Contacts of the helix formed by residues 465 - 474 (chain D) in PDB entry 4CYM
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 465 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456D PRO 4.0 13.0 - - - +
457D PHE* 4.8 3.1 - - - +
458D SER 3.5 13.2 - - - +
459D ARG* 3.7 27.1 - - - +
463D GLY 3.5 0.6 + - - -
464D HIS* 1.3 74.2 - - - +
466D PRO* 1.3 72.0 - - - +
467D LEU* 3.5 12.3 + - - +
468D HIS* 2.8 44.5 + - - +
469D VAL* 3.1 13.8 + - - +
488D MET* 5.1 2.9 + - + +
491D ALA* 4.2 13.6 - - + +
499D PRO* 4.8 0.2 - - - +
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Residues in contact with PRO 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D VAL* 5.4 2.7 - - + -
455D THR 3.7 20.2 - - - +
456D PRO* 3.9 10.3 - - + +
458D SER* 3.4 23.6 - - - +
464D HIS 4.4 1.3 - - - +
465D THR* 1.3 83.8 - - - +
467D LEU* 1.3 59.2 + - - +
469D VAL* 2.9 11.5 + - + +
470D ALA* 2.7 30.7 + - - +
482D LEU* 3.6 26.9 - - + +
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Residues in contact with LEU 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456D PRO 5.2 0.8 + - - -
465D THR* 3.1 12.6 + - - +
466D PRO* 1.3 78.3 - - - +
468D HIS* 1.3 62.4 + - - +
470D ALA* 4.3 0.4 - - - -
471D ALA* 3.0 23.0 + - - +
479D ILE* 4.1 30.3 - - + -
482D LEU* 3.5 27.9 - - + +
483D VAL* 4.3 6.5 - - + -
487D ALA* 4.4 14.3 - - + +
488D MET 3.8 10.1 - - - +
489D VAL* 3.7 36.6 - - + +
499D PRO* 3.9 18.0 - - + +
515D LEU* 4.7 7.9 - - + -
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Residues in contact with HIS 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D ARG* 4.5 0.2 - - - -
463D GLY 3.9 9.2 - - - -
464D HIS* 3.8 22.6 - + + -
465D THR* 2.8 43.7 + - - +
467D LEU* 1.3 75.9 - - - +
469D VAL* 1.3 63.6 + - - +
471D ALA* 3.2 1.4 + - - +
472D VAL* 3.0 20.1 + - - +
491D ALA* 3.4 28.8 + - + -
492D THR 4.0 0.4 - - - -
493D ASP* 3.7 11.9 + - + -
497D ALA 2.7 28.3 + - - -
498D THR 3.8 0.4 - - - -
499D PRO* 3.5 22.2 - - + +
502D LEU* 3.5 32.1 - - + +
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Residues in contact with VAL 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D HIS* 4.7 13.9 - - + +
465D THR 3.1 15.2 + - - +
466D PRO* 2.9 10.4 + - + +
468D HIS* 1.3 72.0 - - - +
470D ALA* 1.3 67.1 + - - +
472D VAL* 3.0 20.5 + - + +
473D CYS* 3.0 31.2 + - - -
475D GLN* 5.7 1.6 - - - +
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Residues in contact with ALA 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D PRO 2.7 18.8 + - - +
467D LEU 3.9 3.6 - - - +
469D VAL* 1.3 74.5 - - - +
471D ALA* 1.3 60.7 + - - +
473D CYS* 3.9 4.6 - - - +
474D GLY 3.1 16.8 + - - -
475D GLN* 3.1 13.1 + - - +
478D LEU* 3.9 33.7 - - + +
479D ILE* 4.0 17.5 - - + +
482D LEU* 3.9 14.1 - - + -
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Residues in contact with ALA 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D LEU 3.0 20.2 + - - +
468D HIS 3.6 4.3 - - - +
469D VAL 3.1 0.2 - - - -
470D ALA* 1.3 75.7 - - - +
472D VAL* 1.3 64.9 + - - +
474D GLY* 3.2 13.2 + - - -
479D ILE* 4.3 5.6 - - + +
499D PRO* 3.8 30.7 - - + +
502D LEU* 4.7 0.7 - - + -
503D ALA* 4.7 6.5 - - - +
508D TYR* 3.8 9.7 - - - -
511D VAL* 4.3 24.7 - - + +
515D LEU* 4.6 2.0 - - + -
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Residues in contact with VAL 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D HIS 3.0 13.2 + - - +
469D VAL* 3.0 16.8 + - + +
471D ALA* 1.3 77.9 - - - +
473D CYS* 1.3 67.4 + - - +
502D LEU* 4.1 32.5 - - + +
505D GLN* 6.2 0.9 - - - +
506D LYS* 3.5 41.6 - - + -
508D TYR* 3.5 4.4 + - - -
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Residues in contact with CYS 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469D VAL* 3.0 34.6 + - - +
470D ALA 3.9 2.2 - - - +
472D VAL* 1.3 82.7 - - - +
474D GLY* 1.3 58.7 + - - +
475D GLN* 3.5 33.6 - - + +
508D TYR* 3.2 14.7 + - - -
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Residues in contact with GLY 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470D ALA 3.1 4.9 + - - -
471D ALA 3.2 6.1 + - - -
473D CYS* 1.3 78.4 - - - +
475D GLN* 1.3 60.8 + - - +
476D ALA* 2.8 11.9 + - - +
508D TYR* 3.4 23.1 - - - -
511D VAL* 4.0 12.5 - - - +
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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