Contacts of the helix formed by residues 456 - 466 (chain A) in PDB entry 5IKP
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 ALA 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A VAL* 1.3 79.8 - - - +
457A ARG* 1.3 57.5 + - - +
458A ILE* 4.0 10.3 - - + -
459A HIS* 2.9 5.7 + - + +
460A SER* 2.7 31.7 + - - -
481A ASN* 3.2 4.9 - - - -
483A THR* 4.0 4.5 - - + -
673A ALA 3.4 25.1 - - - +
674A SER* 3.9 11.4 - - - +
694A GLY 4.9 3.6 - - - -
695A ALA* 5.8 0.7 - - - -
698A GLU* 3.5 12.8 - - - +
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Residues in contact with ARG 457 (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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456A ALA* 1.3 69.4 - - - +
458A ILE* 1.3 65.5 - - - +
460A SER* 3.4 2.5 + - - -
461A GLU* 3.1 39.1 + - - +
481A ASN* 3.2 30.2 + - + +
483A THR* 3.7 1.2 + - - -
697A VAL* 5.3 0.4 - - - +
698A GLU* 2.8 43.7 + - - +
701A GLU* 2.8 42.8 + - - -
810A LYS* 4.4 16.6 - - - +
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Residues in contact with ILE 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A ALA* 4.0 11.0 - - + -
457A ARG* 1.3 76.9 - - + +
459A HIS* 1.4 60.1 + - - +
461A GLU* 3.3 15.6 + - + +
462A ILE* 3.3 24.0 + - + +
673A ALA 4.9 0.7 - - - +
694A GLY* 3.5 30.3 - - - +
697A VAL* 3.8 31.6 - - + -
698A GLU* 3.3 24.2 - - + +
715A VAL* 6.3 2.7 - - + -
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Residues in contact with HIS 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASN* 3.0 31.7 + - - -
377A HIS 3.4 13.3 + - - -
379A VAL* 3.6 30.2 - - + +
454A GLY* 4.0 0.6 - - - -
455A VAL* 3.2 26.9 + - + +
456A ALA* 2.9 9.3 + - + +
458A ILE* 1.4 73.9 - - - +
460A SER* 1.3 58.0 + - - +
462A ILE* 2.9 33.4 + - - +
463A VAL* 3.0 30.5 + - + +
673A ALA* 3.5 40.2 - - + +
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Residues in contact with SER 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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454A GLY* 3.2 17.8 - - - -
456A ALA 2.7 18.1 + - - -
457A ARG 3.4 6.3 - - - -
459A HIS* 1.3 71.2 - - - +
461A GLU* 1.3 62.1 + - - +
463A VAL* 3.4 12.2 - - - +
464A LYS* 3.3 29.8 + - - +
480A GLN 3.8 10.9 - - - +
481A ASN* 2.7 42.1 + - - -
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Residues in contact with GLU 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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457A ARG* 3.1 31.0 + - - +
458A ILE* 3.5 11.9 - - - +
459A HIS 3.2 0.4 - - - -
460A SER* 1.3 77.6 - - - +
462A ILE* 1.3 52.9 + - + +
464A LYS* 3.3 32.7 + - + +
465A GLN* 2.9 43.9 + - + +
472A TYR* 5.4 1.6 + - - -
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Residues in contact with ILE 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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379A VAL* 4.3 21.8 - - + -
380A LEU* 5.5 1.6 - - - +
458A ILE* 3.3 26.5 - - + +
459A HIS* 2.9 18.5 + - - +
461A GLU* 1.3 73.2 - - + +
463A VAL* 1.3 58.9 + - - +
465A GLN* 4.8 6.7 - - - +
466A SER* 2.7 51.0 + - - +
467A VAL* 2.9 13.9 + - + -
715A VAL* 6.6 0.4 - - + -
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Residues in contact with VAL 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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376A ASN* 4.3 14.4 - - + +
379A VAL* 6.2 0.2 - - - -
452A VAL* 4.7 7.9 - - + -
453A ASN 5.2 5.8 - - - +
454A GLY* 4.8 3.1 - - - -
459A HIS* 3.0 42.3 + - + +
460A SER* 3.4 12.8 - - - +
462A ILE* 1.3 74.7 - - - +
464A LYS* 1.3 56.8 - - - +
467A VAL* 3.7 13.0 - - + -
468A PHE* 2.8 60.3 + - + +
479A PHE* 4.2 11.9 - - + -
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Residues in contact with LYS 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 SER* 3.3 17.3 + - - +
461A GLU* 3.4 36.3 + - + +
463A VAL* 1.3 77.3 - - - +
465A GLN* 1.3 65.6 + - + +
469A LYS* 3.3 19.8 + - - -
472A TYR* 3.3 46.2 + - + +
476A PRO 5.2 0.7 - - - -
479A PHE* 3.7 51.3 + - + -
480A GLN* 4.4 11.5 + - - +
481A ASN* 5.7 2.4 - - - +
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Residues in contact with GLN 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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461A GLU* 2.9 22.7 + - + +
462A ILE* 4.7 6.9 - - - +
464A LYS* 1.3 76.9 - - + +
466A SER* 1.3 65.0 - - - +
469A LYS* 3.3 24.8 - - - +
472A TYR* 4.9 7.4 - - + -
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Residues in contact with SER 466 (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* 4.7 4.3 - - - +
462A ILE* 2.7 46.3 + - - +
464A LYS 3.4 0.2 - - - -
465A GLN* 1.3 84.6 - - - +
467A VAL* 1.3 66.3 + - - +
468A PHE 3.4 1.9 + - - -
469A LYS* 3.6 12.5 + - - +
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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