Contacts of the helix formed by residues 453 - 459 (chain A) in PDB entry 2CKH
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 THR 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A GLN 3.7 9.4 - - - -
441A ASP* 3.9 14.6 - - - +
442A GLU 3.2 19.5 - - - +
443A VAL* 4.5 5.2 - - - +
444A LEU* 3.7 4.0 - - - -
451A THR* 4.9 9.4 - - + +
452A ILE* 1.3 77.0 - - - +
454A ARG* 1.3 56.4 + - - +
455A LYS* 3.0 24.5 - - + +
456A ASP* 2.7 25.4 + - - +
457A ILE* 2.7 35.7 + - - +
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Residues in contact with ARG 454 (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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433A ASN* 3.8 28.7 + - - +
434A VAL* 3.5 25.1 + - - +
436A ARG 3.5 23.8 + - - -
438A GLY* 3.8 17.0 - - - +
439A ASN 3.4 35.7 + - - +
440A GLN* 3.9 12.5 + - - +
442A GLU* 2.9 43.3 + - + +
444A LEU* 3.4 21.8 - - + +
453A THR* 1.3 72.9 - - - +
455A LYS* 1.3 56.9 + - - +
457A ILE* 3.7 3.7 - - - +
458A GLN* 2.8 32.0 + - - +
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Residues in contact with LYS 455 (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 GLN* 3.1 28.7 + - + +
441A ASP* 4.2 12.8 - - - +
453A THR* 3.0 17.4 - - + +
454A ARG* 1.3 75.1 - - - +
456A ASP* 1.3 77.8 + - - +
458A GLN* 3.3 18.7 + - - +
459A THR* 3.7 9.9 - - - +
55B ARG* 3.7 36.7 + - - +
58B ARG* 5.8 1.1 - - - +
88B GLN* 3.0 30.9 - - - +
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Residues in contact with ASP 456 (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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451A THR 3.4 13.2 - - - +
452A ILE* 4.3 4.7 - - + -
453A THR* 2.7 37.9 + - - +
455A LYS* 1.3 87.1 + - - +
457A ILE* 1.3 63.5 + - - +
459A THR* 2.6 31.7 + - - -
467A ASN* 3.5 25.6 + - - +
469A GLU* 4.1 9.8 - - + +
470A ILE* 3.3 22.3 - - + +
58B ARG* 3.6 11.1 + - - -
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Residues in contact with ILE 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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434A VAL* 4.0 23.3 - - + +
435A PHE* 3.3 16.9 - - + -
444A LEU* 3.8 17.3 - - + -
452A ILE* 3.6 22.0 - - + -
453A THR 2.7 20.7 + - - +
454A ARG* 3.7 6.3 - - - +
456A ASP* 1.3 74.6 - - - +
458A GLN* 1.3 63.8 + - - +
459A THR 2.9 1.6 + - - -
460A LEU* 2.9 25.4 + - + +
470A ILE* 4.6 4.3 - - + -
634A VAL* 3.8 32.8 - - + -
637A ILE* 4.8 12.3 - - + -
638A LEU* 5.0 7.9 - - + -
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Residues in contact with GLN 458 (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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434A VAL 4.0 3.2 + - - -
435A PHE* 3.0 40.5 + - - +
436A ARG 4.7 1.6 + - - -
437A ASN* 5.3 1.4 - - - +
440A GLN* 4.4 12.1 + - - +
454A ARG* 2.8 27.8 + - - +
455A LYS* 3.3 12.3 - - - +
456A ASP 3.2 0.6 - - - -
457A ILE* 1.3 75.7 - - - +
459A THR* 1.3 57.4 + - + +
461A ASN* 3.0 41.2 + - - +
464A ASN* 2.8 29.6 + - - +
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Residues in contact with THR 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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455A LYS 3.7 10.3 - - - +
456A ASP* 2.6 21.2 + - - +
457A ILE 2.9 1.8 + - - -
458A GLN* 1.3 76.0 - - + +
460A LEU* 1.3 59.0 + - - +
461A ASN 3.4 0.4 - - - -
464A ASN* 3.3 23.8 - - + +
465A TRP 3.4 20.9 - - - +
466A LEU* 3.1 21.0 - - - +
467A ASN* 3.8 23.9 + - + +
470A ILE* 3.3 19.8 - - - +
630A ARG* 3.9 0.2 + - - -
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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