Contacts of the helix formed by residues 521 - 544 (chain A) in PDB entry 2WKP
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 ARG 521 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A HIS* 4.0 36.5 + - + +
520A VAL* 1.3 82.8 - - - +
522A ASP* 1.3 86.7 + - - +
523A ALA 3.2 0.5 + - - -
524A ALA* 3.1 17.3 + - - +
525A GLU* 3.2 11.1 + - - +
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Residues in contact with ASP 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ARG* 1.3 82.2 - - - +
523A ALA* 1.3 66.2 + - - +
525A GLU* 3.5 9.7 + - - +
526A ARG* 3.0 29.5 + - - +
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Residues in contact with ALA 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A ARG 3.2 0.2 + - - -
522A ASP* 1.3 80.6 - - + +
524A ALA* 1.3 63.4 + - - +
526A ARG* 3.3 29.6 + - - +
527A GLU* 3.0 36.8 + - - +
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Residues in contact with ALA 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A VAL* 4.0 23.7 - - + +
521A ARG 3.1 9.2 + - - +
523A ALA* 1.3 78.6 - - - +
525A GLU* 1.3 62.7 + - - +
527A GLU* 3.4 11.7 + - - +
528A GLY* 3.0 20.3 + - - -
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Residues in contact with GLU 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A GLN* 3.3 25.4 + - - +
493A LEU* 4.4 2.8 - - + +
519A HIS* 5.0 2.3 + - - -
520A VAL* 3.7 16.2 - - + +
521A ARG* 3.2 17.8 + - - +
522A ASP* 3.5 18.7 + - - +
524A ALA* 1.3 79.2 - - - +
526A ARG* 1.3 64.7 + - - +
528A GLY* 3.2 1.4 + - - -
529A VAL* 2.9 42.9 + - + +
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Residues in contact with ARG 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ASP* 3.0 11.8 + - - +
523A ALA* 3.6 36.3 + - - +
525A GLU* 1.3 78.7 - - - +
527A GLU* 1.3 65.1 + - - +
529A VAL* 3.5 5.9 + - - +
530A MET* 3.2 34.6 + - + +
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Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ALA* 3.0 30.6 + - + +
524A ALA* 3.7 7.8 - - - +
526A ARG* 1.3 79.6 + - + +
528A GLY* 1.3 63.7 + - - +
530A MET* 3.3 8.3 + - - +
531A LEU* 3.0 37.8 + - + +
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Residues in contact with GLY 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LEU* 3.6 21.8 - - - -
514A LEU* 3.7 14.8 - - - -
524A ALA 3.0 14.0 + - - -
525A GLU 3.7 0.9 - - - -
527A GLU* 1.3 76.8 - - - +
529A VAL* 1.3 61.4 + - - +
531A LEU* 3.2 7.1 + - - +
532A ILE* 3.1 27.2 + - - +
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Residues in contact with VAL 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A THR* 4.0 24.0 - - + +
493A LEU* 3.8 9.2 - - + +
525A GLU* 2.9 35.4 + - + +
526A ARG* 3.8 6.1 - - - +
528A GLY* 1.3 76.2 - - - +
530A MET* 1.3 63.2 + - - +
532A ILE* 3.3 8.9 - - - +
533A LYS* 3.0 53.7 + - + +
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Residues in contact with MET 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 ARG* 3.2 25.8 + - + +
527A GLU* 3.5 11.2 - - - +
529A VAL* 1.3 79.0 - - - +
531A LEU* 1.3 68.1 + - + +
533A LYS* 3.5 6.1 + - - +
534A LYS* 3.2 23.5 + - + +
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Residues in contact with LEU 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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413A LYS* 6.1 4.5 - - - +
514A LEU* 4.6 17.9 - - + -
527A GLU* 3.0 30.6 + - + +
528A GLY* 3.2 8.7 + - - +
530A MET* 1.3 85.5 - - + +
532A ILE* 1.3 61.0 + - + +
534A LYS* 3.3 5.8 + - - +
535A THR* 3.0 30.9 + - - +
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Residues in contact with ILE 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A THR* 4.0 11.2 - - + -
493A LEU* 3.7 34.3 - - + +
495A HIS* 3.5 30.7 - - + +
512A VAL* 3.8 29.4 - - + +
513A GLN 4.8 0.2 - - - -
514A LEU* 3.7 30.1 - - + -
528A GLY 3.1 9.1 + - - +
529A VAL* 3.3 13.5 - - - +
531A LEU* 1.3 80.7 - - + +
533A LYS* 1.3 61.7 + - + +
535A THR* 3.3 4.2 + - - -
536A ALA* 2.9 28.8 + - - +
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Residues in contact with LYS 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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475A GLU* 4.0 15.9 + - - +
477A THR* 3.9 15.5 - - - -
495A HIS* 3.9 30.7 - - + +
497A GLN* 4.7 1.5 - - - +
529A VAL* 3.0 42.7 + - + +
530A MET* 4.0 5.6 - - - +
532A ILE* 1.3 77.1 - - + +
534A LYS* 1.3 62.2 + - - +
536A ALA* 3.3 3.1 + - - +
537A GLU* 3.1 28.0 + - + +
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Residues in contact with LYS 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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530A MET* 3.2 14.3 + - + +
531A LEU* 3.5 10.1 - - - +
533A LYS* 1.3 72.7 - - - +
535A THR* 1.3 67.2 + - - +
537A GLU* 3.2 12.0 + - + +
538A ASN* 3.1 44.7 + - - +
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Residues in contact with THR 535 (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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411A ILE* 4.2 6.5 - - + -
413A LYS* 3.7 48.0 - - + +
512A VAL* 4.0 11.6 - - + +
531A LEU* 3.0 15.8 + - - +
532A ILE* 3.5 11.3 - - - -
534A LYS* 1.3 78.3 - - - +
536A ALA* 1.3 63.3 + - - +
538A ASN* 3.0 12.8 + - - +
539A ILE* 3.0 38.0 + - + +
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Residues in contact with ALA 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A HIS* 3.7 12.3 - - + +
497A GLN* 3.5 33.2 + - + +
510A ILE* 3.9 8.7 - - + +
512A VAL* 4.0 14.5 - - + +
532A ILE 2.9 14.2 + - - +
533A LYS 3.6 7.2 - - - +
534A LYS 3.3 0.2 - - - -
535A THR* 1.3 76.7 - - - +
537A GLU* 1.3 56.9 + - - +
539A ILE* 3.2 7.5 + - - +
540A ASP* 3.0 28.1 + - - +
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Residues in contact with GLU 537 (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 GLN* 3.0 26.5 + - - +
533A LYS 3.1 14.7 + - - +
534A LYS* 3.6 13.7 - - + +
535A THR 3.2 0.2 - - - -
536A ALA* 1.3 76.4 - - - +
538A ASN* 1.3 62.9 + - - +
540A ASP* 3.4 11.3 + - - +
541A GLU* 3.2 21.7 + - - +
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Residues in contact with ASN 538 (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 THR* 5.1 5.6 - - + +
411A ILE* 3.7 19.1 - - + +
534A LYS* 3.1 40.9 + - - +
535A THR* 3.0 12.8 + - - +
537A GLU* 1.3 73.4 - - - +
539A ILE* 1.3 66.2 + - - +
541A GLU* 3.4 15.5 + - - +
542A ALA* 3.0 23.6 + - - +
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Residues in contact with ILE 539 (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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408A LEU* 4.0 6.7 - - + -
411A ILE* 3.8 20.0 - - + -
415A PHE* 3.4 45.3 - - + -
417A ILE* 3.9 23.8 - - + -
510A ILE* 3.8 23.3 - - + -
512A VAL* 3.7 18.8 - - + -
535A THR* 3.0 26.3 + - + +
536A ALA 3.2 5.6 + - - +
538A ASN* 1.3 72.7 - - - +
540A ASP* 1.3 57.7 + - - +
542A ALA* 3.9 0.6 - - - +
543A ALA* 2.7 38.6 + - - +
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Residues in contact with ASP 540 (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 GLN* 4.7 7.3 + - - +
498A PRO 4.6 2.8 - - - +
499A MET* 3.4 32.8 - - - +
500A ARG 4.7 1.4 + - - +
510A ILE* 3.6 14.2 - - + +
536A ALA 3.0 17.2 + - - +
537A GLU* 3.6 14.4 - - - +
539A ILE* 1.3 78.6 - - - +
541A GLU* 1.3 64.9 + - - +
543A ALA* 3.4 2.1 + - - +
544A LYS* 3.3 37.6 + - - +
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Residues in contact with GLU 541 (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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405A ALA* 3.5 32.0 - - + +
406A THR* 5.5 3.8 - - - +
537A GLU 3.2 9.7 + - - +
538A ASN* 3.7 17.0 - - - +
539A ILE 3.3 0.2 - - - -
540A ASP* 1.3 83.2 + - - +
542A ALA* 1.3 62.2 + - - +
544A LYS* 3.3 29.0 + - + +
545A GLU* 4.4 2.9 + - - +
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Residues in contact with ALA 542 (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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405A ALA* 4.9 1.8 - - - -
406A THR* 3.2 30.8 - - + +
407A THR* 4.1 7.6 - - - -
408A LEU* 3.9 21.1 - - + +
411A ILE* 4.1 10.5 - - + -
538A ASN 3.0 16.8 + - - +
539A ILE 3.9 2.2 - - - +
541A GLU* 1.3 77.5 - - - +
543A ALA* 1.3 63.3 + - - +
545A GLU* 3.1 19.7 + - - +
546A LEU 3.9 2.6 + - - -
595A ASN* 5.0 3.5 - - - +
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Residues in contact with ALA 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 4.1 6.0 - - + +
417A ILE* 4.0 19.3 - - + -
499A MET* 3.4 34.4 - - + +
508A TYR* 4.9 8.9 - - + -
539A ILE 2.7 21.9 + - - +
542A ALA* 1.3 68.4 - - - +
544A LYS* 1.3 64.5 + - - +
545A GLU 3.0 2.5 - - - -
546A LEU* 3.0 26.9 + - + +
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Residues in contact with LYS 544 (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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499A MET* 5.3 7.2 - - + -
500A ARG 5.6 7.0 - - - +
540A ASP* 3.3 30.2 + - - +
541A GLU* 3.3 20.7 + - + +
542A ALA 3.2 0.6 - - - -
543A ALA* 1.3 77.2 - - - +
545A GLU* 1.3 72.2 + - - +
546A LEU 3.3 3.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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