 5.8 - - + +
584A PRO 3.4 28.3 - - - +
585A ASP* 4.2 1.3 - - - -
586A PHE* 3.4 37.4 - - + +
589A VAL* 3.9 11.0 - - + -
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Residues in contact with TRP 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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504A LYS 4.7 2.8 + - - -
505A TRP 3.3 19.6 + - - -
506A TYR 3.4 11.2 + - - -
507A ALA* 3.6 18.2 - - + -
508A PRO* 3.6 31.4 - - + -
519A ARG 3.6 1.8 + - - -
520A SER 3.4 12.9 + - - +
521A ASP 2.9 0.6 - - - -
522A VAL* 1.3 78.3 - - - +
524A SER* 1.3 59.3 + - - +
525A TYR 3.2 0.2 - - - -
526A GLY* 3.0 15.1 + - - -
527A VAL* 3.0 23.0 + - + +
540A TYR* 4.5 6.9 + - - -
552A ILE* 4.1 18.8 - - + -
557A ARG* 4.0 20.2 - - - -
575A CYS 3.6 11.2 + - - +
576A TRP* 3.4 51.2 + + + -
577A ILE 3.9 8.1 - - - -
578A TYR* 4.6 1.8 - - - -
583A ARG* 3.6 23.8 - - - +
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Residues in contact with SER 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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460A ARG 5.3 2.9 + - - -
461A ASN* 5.7 0.2 - - - -
462A LEU* 3.4 35.8 + - - -
505A TRP* 2.9 26.6 + - - +
506A TYR* 4.5 5.7 - - - -
520A SER 3.7 10.2 + - - -
521A ASP* 2.8 11.6 + - - -
523A TRP* 1.3 74.7 - - - +
525A TYR* 1.3 55.2 + - - +
527A VAL* 3.2 5.7 + - - +
528A THR* 2.7 37.4 + - - -
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Residues in contact with TYR 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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442A LEU* 2.5 38.1 + - + +
445A VAL* 3.8 23.8 - - + -
446A SER* 3.7 13.5 - - - -
462A LEU* 3.1 26.8 - - + +
521A ASP 2.9 5.1 + - - +
522A VAL 3.6 8.5 - - - +
523A TRP 3.2 0.2 - - - -
524A SER* 1.3 74.3 - - - +
526A GLY* 1.3 62.6 + - - +
528A THR* 3.6 5.5 - - - -
529A MET* 2.8 66.6 + - + +
575A CYS* 4.3 6.1 - - - -
586A PHE* 3.8 19.7 - + + -
589A VAL* 3.8 24.2 - - + -
593A MET* 3.1 20.4 - - + +
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Residues in contact with GLY 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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522A VAL 3.2 4.6 + - - -
523A TRP 3.0 9.5 + - - -
525A TYR* 1.3 82.1 - - - +
527A VAL* 1.3 60.0 + - - +
529A MET* 3.3 6.7 + - - +
530A TRP 3.2 14.9 + - - -
572A MET* 3.4 6.4 - - - +
575A CYS* 3.7 20.6 - - - -
576A TRP* 3.3 25.2 - - - -
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Residues in contact with VAL 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A LYS 4.1 7.2 - - - +
505A TRP* 3.5 39.5 - - + +
523A TRP* 3.0 36.5 + - + +
524A SER* 3.5 8.3 - - - +
526A GLY* 1.3 73.9 - - - +
528A THR* 1.3 67.1 - - - +
530A TRP* 3.1 6.1 + - - +
531A GLU* 2.9 20.1 + - - +
539A PRO* 4.0 21.3 - - + -
540A TYR* 5.0 4.3 - - + +
558A MET* 4.5 6.7 - - + -
576A TRP* 3.4 13.9 - - + +
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Residues in contact with THR 528 (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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422A LEU* 4.8 5.2 - - + -
442A LEU* 4.3 14.8 - - + -
445A VAL* 5.3 4.3 - - + -
462A LEU* 3.9 6.8 - - + +
463A ALA* 3.2 28.0 + - - -
464A ALA* 4.0 20.2 - - + +
467A VAL* 4.4 12.8 - - + -
505A TRP* 4.1 0.2 - - - -
524A SER 2.7 22.6 + - - -
525A TYR* 3.6 9.9 - - + -
527A VAL* 1.3 68.8 - - - +
529A MET* 1.3 68.8 + - - +
531A GLU* 3.1 11.7 + - - +
532A ALA* 3.0 21.0 + - - +
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Residues in contact with MET 529 (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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442A LEU* 3.8 19.7 - - + -
525A TYR* 2.8 53.0 + - + +
526A GLY* 3.4 9.0 - - - +
528A THR* 1.3 74.0 - - - +
530A TRP* 1.3 52.8 + - - +
532A ALA* 3.1 1.4 + - - +
533A LEU* 2.7 46.1 + - + +
568A LEU* 3.4 26.9 - - - +
571A LEU* 4.0 13.2 - - + -
572A MET* 3.4 29.6 - - + +
575A CYS* 5.0 0.7 - - - -
593A MET* 3.5 23.6 - - + -
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Residues in contact with TRP 530 (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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526A GLY 3.2 7.6 + - - +
527A VAL 3.1 10.0 + - - +
529A MET* 1.3 79.4 - - - +
531A GLU* 1.3 68.3 + - - +
533A LEU* 4.7 1.8 - - - -
534A SER* 2.9 45.8 + - - -
537A GLN* 3.3 41.5 - - + -
538A LYS 3.7 17.7 - - - -
539A PRO* 4.0 6.7 - - + -
540A TYR 5.1 0.7 - - - -
558A MET* 3.5 37.0 - - + +
559A GLU* 2.8 43.4 + - - -
561A PRO* 3.4 22.2 - - + +
569A TYR* 5.3 0.2 - + - -
572A MET* 3.5 21.2 - - - +
576A TRP* 4.0 5.8 - + + -
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Residues in contact with GLU 531 (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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423A HIS* 4.2 16.3 - - + +
464A ALA* 2.8 49.6 + - + +
465A ARG* 4.7 1.7 + - - +
505A TRP* 2.9 34.7 + - + -
527A VAL 2.9 11.4 + - - +
528A THR* 3.4 10.0 - - - +
530A TRP* 1.3 82.9 - - - +
532A ALA* 1.3 59.5 + - - +
534A SER* 3.6 1.9 + - - -
535A TYR 3.5 2.1 + - - -
536A GLY* 2.8 29.8 + - - -
537A GLN 4.1 10.8 - - - +
538A LYS* 5.8 0.3 - - - +
539A PRO* 3.7 23.8 - - + +
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Residues in contact with ALA 532 (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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422A LEU* 3.8 28.5 - - + -
423A HIS* 6.3 1.1 - - - +
426A LEU* 3.7 15.3 - - + +
438A VAL* 3.9 21.4 - - + +
442A LEU* 4.1 9.9 - - + -
528A THR 3.0 11.7 + - - +
529A MET 3.5 5.2 - - - +
531A GLU* 1.3 74.4 - - - +
533A LEU* 1.3 58.5 + - - +
534A SER 3.1 2.0 - - - -
535A TYR* 2.7 29.6 + - - -
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Residues in contact with LEU 533 (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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430A ARG* 3.1 18.5 + - - -
435A VAL* 5.5 11.4 - - + +
438A VAL* 4.1 19.5 - - + -
439A ALA 5.5 2.5 - - - +
442A LEU* 4.1 9.0 - - + -
529A MET* 2.7 26.3 + - + +
530A TRP 4.1 1.6 - - - +
532A ALA* 1.3 73.1 - - - +
534A SER* 1.3 57.4 + - - +
535A TYR* 3.2 9.9 - - + -
561A PRO* 4.1 12.5 - - + +
562A PRO 4.3 1.7 - - - +
563A GLU 5.6 0.5 - - - +
564A CYS* 3.6 25.3 - - + +
565A PRO* 5.3 1.6 - - + -
568A LEU* 3.6 37.9 - - + -
572A MET* 3.6 26.2 - - + -
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Residues in contact with SER 534 (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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430A ARG* 3.9 9.4 - - - +
530A TRP* 2.9 34.6 + - - -
531A GLU 3.6 3.1 + - - -
533A LEU* 1.3 75.4 - - - +
535A TYR* 1.3 71.8 + - - +
536A GLY 3.6 0.4 + - - -
537A GLN* 3.2 45.8 + - - +
561A PRO* 3.8 18.8 - - - -
562A PRO* 4.9 3.4 - - - -
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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