Contacts of the helix formed by residues 475 - 485 (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 GLN 475 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469D VAL* 5.7 1.6 - - - +
470D ALA* 3.1 10.0 + - - +
473D CYS* 3.5 32.1 - - + +
474D GLY* 1.3 75.9 - - - +
476D ALA* 1.3 63.3 + - - +
477D SER* 3.3 6.5 - - - +
478D LEU* 3.0 43.8 + - + +
479D ILE* 3.0 15.1 + - - +
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Residues in contact with ALA 476 (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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91A MET* 5.4 9.0 - - - -
93A ARG* 6.3 0.2 - - - +
474D GLY 2.8 11.5 + - - +
475D GLN* 1.3 72.1 - - - +
477D SER* 1.3 62.7 + - - +
479D ILE* 3.2 15.4 + - - +
480D ASP* 3.0 26.3 + - - +
510D SER* 5.6 6.1 - - - -
511D VAL* 4.8 9.6 - - + -
514D LEU* 3.7 16.6 - - + +
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Residues in contact with SER 477 (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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90A ASN* 6.4 0.2 - - - -
475D GLN* 4.4 4.7 - - - +
476D ALA* 1.3 78.2 + - - +
478D LEU* 1.3 56.9 + - - +
480D ASP* 3.4 14.9 - - - +
481D LEU* 3.1 26.3 + - - +
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Residues in contact with LEU 478 (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* 6.4 0.9 - - + -
470D ALA* 3.9 22.2 - - + -
475D GLN* 3.0 46.1 + - + +
477D SER* 1.3 80.1 + - - +
479D ILE* 1.3 54.1 + - - +
481D LEU* 3.1 23.0 + - + +
482D LEU* 2.8 52.1 + - + +
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Residues in contact with ILE 479 (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* 4.1 18.2 - - + -
470D ALA* 4.0 15.2 - - + +
471D ALA* 4.3 11.0 - - + +
475D GLN 3.0 12.9 + - - +
476D ALA* 3.3 10.3 - - - +
478D LEU* 1.3 71.5 - - - +
480D ASP* 1.3 67.5 + - - +
481D LEU 3.0 0.2 + - - -
482D LEU* 3.1 1.2 + - - -
483D VAL* 2.9 38.8 + - + +
511D VAL* 3.6 40.4 - - + -
514D LEU* 3.8 22.0 - - + -
515D LEU* 4.3 14.4 - - + -
518D TYR* 4.2 4.5 - - + -
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Residues in contact with ASP 480 (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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93A ARG* 3.1 31.7 + - - -
476D ALA* 3.0 21.9 + - - +
477D SER* 3.4 14.7 - - - +
479D ILE* 1.3 73.4 - - - +
481D LEU* 1.3 64.2 + - - +
483D VAL* 3.5 1.7 + - - +
484D SER* 3.0 24.8 + - - -
514D LEU* 3.7 4.8 - - - +
518D TYR* 2.5 39.4 + - - +
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Residues in contact with LEU 481 (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* 5.0 9.4 - - + -
477D SER 3.1 10.7 + - - +
478D LEU* 3.4 25.8 - - + +
479D ILE 3.1 1.0 - - - -
480D ASP* 1.3 81.7 - - - +
482D LEU* 1.3 67.7 + - + +
484D SER* 2.5 26.3 + - - +
485D LYS* 3.1 32.3 + - + +
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Residues in contact with LEU 482 (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* 3.9 29.8 - - + -
456D PRO* 4.2 11.0 - - + +
466D PRO* 3.6 22.4 - - + +
467D LEU* 3.5 38.8 - - + +
470D ALA* 3.9 12.3 - - + -
478D LEU* 2.8 34.2 + - + +
479D ILE 3.8 3.1 - - - +
481D LEU* 1.3 76.2 - - + +
483D VAL* 1.3 61.6 + - - +
485D LYS* 3.0 16.2 + - - +
486D GLY 3.3 0.2 + - - -
487D ALA* 3.0 28.7 + - + +
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Residues in contact with VAL 483 (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* 4.3 11.7 - - + -
479D ILE* 2.9 26.5 + - + +
480D ASP 3.8 2.7 - - - +
482D LEU* 1.3 74.4 - - - +
484D SER* 1.3 64.0 + - - +
486D GLY* 3.0 15.9 + - - -
487D ALA* 3.9 9.2 + - + +
489D VAL* 4.3 21.1 - - + -
515D LEU* 5.7 1.1 - - + -
518D TYR* 3.6 51.4 - - + -
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Residues in contact with SER 484 (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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480D ASP 3.0 13.7 + - - -
481D LEU* 2.5 27.1 + - - +
483D VAL* 1.3 77.4 - - - +
485D LYS* 1.3 68.4 + - - +
486D GLY 3.3 1.6 + - - -
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Residues in contact with LYS 485 (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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453D VAL* 3.9 32.7 - - + +
454D VAL* 3.5 24.5 - - + +
456D PRO* 3.3 20.7 - - + +
481D LEU* 3.1 30.4 + - + +
482D LEU* 3.0 12.3 + - - +
484D SER* 1.3 83.0 + - - +
486D GLY* 1.3 57.3 + - - +
487D ALA 3.5 1.6 - - - -
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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