Contacts of the helix formed by residues 435 - 450 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434B LEU* 1.3 75.6 - - - +
436B GLN* 1.3 61.9 + - - +
437B GLU* 3.2 24.1 + - - +
438B GLN* 2.8 59.4 + - - +
439B LYS* 3.1 23.2 + - - +
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Residues in contact with GLN 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B ASN* 1.3 74.2 - - - +
437B GLU* 1.3 67.8 + - - +
439B LYS* 3.3 15.8 + - - +
440B LYS* 3.1 30.7 + - - +
487B LYS* 5.0 3.6 - - - +
491B GLU* 2.9 35.1 + - - +
495B TYR* 2.7 41.1 + - - +
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B ASN* 3.2 24.4 + - - +
436B GLN* 1.3 84.6 + - - +
438B GLN* 1.4 56.5 + - + +
440B LYS* 3.6 6.4 + - - +
441B GLU* 3.1 41.3 + - - +
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Residues in contact with GLN 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B GLN 6.0 1.2 - - - +
356B GLU* 6.2 3.3 - - - +
433B ASP 4.8 0.3 - - - +
434B LEU* 3.4 30.6 - - + +
435B ASN* 2.8 54.5 + - - +
437B GLU* 1.4 74.5 - - + +
439B LYS* 1.3 58.1 + - - +
441B GLU* 3.3 10.6 + - - +
442B ILE* 3.0 37.9 + - + +
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Residues in contact with LYS 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B PRO 4.5 9.2 + - - -
434B LEU* 3.4 34.2 + - + -
435B ASN 3.1 14.2 + - - +
436B GLN* 3.3 23.1 + - - +
438B GLN* 1.3 73.9 - - - +
440B LYS* 1.3 56.1 + - - +
442B ILE* 3.4 8.8 + - - +
443B ALA* 3.0 29.3 + - - +
488B PHE* 3.7 33.8 - - + +
491B GLU* 2.8 34.0 + - + +
492B MET* 3.7 13.6 - - - +
495B TYR* 3.8 14.6 - - + -
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Residues in contact with LYS 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B GLN 3.1 17.6 + - - +
437B GLU* 3.8 7.2 - - - +
439B LYS* 1.3 73.2 - - - +
441B GLU* 1.4 65.4 + - + +
443B ALA* 3.3 4.2 + - - +
444B ASP* 3.1 55.5 + - - +
495B TYR* 4.0 40.3 + - + +
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Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B GLU* 5.4 2.9 - - - +
357B ALA* 3.9 26.9 + - + +
437B GLU* 3.1 27.3 + - - +
438B GLN* 3.3 10.1 + - - +
440B LYS* 1.4 77.7 - - + +
442B ILE* 1.3 61.5 + - + +
444B ASP* 3.4 11.4 + - - +
445B VAL* 3.2 26.2 + - - +
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B GLN* 3.3 36.1 - - + +
357B ALA* 5.2 3.4 - - - +
360B LEU* 3.8 21.3 - - + -
430B LEU* 4.1 16.4 - - + -
434B LEU* 3.7 31.9 - - + -
438B GLN* 3.0 24.2 + - + +
439B LYS* 3.6 5.6 - - - +
441B GLU* 1.3 73.7 - - + +
443B ALA* 1.4 59.9 + - - +
445B VAL* 3.0 10.0 + - - +
446B LEU* 2.9 41.0 + - + +
492B MET* 4.0 15.0 - - + -
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Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B LYS 3.0 10.5 + - - +
440B LYS 3.5 8.5 - - - +
442B ILE* 1.4 74.2 - - - +
444B ASP* 1.4 58.1 + - - +
446B LEU* 3.2 4.5 + - - +
447B LEU* 3.1 34.4 + - - +
492B MET* 3.9 7.2 - - + +
495B TYR* 3.4 41.3 - - + +
496B THR* 3.7 17.9 - - + +
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Residues in contact with ASP 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B LYS* 3.1 51.0 + - - +
441B GLU* 3.6 11.9 - - - +
443B ALA* 1.4 76.4 - - - +
445B VAL* 1.3 62.6 + - + +
447B LEU* 3.5 13.0 + - - +
448B GLU* 3.2 25.1 + - - +
495B TYR 4.8 3.6 - - - +
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Residues in contact with VAL 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B ALA* 3.5 29.8 - - + +
360B LEU* 4.3 7.6 - - + -
361B LYS* 3.7 41.7 - - + +
364B ILE* 4.2 16.2 - - + -
441B GLU 3.2 13.7 + - - +
442B ILE* 3.0 10.9 + - - +
444B ASP* 1.3 77.5 - - + +
446B LEU* 1.3 55.8 + - - +
448B GLU* 3.3 7.4 + - - +
449B THR* 2.9 35.8 + - + +
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B LEU* 4.2 10.1 - - + -
364B ILE* 3.7 26.7 - - + -
428B VAL* 3.8 26.5 - - + -
430B LEU* 4.6 0.9 - - + -
442B ILE* 2.9 31.6 + - + +
443B ALA* 3.2 7.4 + - - +
445B VAL* 1.3 76.4 - - - +
447B LEU* 1.3 55.2 + - - +
449B THR* 3.9 2.7 - - - -
450B ASN* 3.1 23.4 + - - -
451B ILE* 3.3 26.8 + - + -
454B MET* 3.6 31.0 - - + -
492B MET* 4.4 4.7 - - + -
496B THR* 4.6 1.8 - - + -
500B ILE* 3.7 13.5 - - + +
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Residues in contact with LEU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B ALA 3.1 20.9 + - - +
444B ASP* 3.8 11.4 - - - +
446B LEU* 1.3 76.4 - - - +
448B GLU* 1.3 60.8 + - - +
450B ASN* 3.5 11.4 + - - +
495B TYR 4.1 4.9 - - - +
496B THR* 3.4 34.1 - - - +
497B ASN* 4.0 21.8 - - - +
499B GLN* 3.6 22.2 - - + -
500B ILE* 4.4 10.4 - - + +
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Residues in contact with GLU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B LYS* 3.2 40.9 + - - +
365B LEU* 5.7 0.2 - - - +
444B ASP 3.2 18.6 + - - +
445B VAL* 3.8 7.0 - - - +
447B LEU* 1.3 78.1 - - - +
449B THR* 1.3 59.9 + - + +
450B ASN* 3.5 2.3 + - - +
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Residues in contact with THR 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B LYS* 3.8 35.0 - - + +
364B ILE* 3.5 30.5 - - + +
365B LEU* 3.9 26.7 - - + +
368B LYS* 3.5 18.5 - - - +
445B VAL* 2.9 33.4 + - + +
446B LEU* 3.7 5.4 + - - -
448B GLU* 1.3 73.9 - - + +
450B ASN* 1.3 69.9 + - - +
451B ILE 3.5 2.1 + - - -
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Residues in contact with ASN 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B LYS* 5.3 7.8 - - - -
368B LYS* 3.6 15.5 - - - +
446B LEU 3.1 9.2 + - - -
447B LEU 3.5 7.5 + - - +
448B GLU 3.3 5.8 - - - +
449B THR* 1.3 81.1 - - - +
451B ILE* 1.4 71.6 + - - +
452B ASP* 3.6 7.3 + - - +
500B ILE* 5.1 4.8 - - - +
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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