Contacts of the helix formed by residues 530 - 539 (chain A) in PDB entry 4KYI
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 TRP 530 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A VAL* 4.2 8.1 - - + -
471A GLN* 3.3 64.6 + - + +
474A LEU* 4.2 9.4 - - + -
475A ASP* 5.8 0.4 - - - -
514A TYR* 3.6 36.9 + + - -
515A LEU* 3.6 29.2 - - + -
518A VAL* 3.4 21.6 - - + +
529A SER* 1.3 81.0 + - - +
531A ALA* 1.3 64.0 + - - +
532A THR 3.0 10.0 + - - -
533A LYS* 3.5 9.2 + - - +
534A ILE* 3.3 33.4 + - + +
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Residues in contact with ALA 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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515A LEU* 3.5 43.7 - - + +
518A VAL* 4.2 12.1 - - + -
519A GLU* 4.2 9.0 - - + -
529A SER* 3.2 10.7 + - - +
530A TRP* 1.3 85.8 - - + +
532A THR* 1.3 61.4 + - - +
533A LYS 3.5 0.2 - - - -
534A ILE* 4.0 2.7 - - - -
535A LEU* 3.1 30.3 + - - +
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Residues in contact with THR 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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338A ARG* 3.3 3.6 + - - -
342A LEU* 4.3 16.6 - - + -
519A GLU* 3.7 24.6 + - - +
529A SER* 3.5 28.4 + - - -
530A TRP 3.0 0.8 - - - -
531A ALA* 1.3 79.1 - - - +
533A LYS* 1.3 59.3 + - + +
536A ASN* 2.9 43.2 + - - +
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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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478A GLU* 3.3 33.9 + - - -
492A LYS* 5.5 2.0 - - - +
493A GLU* 5.1 11.0 - - - +
496A PHE* 4.8 5.2 - - - -
530A TRP 3.5 7.3 + - - +
532A THR* 1.3 78.2 - - + +
534A ILE* 1.3 76.6 + - - +
536A ASN* 3.3 12.7 + - + +
537A LEU* 3.1 35.9 + - + +
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Residues in contact with ILE 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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474A LEU* 4.1 21.3 - - + -
475A ASP* 6.0 1.6 - - - +
478A GLU* 5.5 0.4 - - - +
496A PHE* 3.8 32.3 - - + -
500A ILE* 3.6 25.9 - - + +
511A LEU* 5.3 0.4 - - + -
515A LEU* 3.6 28.7 - - + -
530A TRP* 3.3 36.1 - - + +
531A ALA 4.2 0.2 - - - +
532A THR 3.4 0.4 - - - -
533A LYS* 1.3 87.5 - - - +
535A LEU* 1.3 57.5 + - - +
537A LEU* 3.7 0.4 + - + -
538A LEU* 3.0 26.2 + - - +
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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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338A ARG* 3.3 30.3 - - - +
512A GLU* 4.2 17.3 - - + -
515A LEU* 3.3 45.8 - - + +
516A ASN* 3.3 27.8 - - - +
519A GLU* 3.5 8.3 - - - +
531A ALA 3.1 18.4 + - - +
534A ILE* 1.3 76.3 - - - +
536A ASN* 1.3 64.5 + - - +
538A LEU* 3.3 9.7 + - + +
539A TRP* 3.0 39.0 + - - +
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Residues in contact with ASN 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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335A PHE* 3.4 14.9 - - + -
338A ARG* 2.4 29.2 + - - +
339A MET* 3.3 38.4 - - + +
342A LEU* 4.1 5.3 - - - +
532A THR* 2.9 34.9 + - - +
533A LYS* 3.3 14.0 + - + +
535A LEU* 1.3 77.8 - - - +
537A LEU* 1.3 59.6 + - + +
539A TRP* 3.1 4.5 + - - +
540A ALA 3.1 20.6 + - - -
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Residues in contact with LEU 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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493A GLU* 3.2 43.5 - - + +
496A PHE* 3.6 39.3 - - + -
497A ALA* 3.5 26.4 - - + +
500A ILE* 3.8 13.2 - - + -
501A LYS* 3.7 5.5 - - - -
533A LYS* 3.1 27.4 + - + +
536A ASN* 1.3 74.3 - - + +
538A LEU* 1.3 65.1 + - - +
539A TRP 3.1 1.8 - - - -
540A ALA* 3.1 23.0 + - + +
544A TRP* 5.3 4.0 - - + -
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Residues in contact with LEU 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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357A SER* 3.6 32.9 + - - +
500A ILE* 3.9 19.2 - - + +
501A LYS* 3.1 34.0 + - + -
504A ASN* 3.3 36.3 - - + +
511A LEU* 6.0 0.2 - - + -
512A GLU* 4.0 13.2 - - + -
515A LEU* 5.0 4.0 - - + -
534A ILE 3.0 19.4 + - - +
535A LEU* 3.4 14.6 - - + +
537A LEU* 1.3 77.7 - - - +
539A TRP* 1.3 70.4 + - + +
540A ALA 3.4 0.2 - - - -
603A GOL 4.9 1.6 - - - +
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Residues in contact with TRP 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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331A ALA 4.5 2.3 - - - +
334A TRP* 3.9 51.3 - + + +
335A PHE* 3.2 24.2 + - + +
338A ARG* 3.8 35.1 - - + +
355A THR 4.1 9.0 - - - -
356A SER* 3.5 29.2 - - - -
357A SER* 3.4 29.2 - - - -
359A LEU* 4.9 7.9 - - + -
501A LYS* 4.5 0.2 - - - -
512A GLU* 3.5 12.5 + - - -
516A ASN* 5.5 1.8 + - - +
535A LEU* 3.0 35.3 + - + +
536A ASN* 3.8 4.0 - - - +
537A LEU 3.1 0.4 - - - -
538A LEU* 1.3 87.9 - - + +
540A ALA* 1.3 64.9 + - - +
541A PRO* 4.5 0.3 - - - +
601A EDO 4.4 12.9 + - - -
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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