Contacts of the helix formed by residues 435 - 450 (chain A) in PDB entry 4CQ8
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 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A LEU* 1.3 75.5 - - - +
436A GLN* 1.3 61.9 - - - +
437A GLU* 3.2 17.7 + - - +
438A GLN* 2.8 59.8 + - - +
439A LYS* 3.1 22.8 + - - +
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Residues in contact with GLN 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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435A ASN* 1.3 70.8 - - - +
437A GLU* 1.3 63.3 + - - +
439A LYS* 3.3 14.6 + - - +
440A LYS* 3.1 26.0 + - - +
487A LYS* 4.8 5.7 - - - +
491A GLU* 2.9 36.7 + - - +
495A TYR* 2.7 41.5 + - - +
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Residues in contact with GLU 437 (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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435A ASN* 3.2 15.0 + - - +
436A GLN* 1.3 77.2 - - - +
438A GLN* 1.3 57.2 + - + +
440A LYS* 3.6 5.6 + - - +
441A GLU* 3.1 50.2 + - - +
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Residues in contact with GLN 438 (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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355A GLN 6.0 1.2 - - - +
356A GLU* 6.2 3.7 - - - +
433A ASP 4.8 0.5 - - - +
434A LEU* 3.4 30.0 - - + +
435A ASN* 2.8 55.7 + - - +
437A GLU* 1.3 74.6 - - + +
439A LYS* 1.3 58.4 + - - +
441A GLU* 3.3 10.5 + - - +
442A ILE* 3.0 38.5 + - + +
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Residues in contact with LYS 439 (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 PRO 4.6 8.8 + - - -
434A LEU* 3.4 33.6 + - + -
435A ASN 3.1 12.9 + - - +
436A GLN* 3.3 23.0 + - - +
438A GLN* 1.3 74.9 - - - +
440A LYS* 1.3 55.4 + - - +
442A ILE* 3.4 9.0 + - - +
443A ALA* 3.0 28.9 + - - +
487A LYS* 5.8 1.0 - - - +
488A PHE* 3.7 34.3 - - + +
491A GLU* 2.8 33.7 + - + +
492A MET* 3.6 14.2 - - - +
495A TYR* 3.8 14.8 - - + -
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Residues in contact with LYS 440 (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 GLN 3.1 17.5 + - - +
437A GLU* 3.8 7.4 - - - +
439A LYS* 1.3 72.8 - - - +
441A GLU* 1.4 65.4 + - + +
443A ALA* 3.3 3.8 + - - +
444A ASP* 3.1 56.8 + - - +
495A TYR* 4.0 40.8 + - + +
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Residues in contact with GLU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLU* 5.4 3.3 - - - +
357A ALA* 3.9 28.2 + - + +
437A GLU* 3.1 44.7 + - + +
438A GLN* 3.3 10.7 + - - +
440A LYS* 1.4 77.1 - - + +
442A ILE* 1.4 61.2 + - + +
444A ASP* 3.4 10.6 + - - +
445A VAL* 3.2 26.0 + - - +
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Residues in contact with ILE 442 (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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355A GLN* 3.3 35.7 - - + +
357A ALA* 5.2 3.1 - - - +
360A LEU* 3.8 20.4 - - + -
430A LEU* 4.1 16.4 - - + -
434A LEU* 3.7 32.1 - - + -
438A GLN* 3.0 24.2 + - + +
439A LYS* 3.6 5.6 - - - +
441A GLU* 1.4 73.5 - - - +
443A ALA* 1.4 55.0 + - - +
445A VAL* 3.0 10.3 + - - +
446A LEU* 2.9 50.7 + - + +
492A MET* 4.0 13.0 - - + -
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Residues in contact with ALA 443 (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 LYS 3.0 10.9 + - - +
440A LYS* 3.3 8.7 + - + +
442A ILE* 1.4 73.6 - - - +
444A ASP* 1.3 57.9 + - - +
446A LEU* 3.2 4.6 + - - +
447A LEU* 3.1 34.7 + - - +
492A MET* 4.0 7.0 - - + -
495A TYR* 3.4 42.2 - - + +
496A THR* 3.7 17.1 - - + +
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Residues in contact with ASP 444 (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 LYS* 3.1 50.8 + - - +
441A GLU* 3.6 12.8 - - - +
443A ALA* 1.3 76.2 - - - +
445A VAL* 1.3 61.6 + - + +
447A LEU* 3.5 11.6 + - - +
448A GLU* 3.2 25.1 + - - +
495A TYR 4.8 3.6 - - - +
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Residues in contact with VAL 445 (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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357A ALA* 3.5 30.3 - - + +
360A LEU* 4.3 7.9 - - + -
361A LYS* 3.7 41.5 - - + +
364A ILE* 4.2 16.2 - - + -
441A GLU 3.2 12.8 + - - +
442A ILE* 3.0 11.3 + - - +
444A ASP* 1.3 75.6 - - + +
446A LEU* 1.4 60.1 + - - +
448A GLU* 3.3 8.2 + - - +
449A THR* 2.9 35.7 + - + +
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Residues in contact with LEU 446 (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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360A LEU* 4.2 9.9 - - + -
364A ILE* 3.7 27.6 - - + -
428A VAL* 3.9 26.2 - - + -
430A LEU* 4.6 0.9 - - + -
442A ILE* 2.9 32.0 + - + +
443A ALA* 3.2 8.2 + - - +
445A VAL* 1.4 75.7 - - - +
447A LEU* 1.4 54.7 + - - +
449A THR* 3.9 2.9 - - - -
450A ASN* 3.1 22.9 + - - -
451A ILE* 3.3 27.6 + - + -
454A MET* 3.6 31.2 - - + -
492A MET* 4.4 4.9 - - + -
496A THR* 4.6 0.7 - - + -
500A ILE* 3.7 13.4 - - + +
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Residues in contact with LEU 447 (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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443A ALA 3.1 21.3 + - - +
444A ASP* 3.8 11.4 - - - +
446A LEU* 1.4 76.1 - - - +
448A GLU* 1.3 62.0 - - - +
450A ASN* 3.6 11.3 + - - +
495A TYR 4.1 5.2 - - - +
496A THR* 3.4 33.9 - - - +
497A ASN* 4.0 22.4 - - - +
499A GLN* 3.7 22.7 - - + -
500A ILE* 4.4 10.3 - - + +
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Residues in contact with GLU 448 (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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361A LYS* 3.2 41.3 + - - +
444A ASP 3.2 17.7 + - - +
445A VAL* 3.3 7.3 + - - +
447A LEU* 1.3 78.0 - - - +
449A THR* 1.4 60.1 + - + +
450A ASN* 3.5 2.6 + - - +
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Residues in contact with THR 449 (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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361A LYS* 3.8 34.5 - - + +
364A ILE* 3.5 28.9 - - + +
365A LEU* 3.9 27.1 - - + +
368A LYS* 3.5 18.9 - - - +
445A VAL* 2.9 34.8 + - + +
446A LEU* 3.7 4.9 + - - -
448A GLU* 1.4 72.7 - - + +
450A ASN* 1.3 69.7 + - - +
451A ILE 4.0 2.3 + - - -
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Residues in contact with ASN 450 (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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213A LYS* 5.3 8.4 - - - +
368A LYS* 3.7 16.0 - - - +
446A LEU 3.1 9.6 + - - -
447A LEU 3.6 6.9 + - - +
448A GLU 3.3 5.8 - - - +
449A THR* 1.3 80.9 - - - +
451A ILE* 1.3 69.4 + - - +
452A ASP* 3.6 8.5 + - - +
500A ILE* 5.1 5.4 - - - +
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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