Contacts of the helix formed by residues 513 - 525 (chain A) in PDB entry 1KK8
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 GLY 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486A GLN* 5.0 2.6 + - - -
512A PHE* 1.3 96.1 - - - +
514A MET* 1.3 63.8 + - - +
515A ASP 3.6 1.6 - - - -
516A LEU* 4.3 13.5 - - - +
517A GLN* 3.7 21.0 + - - +
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Residues in contact with MET 514 (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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511A ASP* 3.6 39.9 - - + +
512A PHE 3.9 2.6 + - - +
513A GLY* 1.3 75.9 - - - +
515A ASP* 1.3 69.2 + - - +
516A LEU 3.3 0.2 - - - -
517A GLN* 3.5 4.3 + - - +
518A MET* 2.8 32.3 + - - +
560A ARG* 6.1 0.7 - - - +
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Residues in contact with ASP 515 (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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513A GLY* 4.6 0.2 - - - -
514A MET* 1.3 79.8 + - - +
516A LEU* 1.3 60.2 + - - +
518A MET* 3.8 2.7 - - - -
519A CYS* 2.9 27.4 + - - +
560A ARG* 3.5 26.0 + - - -
561A MET* 3.2 27.0 - - + +
583A TYR* 6.5 0.4 - - + -
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Residues in contact with LEU 516 (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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482A GLU* 3.4 43.7 - - + +
485A GLN* 4.3 4.9 - - + -
486A GLN* 3.6 41.3 - - + +
489A ASN* 4.5 10.3 - - + -
513A GLY* 4.2 15.1 + - - +
514A MET 3.3 0.4 - - - -
515A ASP* 1.3 80.5 - - - +
517A GLN* 1.3 62.5 + - - +
519A CYS* 3.3 3.7 + - - +
520A ILE* 3.1 28.0 + - + +
583A TYR* 3.9 36.5 - - + -
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Residues in contact with GLN 517 (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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486A GLN* 3.4 22.8 - - - +
513A GLY 3.7 15.7 + - - +
514A MET* 3.5 5.5 + - - +
515A ASP 3.3 0.2 - - - -
516A LEU* 1.3 79.6 - - - +
518A MET* 1.3 57.8 + - - +
520A ILE* 3.2 17.0 + - - +
521A ASP* 2.8 53.3 + - - +
525A LYS* 4.8 3.9 + - - +
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Residues in contact with MET 518 (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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514A MET* 2.8 19.8 + - - +
515A ASP* 3.4 7.2 - - - +
516A LEU 3.2 0.2 - - - -
517A GLN* 1.3 77.6 - - - +
519A CYS* 1.3 60.4 + - - +
521A ASP* 3.4 7.7 + - - +
522A LEU* 3.1 23.0 + - - +
559A ASN* 3.5 19.4 + - - +
560A ARG* 2.7 57.2 - - + +
561A MET* 3.2 29.3 - - + +
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Residues in contact with CYS 519 (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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482A GLU* 3.3 41.5 - - - +
515A ASP 2.9 16.3 + - - +
516A LEU* 3.3 4.2 + - - +
518A MET* 1.3 75.7 - - - +
520A ILE* 1.3 62.3 + - - +
522A LEU* 3.4 6.7 + - - +
523A ILE* 3.3 30.7 + - - +
561A MET* 4.3 14.1 - - + +
580A LEU* 5.3 4.7 - - - -
581A HIS 4.1 17.9 - - - +
582A HIS* 4.0 14.6 - - - -
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Residues in contact with ILE 520 (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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479A TYR* 4.6 4.7 - - + -
482A GLU* 3.9 33.9 - - + +
483A ARG* 3.8 18.6 - - + -
486A GLN* 3.6 37.0 - - - +
516A LEU* 3.1 21.0 + - + +
517A GLN* 3.2 16.8 + - - +
519A CYS* 1.3 77.9 - - - +
521A ASP* 1.3 58.7 + - - +
523A ILE* 3.2 7.2 + - - +
524A GLU* 2.9 55.4 + - + +
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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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517A GLN* 2.8 51.7 + - - +
518A MET* 3.8 7.9 + - - +
519A CYS 3.3 0.2 - - - -
520A ILE* 1.3 71.9 - - - +
522A LEU* 1.3 66.2 + - - +
523A ILE 3.0 1.8 - - - -
525A LYS* 2.8 72.8 + - + +
528A GLY* 4.2 1.6 - - - -
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Residues in contact with LEU 522 (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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518A MET 3.1 13.7 + - - +
519A CYS* 3.5 11.9 - - - +
521A ASP* 1.3 77.1 - - - +
523A ILE* 1.3 57.4 + - + +
528A GLY* 3.1 4.3 - - - -
529A ILE* 2.8 30.8 + - + +
555A HIS* 3.6 39.9 - - + +
559A ASN* 3.8 18.2 - - - +
561A MET* 3.8 20.9 - - + -
562A PHE* 4.0 11.7 - - + +
580A LEU* 3.3 34.3 - - + -
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Residues in contact with ILE 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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475A LEU* 3.9 15.5 - - + -
479A TYR* 3.8 35.9 - - + -
519A CYS* 3.3 20.9 - - - +
520A ILE* 3.2 6.2 + - - +
521A ASP 3.0 0.6 - - - -
522A LEU* 1.3 79.8 - - - +
524A GLU* 1.3 60.2 + - - +
525A LYS 3.8 0.4 - - - -
528A GLY 3.9 0.7 - - - -
529A ILE* 3.5 22.4 + - + +
530A LEU* 3.1 49.0 + - + +
531A SER 4.5 0.2 + - - -
580A LEU* 3.2 35.9 - - + -
582A HIS* 5.4 2.0 - - + -
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Residues in contact with GLU 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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479A TYR* 2.3 46.5 + - + +
483A ARG* 2.9 23.6 + - - -
520A ILE* 2.9 40.9 + - + +
523A ILE* 1.3 74.8 - - + +
525A LYS* 1.3 90.3 + - - +
526A PRO* 4.6 0.3 - - - +
530A LEU* 4.9 1.3 - - - -
650A ARG* 3.3 30.1 + - + +
654A ASN* 5.2 1.8 - - - +
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Residues in contact with LYS 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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517A GLN* 4.8 4.8 - - - +
521A ASP* 2.8 61.0 + - + +
524A GLU* 1.3 105.2 + - - +
526A PRO* 1.4 71.1 - - + +
527A MET* 3.1 11.2 - - + +
528A GLY* 2.7 21.5 + - - +
531A SER* 2.9 9.8 + - - -
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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