Contacts of the helix formed by residues 523 - 535 (chain I) in PDB entry 6KC4
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 ASN 523 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468G ILE* 4.4 17.9 - - + +
469G GLU* 6.5 0.4 - - + -
514I TYR* 3.8 11.7 - - - -
521I PHE* 3.2 9.1 - - - +
522I SER* 1.3 97.3 + - - +
524I ILE* 1.3 63.2 + - - +
525I PRO* 3.3 16.0 - - + +
526I GLN* 2.9 43.8 + - - +
527I LEU* 3.4 14.4 + - - +
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Residues in contact with ILE 524 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455I LEU* 4.1 20.9 - - + -
460I TRP* 4.3 4.7 - - + -
482I VAL* 4.5 3.1 - - + -
492I TYR* 3.4 52.7 - - + -
507I ILE* 4.0 21.3 - - + -
514I TYR* 3.5 32.0 - - + -
523I ASN* 1.3 70.4 - - - +
525I PRO* 1.3 75.0 - - + +
527I LEU* 3.0 8.0 + - + +
528I ILE* 2.9 38.6 + - + +
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Residues in contact with PRO 525 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469G GLU* 5.7 1.1 - - - +
453I LYS 3.8 13.9 - - - +
455I LEU* 4.1 22.7 - - + +
458I GLN* 3.7 33.0 - - + +
460I TRP* 3.9 12.3 - - + -
523I ASN* 3.3 17.3 - - + +
524I ILE* 1.3 91.4 - - + +
526I GLN* 1.3 59.7 + - - +
528I ILE* 3.5 1.4 + - - +
529I ASP* 2.9 31.0 + - - +
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Residues in contact with GLN 526 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A LYS* 3.1 41.2 + - - +
497A TYR* 3.3 24.3 + - - +
502A ARG* 4.4 12.2 - - - +
521I PHE* 3.7 18.7 - - + -
522I SER* 5.5 2.0 - - - +
523I ASN* 2.9 33.7 + - - +
524I ILE 3.2 0.2 - - - -
525I PRO* 1.3 77.4 - - + +
527I LEU* 1.3 66.5 + - - +
529I ASP* 3.9 11.3 - - - +
530I HIS* 3.0 23.9 + - - +
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Residues in contact with LEU 527 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507I ILE* 3.7 33.7 - - + -
514I TYR* 4.3 2.9 - - + -
515I ARG* 4.1 18.6 - - - +
516I PHE* 3.7 31.2 - - + +
519I THR 4.9 0.7 - - - +
521I PHE* 3.5 40.7 - - + -
523I ASN 3.4 8.1 + - - +
524I ILE* 3.0 10.0 + - - +
526I GLN* 1.3 77.9 - - - +
528I ILE* 1.3 64.4 + - + +
530I HIS* 3.3 9.0 + - - +
531I HIS* 3.3 38.4 + - + +
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Residues in contact with ILE 528 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460I TRP* 3.9 29.4 - - + +
480I PHE* 3.8 29.4 - - + -
482I VAL* 4.0 16.6 - - + -
494I LEU* 4.1 23.3 - - + -
507I ILE* 4.8 3.1 - - + -
516I PHE* 4.7 12.6 - - + -
524I ILE* 2.9 34.1 + - + +
525I PRO 3.9 3.1 - - - +
527I LEU* 1.3 76.2 - - + +
529I ASP* 1.3 59.7 + - - +
531I HIS* 3.1 5.6 + - - +
532I TYR* 2.8 26.9 + - + +
546I LEU* 4.1 8.6 - - + +
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Residues in contact with ASP 529 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A LYS 4.4 5.1 - - - +
476A LYS* 2.9 45.2 + - - +
525I PRO 2.9 19.3 + - - +
526I GLN* 4.0 13.2 - - - +
528I ILE* 1.3 74.4 - - - +
530I HIS* 1.3 60.9 + - - +
532I TYR* 4.2 16.2 - - - +
533I THR* 2.8 43.4 + - - -
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Residues in contact with HIS 530 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A GLN* 4.9 0.4 + - - -
497A TYR* 5.2 6.2 - - + +
499A ASP* 3.8 28.7 - - + -
500A GLY* 3.6 13.8 + - - -
519I THR* 5.8 0.8 + - - -
521I PHE* 3.7 25.4 - + + -
526I GLN 3.0 14.2 + - - +
527I LEU 3.5 8.3 - - - +
528I ILE 3.2 0.4 - - - -
529I ASP* 1.3 77.2 - - - +
531I HIS* 1.3 81.2 + + - +
533I THR* 4.9 1.6 - - - -
534I THR* 2.8 61.4 + - + +
536I GLN* 4.2 15.8 - - + +
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Residues in contact with HIS 531 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516I PHE* 3.8 16.5 - + + +
527I LEU* 3.3 34.7 + - + +
528I ILE* 3.1 7.2 + - - +
530I HIS* 1.3 94.2 - + - +
532I TYR* 1.3 58.2 + - - +
534I THR* 4.1 3.4 - - - -
535I LYS* 2.9 31.0 + - - +
536I GLN* 2.9 27.7 + - + +
537I VAL 3.2 22.2 + - - -
538I ILE* 3.7 23.5 - - + +
546I LEU* 3.9 23.5 + - + +
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Residues in contact with TYR 532 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480I PHE* 3.9 24.5 - + + -
528I ILE* 2.8 17.7 + - + +
529I ASP* 4.0 18.4 - - - +
531I HIS* 1.3 77.2 - - - +
533I THR* 1.3 64.1 + - - +
535I LYS* 2.9 43.1 + - - +
546I LEU* 3.9 10.7 - - + +
547I LEU 3.3 29.3 + - - -
549I PRO* 3.9 21.1 - - + +
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Residues in contact with THR 533 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LYS* 4.4 11.9 + - + +
477A GLN* 3.9 32.8 - - + +
529I ASP* 2.8 37.9 + - - -
530I HIS* 4.1 2.7 - - - -
532I TYR* 1.3 84.5 - - - +
534I THR* 1.3 61.5 + - - +
535I LYS* 3.5 5.1 + - - +
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Residues in contact with THR 534 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A GLN* 3.7 40.6 - - + +
499A ASP* 4.9 2.2 - - - +
530I HIS* 2.8 37.5 + - + +
533I THR* 1.3 78.9 - - - +
535I LYS* 1.3 67.5 + - - +
536I GLN* 3.1 39.3 + - - +
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Residues in contact with LYS 535 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531I HIS 2.9 12.8 + - - +
532I TYR* 2.9 40.3 + - - +
533I THR 4.5 4.0 - - - +
534I THR* 1.3 79.2 - - - +
536I GLN* 1.3 67.5 + - - +
537I VAL* 3.5 2.9 + - - +
545I VAL* 3.9 30.9 - - + +
546I LEU 2.8 29.2 + - - +
547I LEU* 4.0 16.1 + - + +
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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