Contacts of the helix formed by residues 481 - 496 (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 LEU 481 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B PRO* 4.1 8.1 - - + -
457B SER* 4.3 4.9 - - - +
458B ASN 3.8 19.7 - - - +
459B THR* 4.3 0.7 - - - -
460B THR* 3.7 29.8 - - + -
463B ILE* 4.3 2.2 - - + +
476B VAL 3.7 21.8 - - - +
477B SER* 4.1 3.6 - - - -
478B GLY 2.9 14.3 + - - +
480B LYS* 1.3 77.7 - - - +
482B LYS* 1.4 63.1 + - - +
483B ASP 3.5 1.3 - - - -
484B ILE* 3.4 13.0 + - + -
485B SER* 3.1 23.5 + - - +
505B SER 4.9 0.4 - - - +
506B GLY* 3.9 14.1 - - - -
507B GLY 4.8 0.4 - - - +
800B FMN 3.7 29.6 - - - +
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Residues in contact with LYS 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B GLY 3.5 3.4 + - - -
479B ALA* 3.3 15.6 + - - +
480B LYS 3.6 0.2 - - - -
481B LEU* 1.4 76.5 - - - +
483B ASP* 1.4 75.6 + - - +
486B THR* 2.9 41.6 + - - +
506B GLY 3.4 15.0 + - - +
507B GLY* 3.6 23.1 - - - +
512B LEU* 6.3 0.6 - - - +
513B ASP* 3.0 29.4 + - + +
516B GLU* 2.8 32.3 + - - +
517B LYS* 3.3 7.1 + - - +
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Residues in contact with ASP 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ALA 4.8 1.2 + - - -
480B LYS 5.2 1.4 + - - +
481B LEU 3.5 0.8 - - - -
482B LYS* 1.4 92.2 - - - +
484B ILE* 1.4 63.1 + - + +
486B THR* 3.9 5.6 - - - -
487B LYS* 3.0 26.2 + - - +
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Residues in contact with ILE 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B PRO* 3.6 33.0 - - + +
460B THR* 4.3 13.5 - - + +
462B GLN* 4.5 23.6 - - + +
463B ILE* 4.3 20.6 - - + -
480B LYS 4.1 17.7 + - - +
481B LEU* 3.4 10.3 + - + +
483B ASP* 1.4 77.2 - - + +
485B SER* 1.3 57.5 + - - +
487B LYS* 3.5 5.9 + - - +
488B PHE* 3.0 27.1 + - + +
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Residues in contact with SER 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ILE* 3.8 2.0 + - - +
457B SER* 2.9 25.8 + - - -
481B LEU* 3.1 20.6 + - - +
484B ILE* 1.3 75.9 - - - +
486B THR* 1.4 58.6 + - - +
488B PHE* 3.3 7.1 + - - +
489B ILE* 3.0 31.9 + - - +
505B SER 2.7 25.0 + - - -
506B GLY* 3.8 4.9 - - - -
517B LYS* 3.3 18.8 - - - -
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Residues in contact with THR 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LYS* 2.9 24.1 + - - +
483B ASP* 3.9 6.3 - - - -
484B ILE 3.5 0.2 - - - -
485B SER* 1.4 70.9 - - - +
487B LYS* 1.4 64.5 + - - +
489B ILE* 3.1 10.4 + - - +
490B CYS* 3.1 26.6 + - - -
516B GLU* 4.3 21.5 + - + +
517B LYS* 3.0 20.9 + - + +
520B ALA* 4.1 18.2 - - + -
565B LYS* 4.8 9.2 - - - +
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Residues in contact with LYS 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B GLN* 5.0 2.9 - - - +
483B ASP 3.0 18.4 + - - +
484B ILE* 3.7 6.5 - - - +
486B THR* 1.4 74.5 - - - +
488B PHE* 1.3 57.1 + - - +
490B CYS* 3.2 11.3 + - + +
491B GLU* 3.0 55.1 + - + +
565B LYS* 6.2 0.4 - - - +
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Residues in contact with PHE 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B LEU* 3.9 28.3 - - + -
431B ALA 3.2 30.7 - - - -
432B PRO* 3.7 17.5 - - + +
434B LEU* 4.1 8.3 - - + -
439B LYS* 3.7 37.7 - - + +
456B ILE* 3.4 19.3 - - + -
457B SER* 3.8 8.5 - - - -
484B ILE* 3.0 18.1 + - + +
485B SER* 3.6 6.1 - - - +
486B THR 3.2 0.4 - - - -
487B LYS* 1.3 72.6 - - - +
489B ILE* 1.4 63.5 + - - +
491B GLU* 3.4 10.0 + - - +
492B MET* 3.0 44.0 + - + +
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Residues in contact with ILE 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ILE* 3.6 32.8 - - + +
485B SER 3.0 19.4 + - - +
486B THR* 3.1 8.2 + - - +
488B PHE* 1.4 74.4 - - - +
490B CYS* 1.4 55.6 + - - +
492B MET* 3.3 1.6 + - - -
493B TYR* 2.9 32.9 + - - +
502B ILE* 4.0 16.5 - - + +
504B ALA* 3.8 19.7 - - + -
517B LYS* 3.7 35.2 - - + +
520B ALA* 3.6 30.1 - - + +
521B GLY 3.8 2.7 - - - +
522B ALA* 4.0 9.6 - - + +
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Residues in contact with CYS 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B THR* 3.1 14.3 + - - -
487B LYS* 3.5 11.0 - - + +
489B ILE* 1.4 75.2 - - - +
491B GLU* 1.3 62.8 + - + +
493B TYR* 3.8 1.2 - - - +
494B ASN* 2.9 32.9 + - - +
520B ALA* 3.6 26.5 - - - -
565B LYS* 3.7 27.1 - - - -
566B HIS* 3.7 25.8 - - + -
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Residues in contact with GLU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B GLN* 2.9 32.8 + - - +
439B LYS* 2.8 28.8 + - + -
487B LYS* 3.0 44.2 + - + +
488B PHE* 3.5 17.3 + - + +
489B ILE 3.3 0.2 - - - -
490B CYS* 1.3 76.6 - - + +
492B MET* 1.3 57.7 + - + +
494B ASN* 3.4 5.3 + - - +
495B TYR* 2.8 48.6 + - + -
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Residues in contact with MET 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B LEU* 4.1 11.4 - - + -
439B LYS* 3.7 36.8 - - - +
442B ILE* 4.0 15.9 - - + -
443B ALA* 3.9 21.8 - - + +
446B LEU* 4.4 0.7 - - + -
454B MET* 3.7 15.0 - - + -
456B ILE* 3.6 23.6 - - + -
488B PHE* 3.0 47.6 + - + +
491B GLU* 1.3 73.5 - - - +
493B TYR* 1.3 53.8 + - - +
495B TYR* 4.1 6.7 - - - -
496B THR* 2.7 42.1 + - + +
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Residues in contact with TYR 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ILE 2.9 18.0 + - - +
490B CYS 3.8 3.6 - - - +
492B MET* 1.3 74.7 - - - +
494B ASN* 1.3 59.2 + - - +
496B THR* 3.6 4.3 + - - -
497B ASN 3.4 1.4 + - - -
498B LYS* 2.8 82.4 + - + +
500B ILE 5.0 5.2 - - - -
501B PRO* 6.5 0.2 - - + -
502B ILE* 3.7 14.0 - - + +
520B ALA 3.7 6.1 - - - +
521B GLY* 3.8 22.9 - - - -
562B ILE* 4.0 13.0 + - + +
563B GLY* 3.6 32.0 + - - -
566B HIS* 3.4 26.5 - + - -
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Residues in contact with ASN 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B CYS* 2.9 23.7 + - - +
491B GLU* 3.9 4.0 - - - +
493B TYR* 1.3 77.2 - - - +
495B TYR* 1.4 60.1 + - + +
496B THR 3.3 0.4 - - - -
497B ASN* 3.0 27.9 + - - +
498B LYS* 4.4 13.2 - - - -
566B HIS* 3.1 35.4 + - - +
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Residues in contact with TYR 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B GLN* 2.7 45.0 + - - +
439B LYS* 3.8 22.9 - - + -
440B LYS* 4.0 42.9 + - + +
443B ALA* 3.4 25.4 - - + +
444B ASP* 4.8 4.3 - - - +
447B LEU* 4.1 8.7 - - - +
491B GLU* 2.8 36.9 + - + +
492B MET* 3.4 6.0 + - - +
494B ASN* 1.4 71.7 - - + +
496B THR* 1.3 57.5 + - - +
497B ASN* 3.3 6.3 + - - +
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Residues in contact with THR 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ALA* 3.7 29.4 - - + +
446B LEU* 4.6 2.2 - - + -
447B LEU* 3.4 12.2 - - + +
454B MET* 3.5 27.1 - - + +
492B MET* 2.7 24.6 + - + +
493B TYR* 3.6 7.1 + - - -
495B TYR* 1.3 73.8 - - - +
497B ASN* 1.3 68.6 + - - +
498B LYS* 4.1 2.1 + - - -
499B GLN* 2.9 20.1 + - - +
500B ILE* 3.8 28.4 + - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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