Contacts of the helix formed by residues 424 - 436 (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 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A GLU* 4.5 21.5 - - + +
423A ILE* 1.3 76.3 - - - +
425A GLU* 1.3 68.6 + - - +
426A GLU* 4.4 13.9 + - - +
427A MET* 2.8 50.8 + - + +
428A GLU* 3.3 3.6 + - - +
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Residues in contact with GLU 425 (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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423A ILE 3.8 1.2 + - - -
424A THR* 1.3 71.7 - - - +
426A GLU* 1.3 66.2 + - + +
427A MET 2.8 1.6 + - - -
428A GLU* 3.1 18.7 + - - +
429A LYS* 3.2 26.5 + - + +
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Residues in contact with GLU 426 (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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424A THR* 4.6 12.9 + - - +
425A GLU* 1.3 76.7 - - + +
427A MET* 1.3 65.3 + - + +
429A LYS* 3.9 6.1 + - - +
430A GLU* 3.6 18.5 + - - +
635A TRP* 6.0 0.2 - - - -
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Residues in contact with MET 427 (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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422A GLU 3.2 27.8 - - - +
423A ILE* 3.4 14.4 - - + -
424A THR* 2.8 37.1 + - - +
425A GLU 2.8 0.8 + - - -
426A GLU* 1.3 76.4 - - + +
428A GLU* 1.3 67.0 + - - +
429A LYS 3.0 1.3 - - - -
430A GLU* 2.7 17.5 + - - +
431A ILE* 2.8 24.9 + - + +
632A ARG* 6.3 1.8 - - - -
635A TRP* 4.2 47.6 - - + +
643A LEU* 4.9 15.7 - - + -
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Residues in contact with GLU 428 (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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423A ILE* 3.8 40.4 - - + +
424A THR 3.3 3.1 + - - +
425A GLU* 3.1 8.9 + - - +
427A MET* 1.3 78.6 - - - +
429A LYS* 1.3 59.1 + - + +
431A ILE* 3.5 13.8 - - + +
432A LYS* 2.9 33.6 + - - +
631A LYS* 3.9 29.5 + - - +
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Residues in contact with LYS 429 (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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425A GLU* 3.2 24.2 + - + +
426A GLU* 4.1 6.5 - - - +
427A MET 2.8 1.6 + - - -
428A GLU* 1.3 77.6 - - + +
430A GLU* 1.3 61.7 + - - +
432A LYS* 4.6 3.3 - - - +
433A ASN* 3.4 21.0 + - - +
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Residues in contact with GLU 430 (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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426A GLU 3.6 11.3 + - - +
427A MET* 2.7 11.2 + - - +
429A LYS* 1.3 73.2 - - - +
431A ILE* 1.3 69.0 + - + +
433A ASN* 3.4 8.8 - - + +
434A VAL* 3.2 25.5 + - + +
635A TRP* 4.2 9.7 + - + -
638A LEU* 4.0 21.5 - - + +
639A HIS* 3.2 30.7 + - - -
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Residues in contact with ILE 431 (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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423A ILE* 5.5 5.6 - - + -
427A MET* 2.8 35.7 + - + +
428A GLU* 3.5 18.4 - - + +
430A GLU* 1.3 72.9 - - + +
432A LYS* 1.3 55.7 + - - +
433A ASN 2.7 4.6 + - - -
434A VAL* 2.6 39.9 + - + +
435A PHE* 3.2 31.7 + - + +
631A LYS* 4.3 33.7 - - + +
632A ARG* 5.8 0.4 - - - -
634A VAL* 4.4 18.2 - - + -
635A TRP* 5.2 11.9 - - + +
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Residues in contact with LYS 432 (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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428A GLU 2.9 17.6 + - - +
429A LYS* 4.6 4.0 - - - +
431A ILE* 1.3 77.7 - - - +
433A ASN* 1.3 60.9 + - - +
435A PHE* 3.5 10.2 + - + +
436A ARG* 3.3 31.2 + - + +
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Residues in contact with ASN 433 (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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429A LYS 3.4 20.0 + - - +
430A GLU* 3.4 10.1 + - - +
431A ILE 2.7 4.8 + - - -
432A LYS* 1.3 76.0 - - - +
434A VAL* 1.3 70.3 + - - +
435A PHE 3.1 0.9 + - - -
436A ARG* 3.4 42.0 + - - +
454A ARG* 3.8 22.0 + - - +
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Residues in contact with VAL 434 (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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430A GLU* 3.4 17.0 - - + +
431A ILE* 2.6 29.7 + - + +
433A ASN* 1.3 83.6 - - - +
435A PHE* 1.3 58.7 + - + +
444A LEU* 4.3 28.9 - - + -
454A ARG* 3.5 31.6 - - - +
457A ILE* 4.0 25.4 - - + +
458A GLN* 4.0 2.4 + - - -
634A VAL* 4.3 11.9 - - + -
638A LEU* 4.5 15.5 - - + -
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Residues in contact with PHE 435 (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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431A ILE* 3.2 32.6 + - + +
432A LYS* 3.9 11.9 - - + +
433A ASN 3.1 0.6 - - - -
434A VAL* 1.3 78.6 - - - +
436A ARG* 1.3 65.2 + - - +
437A ASN 3.5 1.6 + - - -
457A ILE* 3.3 36.6 - - + -
458A GLN* 3.0 29.1 + - - +
460A LEU* 3.6 14.1 - - + -
461A ASN* 3.3 60.1 + - + +
631A LYS* 5.3 9.4 - - + -
634A VAL* 4.1 11.4 - - + -
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Residues in contact with ARG 436 (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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432A LYS* 3.3 16.2 + - + +
433A ASN* 3.4 40.7 + - - +
435A PHE* 1.3 80.9 - - - +
437A ASN* 1.3 70.4 + - + +
438A GLY* 2.8 11.4 + - - -
454A ARG* 3.5 16.5 + - - -
458A GLN* 4.7 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