Contacts of the helix formed by residues 520 - 528 (chain A) in PDB entry 2KFN
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 LYS 520 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517A GLN* 3.6 26.3 + - - +
519A HIS* 1.3 71.9 - - - +
521A GLY* 1.3 65.0 + - - +
523A LEU* 3.9 17.1 - - + +
524A ASN* 3.0 24.9 + - - +
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Residues in contact with GLY 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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519A HIS* 4.3 1.0 - - - +
520A LYS* 1.3 77.1 - - - +
522A PRO* 1.3 70.4 - - - +
524A ASN* 3.1 15.0 + - - +
525A VAL* 3.2 10.4 + - - +
816A GLU* 5.2 4.3 - - - -
819A ASP 3.6 7.6 - - - +
820A GLY* 3.6 22.2 - - - -
822A ARG* 5.3 1.7 - - - +
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Residues in contact with PRO 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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448A ILE* 3.2 38.2 - - + +
449A LEU* 5.6 3.4 - - + +
516A LEU* 4.3 9.4 - - + +
519A HIS* 3.7 22.4 - - + +
521A GLY* 1.3 85.5 - - - +
523A LEU* 1.3 64.9 + - - +
525A VAL* 3.3 4.7 + - + +
526A PHE* 3.0 21.7 + - - +
820A GLY 3.7 11.2 - - - +
821A ARG* 5.3 1.1 - - - +
822A ARG* 3.7 31.6 - - + +
824A TYR* 5.8 0.4 - - - +
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Residues in contact with LEU 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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513A TRP* 3.6 36.6 - - + -
516A LEU* 3.4 23.5 + - + +
517A GLN* 4.4 13.0 - - + +
519A HIS 3.3 18.6 + - - +
520A LYS* 3.9 20.0 - - + +
521A GLY 3.2 0.6 - - - -
522A PRO* 1.3 77.7 - - - +
524A ASN* 1.3 59.2 + - - +
526A PHE* 3.4 3.0 + - + +
527A GLU* 3.0 60.4 + - + +
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Residues in contact with ASN 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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520A LYS 3.0 19.7 + - - +
521A GLY* 3.1 3.8 + - - +
523A LEU* 1.3 80.5 - - - +
525A VAL* 1.3 58.3 + - - +
527A GLU* 4.8 0.7 - - - -
528A ASN* 3.0 54.4 + - - +
529A ILE* 4.7 2.4 - - - +
819A ASP* 2.8 44.1 + - - +
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Residues in contact with VAL 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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448A ILE* 3.7 17.0 - - + -
521A GLY 3.2 5.9 + - - +
522A PRO* 3.8 7.0 - - + +
524A ASN* 1.3 76.6 - - - +
526A PHE* 1.3 58.3 + - - +
529A ILE* 3.0 22.5 + - + +
530A GLU* 2.9 28.5 + - + +
819A ASP* 3.5 25.4 - - + +
821A ARG* 3.4 63.9 - - + +
854A ASP* 4.3 1.8 - - - +
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Residues in contact with PHE 526 (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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439A ALA 4.2 1.3 - - - -
440A PHE* 4.0 20.6 - + - -
441A ASP 4.1 1.3 - - - -
444A LEU* 3.9 20.6 - - + -
445A GLU* 3.5 37.0 - - + -
448A ILE* 4.0 13.0 - - + +
513A TRP* 3.9 30.1 - + - -
516A LEU* 4.0 13.5 - - + -
522A PRO 3.0 17.1 + - - +
523A LEU* 3.7 3.4 - - + +
525A VAL* 1.3 78.0 - - - +
527A GLU* 1.3 67.3 + - + +
530A GLU* 4.2 7.0 - - + -
531A MET* 3.0 66.2 + - + +
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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
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440A PHE* 5.9 0.5 - - - -
513A TRP* 4.0 14.0 - - + -
523A LEU* 3.0 50.2 + - + +
524A ASN* 5.5 0.3 - - - -
526A PHE* 1.3 88.4 - - + +
528A ASN* 1.3 76.8 + - - +
531A MET* 4.5 4.5 - - - +
532A PRO* 3.5 16.5 - - - +
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Residues in contact with ASN 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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524A ASN* 3.0 36.7 + - - +
527A GLU* 1.3 94.0 + - - +
529A ILE* 1.3 66.9 + - + +
532A PRO* 3.7 15.1 - - - +
858A ARG* 5.4 1.6 - - - +
861A ILE* 3.8 10.0 - - - +
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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