Contacts of the helix formed by residues 458 - 465 (chain A) in PDB entry 4KSC
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 458 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A PHE* 4.3 3.7 - - - -
375A SER 4.1 9.3 + - - -
376A LYS* 3.7 14.6 + - - +
377A SER 2.5 33.2 + - - +
378A GLY* 4.3 2.7 - - - -
379A HIS 2.6 20.8 + - - +
380A LYS* 3.6 20.1 - - + +
381A PRO* 5.0 0.2 - - - +
457A ILE* 1.3 73.2 - - - +
459A VAL* 1.3 65.7 + - - +
460A ARG* 3.1 13.7 - - - +
461A TYR* 2.8 32.0 + - + +
462A LEU* 3.1 20.4 + - - +
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Residues in contact with VAL 459 (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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372A ASP 4.7 0.4 - - - +
373A SER* 3.2 36.3 - - - +
374A PHE* 4.4 10.1 - - + +
375A SER* 6.2 0.7 - - - -
438A ARG* 3.5 37.7 - - + +
457A ILE 3.4 0.6 + - - -
458A ASN* 1.3 73.1 - - - +
460A ARG* 1.3 68.3 + - - +
462A LEU* 2.9 19.4 + - + +
463A ARG* 3.1 48.4 + - - +
906A LEU* 4.1 9.6 - - + -
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Residues in contact with ARG 460 (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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375A SER* 4.2 33.2 + - - +
380A LYS* 6.4 0.7 - - - -
458A ASN* 3.1 13.5 + - - +
459A VAL* 1.3 79.8 - - - +
461A TYR* 1.3 63.0 + - - +
463A ARG* 3.7 4.2 + - - +
464A GLU* 3.2 39.0 + - - +
906A LEU* 3.4 42.8 + - + +
909A GLU* 5.2 6.1 - - - +
910A GLN* 5.2 11.7 - - - +
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Residues in contact with TYR 461 (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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380A LYS* 3.5 30.5 - - + -
381A PRO* 3.0 52.7 + - + -
384A ILE* 4.0 21.7 + - - +
457A ILE* 5.8 1.1 - - + -
458A ASN* 2.8 23.9 + - + +
460A ARG* 1.3 74.6 - - - +
462A LEU* 1.3 67.3 + - - +
464A GLU* 3.1 29.6 + - - +
465A ILE* 3.1 49.4 + - + +
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Residues in contact with LEU 462 (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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436A MET* 4.2 1.1 - - + +
437A GLN* 4.0 11.7 - - - +
438A ARG* 3.9 20.9 - - + -
449A ILE* 5.0 11.4 - - + -
454A ILE* 3.5 33.4 - - + -
457A ILE* 3.8 24.7 - - + -
458A ASN 3.1 13.5 + - - +
459A VAL* 2.9 13.6 + - + +
461A TYR* 1.3 76.2 - - - +
463A ARG* 1.3 64.6 + - - +
465A ILE* 2.9 25.6 + - + -
466A ILE* 3.0 31.4 + - + +
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Residues in contact with ARG 463 (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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155A GLU* 5.1 1.8 - - - +
156A ILE* 5.1 2.8 - - - +
372A ASP 5.9 0.2 + - - -
373A SER* 4.8 11.7 - - - -
437A GLN* 3.3 26.9 + - - +
438A ARG* 4.5 7.9 + - - +
439A LEU* 3.9 22.0 - - - +
459A VAL* 3.1 37.2 + - - +
460A ARG 4.0 3.6 - - - +
461A TYR 3.4 0.2 - - - -
462A LEU* 1.3 78.3 - - - +
464A GLU* 1.3 55.1 + - - +
466A ILE* 2.7 22.5 - - - +
543A ARG* 2.3 26.7 + - - +
903A VAL* 2.3 53.1 + - - +
904A VAL* 3.2 26.4 - - - +
905A SER 3.8 8.7 - - - +
906A LEU* 3.9 16.5 - - + +
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Residues in contact with GLU 464 (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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460A ARG* 3.2 31.1 - - - +
461A TYR* 3.1 28.0 + - - +
462A LEU 3.0 1.0 - - - -
463A ARG* 1.3 77.9 - - - +
465A ILE* 1.3 64.4 + - + +
466A ILE 3.6 0.3 + - - -
543A ARG* 3.5 36.6 - - - +
545A PRO* 3.9 7.3 - - - +
905A SER 4.9 5.6 - - - +
906A LEU* 5.8 1.0 - - + +
907A THR* 5.3 8.9 - - + +
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Residues in contact with ILE 465 (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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381A PRO* 5.8 0.2 - - + -
384A ILE* 6.4 2.7 - - + -
385A GLN* 6.3 2.9 - - - +
449A ILE* 5.6 6.3 - - + -
461A TYR* 3.2 54.5 - - + +
462A LEU* 2.9 13.7 + - + +
464A GLU* 1.3 82.7 - - + +
466A ILE* 1.3 60.7 + - + +
545A PRO* 3.3 6.9 - - - +
546A LYS* 4.0 33.2 - - + +
547A ILE* 3.0 45.8 + - + +
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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