Contacts of the helix formed by residues 520 - 544 (chain A) in PDB entry 4KZI
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 GLU 520 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A LEU* 5.0 2.4 - - + +
431A SER* 4.1 16.0 + - - +
434A ASP* 3.0 12.7 + - - +
518A LEU* 4.4 0.9 - - - -
519A GLN* 1.3 91.2 - - + +
521A PRO* 1.3 68.1 - - - +
522A ARG 2.9 4.8 + - - -
523A ARG* 2.7 62.9 + - + +
524A VAL* 3.3 10.3 + - - +
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Residues in contact with PRO 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASP* 4.6 10.8 - - - +
515A ARG 5.8 0.7 - - - +
518A LEU* 3.5 37.7 - - + +
519A GLN 3.3 9.6 - - - +
520A GLU* 1.3 88.7 - - - +
522A ARG* 1.3 64.4 + - + +
524A VAL* 3.3 2.9 + - - +
525A GLU* 2.9 36.1 + - - +
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Residues in contact with ARG 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A GLU 2.9 3.8 + - - -
521A PRO* 1.3 79.4 - - + +
523A ARG* 1.3 62.5 + - + +
525A GLU* 3.7 20.9 + - - +
526A GLU* 2.8 28.8 + - - +
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Residues in contact with ARG 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLY 4.8 1.8 + - - -
429A GLU* 3.0 42.4 + - - +
430A LEU* 3.8 26.1 - - + +
431A SER 4.2 1.4 - - - +
520A GLU* 2.7 57.9 + - + +
522A ARG* 1.3 77.5 - - + +
524A VAL* 1.3 62.4 + - - +
526A GLU* 3.3 7.9 + - - +
527A LEU* 3.0 23.2 + - - +
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Residues in contact with VAL 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 4.4 16.4 - - + -
434A ASP* 4.9 3.1 - - + +
438A LEU* 4.1 20.4 - - + -
512A ILE* 3.6 12.3 - - + +
513A THR* 3.6 40.8 - - - +
514A ASP* 4.6 0.7 - - - +
518A LEU* 3.9 26.2 - - + -
520A GLU* 3.9 9.2 - - + +
521A PRO 3.3 7.4 + - - +
522A ARG 3.2 0.6 - - - -
523A ARG* 1.3 75.5 - - - +
525A GLU* 1.4 55.9 + - + +
527A LEU* 3.1 3.4 + - - -
528A GLN* 2.8 32.8 + - - +
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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
----------------------------------------------------------
514A ASP* 2.5 38.6 - - - +
521A PRO* 2.9 25.9 + - - +
522A ARG* 3.8 24.7 + - - +
524A VAL* 1.4 76.2 - - + +
526A GLU* 1.3 54.9 + - - +
528A GLN* 3.1 17.5 + - - +
529A ASN* 2.8 37.7 + - - +
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Residues in contact with GLU 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ARG 2.8 19.0 + - - +
523A ARG* 3.6 9.0 - - - +
524A VAL 3.2 0.2 - - - -
525A GLU* 1.3 75.5 - - - +
527A LEU* 1.3 62.2 + - - +
529A ASN* 3.3 17.4 + - - +
530A ARG* 2.9 64.2 + - - +
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Residues in contact with LEU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 6.0 3.8 - - + -
424A ILE* 5.0 2.5 - - + -
425A PRO 3.4 26.7 - - - +
426A GLY* 4.1 6.7 - - - +
427A PHE* 4.1 16.8 - - + +
430A LEU* 4.7 9.4 - - + -
512A ILE* 3.9 31.0 - - + -
523A ARG 3.0 13.7 + - - +
524A VAL* 3.1 7.1 + - - +
526A GLU* 1.3 73.6 - - - +
528A GLN* 1.3 66.8 + - - +
530A ARG* 3.1 29.6 + - + +
531A ILE* 3.1 36.9 + - + +
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Residues in contact with GLN 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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509A LEU* 3.7 17.6 + - + +
512A ILE* 3.6 26.7 + - - +
513A THR* 3.4 28.9 + - - +
514A ASP* 4.4 12.9 + - - +
524A VAL 2.8 14.4 + - - +
525A GLU* 3.4 19.4 - - - +
527A LEU* 1.3 76.3 - - - +
529A ASN* 1.3 68.2 + - - +
531A ILE* 3.2 1.1 + - - -
532A ALA* 2.9 25.6 + - + +
701A GOL 4.3 8.1 + - - -
703A ZJ0 5.4 0.4 - - - -
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Residues in contact with ASN 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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525A GLU* 2.8 24.5 + - - +
526A GLU* 3.5 22.8 + - - +
527A LEU 3.2 0.2 - - - -
528A GLN* 1.3 80.2 - - - +
530A ARG* 1.3 64.0 + - + +
531A ILE 3.3 0.2 + - - -
532A ALA* 3.3 8.0 + - - +
533A SER* 3.0 26.8 + - - +
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Residues in contact with ARG 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 3.8 17.8 - - + +
425A PRO 5.1 3.2 + - - -
426A GLY* 5.3 5.5 - - - -
526A GLU* 2.9 48.6 + - - +
527A LEU* 3.1 30.9 + - + +
529A ASN* 1.3 78.9 - - + +
531A ILE* 1.3 61.4 + - - +
533A SER* 3.4 6.2 + - - -
534A CYS* 3.0 23.4 + - - +
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Residues in contact with ILE 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 4.4 10.1 - - + -
368A LEU* 4.0 25.1 - - + -
424A ILE* 4.4 8.5 - - + -
505A CYS* 3.7 16.3 - - + +
508A ALA* 4.3 13.2 - - + +
509A LEU* 3.7 26.0 - - + -
512A ILE* 4.0 30.1 - - + -
527A LEU* 3.1 30.4 + - + +
528A GLN* 3.2 1.1 + - - -
530A ARG* 1.3 75.0 - - - +
532A ALA* 1.3 61.5 + - - +
534A CYS* 3.2 6.9 + - - +
535A LEU* 2.9 28.1 + - - +
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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
----------------------------------------------------------
509A LEU* 3.9 18.0 - - + +
528A GLN* 2.9 19.3 + - + +
529A ASN* 3.6 7.9 - - - +
531A ILE* 1.3 77.9 - - - +
533A SER* 1.3 57.0 + - - +
535A LEU* 3.2 4.9 + - - +
536A LYS* 2.8 30.0 + - - +
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Residues in contact with SER 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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529A ASN* 3.0 18.0 + - - +
530A ARG* 3.7 6.9 - - - -
531A ILE 3.3 0.4 - - - -
532A ALA* 1.3 75.0 - - - +
534A CYS* 1.3 63.7 + - - +
536A LYS* 3.3 9.9 + - - +
537A GLU* 3.0 28.5 + - - +
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Residues in contact with CYS 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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362A ALA* 4.2 8.7 - - - -
364A LEU* 4.0 17.5 - - + -
365A LEU* 3.3 51.9 - - - +
368A LEU* 4.5 1.1 - - - -
505A CYS* 4.2 6.3 - - - -
530A ARG 3.0 14.4 + - - +
531A ILE* 3.3 11.0 - - - +
533A SER* 1.3 77.0 - - - +
535A LEU* 1.3 62.3 + - - +
537A GLU* 3.8 6.2 - - - +
538A HIS* 3.1 23.0 + - - +
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Residues in contact with LEU 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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502A ALA* 3.8 36.6 - - + +
505A CYS* 3.7 20.3 - - + -
506A LEU* 3.9 29.2 - - + -
509A LEU* 4.1 14.4 - - + -
531A ILE 2.9 13.9 + - - +
532A ALA* 3.6 8.7 - - - +
534A CYS* 1.3 75.3 - - - +
536A LYS* 1.3 64.8 + - - +
538A HIS* 3.1 8.2 + - + +
539A VAL* 3.0 33.5 + - + +
552A LEU* 4.9 12.6 - - + -
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Residues in contact with LYS 536 (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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532A ALA 2.8 19.7 + - - +
533A SER* 3.6 9.2 - - - +
535A LEU* 1.3 71.8 - - - +
537A GLU* 1.3 63.3 + - - +
539A VAL* 3.2 16.5 + - + +
540A ALA* 3.1 22.7 + - + +
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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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362A ALA* 4.2 24.5 + - + +
533A SER 3.0 18.0 + - - +
534A CYS* 3.8 6.1 - - - +
536A LYS* 1.3 75.6 - - - +
538A HIS* 1.3 58.8 + - - +
540A ALA* 3.3 8.0 + - - +
541A ALA* 3.0 28.8 + - + +
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Residues in contact with HIS 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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365A LEU* 3.7 30.0 - - + +
499A ASP* 3.2 32.5 + - - -
501A PRO* 3.5 23.1 - - + +
502A ALA* 4.0 20.2 - - + -
505A CYS* 5.8 0.4 - - - -
534A CYS 3.1 15.2 + - - +
535A LEU* 3.1 9.4 + - + +
537A GLU* 1.3 76.6 - - - +
539A VAL* 1.3 65.3 + - + +
541A ALA* 4.4 6.3 - - - +
542A VAL* 3.0 53.4 + - + +
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Residues in contact with VAL 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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502A ALA* 5.0 5.6 - - + -
535A LEU* 3.0 40.0 + - + +
536A LYS* 3.2 20.9 - - + +
538A HIS* 1.3 80.5 - - + +
540A ALA* 1.3 57.0 + - + +
542A VAL* 4.8 2.2 - - - +
543A ALA* 3.0 26.8 + - - +
551A CYS* 6.2 5.4 - - + -
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Residues in contact with ALA 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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536A LYS* 3.1 12.3 + - + +
537A GLU* 3.6 10.5 - - - +
538A HIS 3.2 0.2 - - - -
539A VAL* 1.3 76.7 - - + +
541A ALA* 1.3 65.9 + - - +
543A ALA* 3.2 6.0 + - - +
544A GLY 2.9 29.1 + - - +
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Residues in contact with ALA 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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537A GLU* 3.0 18.3 + - + +
538A HIS* 3.4 10.3 + - - +
540A ALA* 1.3 75.1 - - - +
542A VAL* 1.3 62.9 + - + +
544A GLY* 3.1 21.9 + - - -
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Residues in contact with VAL 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ASP* 4.4 13.2 - - - +
538A HIS* 3.0 44.5 + - + +
539A VAL* 4.9 2.2 - - - +
541A ALA* 1.3 76.8 - - + +
543A ALA* 1.3 66.7 + - - +
544A GLY* 3.4 0.3 + - - -
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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
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539A VAL 3.0 23.9 + - - +
540A ALA* 3.2 10.3 + - - +
542A VAL* 1.3 79.3 - - - +
544A GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A ALA* 2.9 17.2 + - - +
541A ALA* 3.1 13.2 + - - -
542A VAL 3.2 0.6 - - - -
543A ALA* 1.3 81.2 - - - +
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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
------------------------------------------------------------
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