Contacts of the helix formed by residues 508 - 518 (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 TYR 508 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471D ALA 3.8 8.7 - - - -
472D VAL 3.5 6.6 + - - -
473D CYS* 3.2 29.8 + - - -
474D GLY* 3.4 21.1 - - - -
503D ALA* 3.2 10.5 + - + +
506D LYS* 3.0 55.5 - - + -
507D GLY* 1.3 77.9 - - - +
509D GLN* 1.3 65.8 + - - +
510D SER* 3.1 3.7 + - - +
511D VAL* 3.1 16.1 + - + +
512D THR* 2.9 24.7 + - - -
544D CYS* 3.7 0.2 - - - -
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Residues in contact with GLN 509 (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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58A ILE 4.7 3.0 + - - -
59A GLY* 4.4 4.2 - - - -
60A VAL* 2.9 48.0 + - - +
62A PHE* 4.1 7.5 - - - -
95A TYR* 4.8 2.8 + - - -
507D GLY 3.3 5.9 + - - -
508D TYR* 1.3 72.7 - - - +
510D SER* 1.3 64.0 + - - +
512D THR* 3.4 2.4 - - - -
513D LEU* 2.9 42.5 + - + +
543D ASP* 3.0 58.1 + - - +
544D CYS* 3.5 9.5 - - - +
546D LYS* 5.4 0.2 - - - +
547D ALA* 4.2 6.7 - - + -
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Residues in contact with SER 510 (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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86A GLU* 5.6 0.3 + - - -
91A MET* 3.2 39.9 - - - +
95A TYR* 4.7 5.5 + - - -
476D ALA* 5.6 6.7 - - - -
508D TYR* 3.1 3.0 + - - -
509D GLN* 1.3 80.6 + - - +
511D VAL* 1.3 62.2 + - - +
513D LEU* 3.4 2.2 + - - -
514D LEU* 3.0 24.0 + - - +
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Residues in contact with VAL 511 (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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471D ALA* 4.3 9.2 - - + +
474D GLY* 4.0 34.1 - - - +
476D ALA* 4.8 6.5 - - + -
479D ILE* 3.6 29.2 - - + -
503D ALA* 3.5 20.4 - - + -
508D TYR* 3.1 17.1 + - + +
510D SER* 1.3 79.8 - - - +
512D THR* 1.3 70.2 + - - +
514D LEU* 2.9 8.8 + - - +
515D LEU* 2.8 31.7 + - + +
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Residues in contact with THR 512 (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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500D LEU* 3.8 15.7 - - + +
503D ALA* 3.7 14.1 - - - +
504D CYS* 3.7 23.3 - - - -
508D TYR 2.9 17.3 + - - -
509D GLN* 3.4 12.1 - - - -
511D VAL* 1.3 75.4 - - - +
513D LEU* 1.3 62.3 + - - +
515D LEU* 3.4 3.2 + - - +
516D LEU* 3.0 39.5 + - + +
544D CYS* 3.6 15.6 - - - +
547D ALA* 4.3 13.9 - - + -
548D LEU* 4.4 5.4 - - + -
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Residues in contact with LEU 513 (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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60A VAL* 4.8 3.6 - - + -
62A PHE* 4.8 5.4 - - + -
80A TRP* 4.8 11.4 - - + -
91A MET* 4.4 2.2 - - + -
94A VAL* 4.0 15.4 - - + +
95A TYR* 3.9 24.0 - - + -
509D GLN* 2.9 47.5 + - + +
510D SER* 3.8 4.5 - - - +
512D THR* 1.3 71.8 - - - +
514D LEU* 1.3 61.7 + - - +
516D LEU* 3.1 7.6 + - + +
517D HIS* 2.7 29.6 + - - +
547D ALA* 3.6 28.5 - - + +
551D TYR* 3.9 26.7 - - + -
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Residues in contact with LEU 514 (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* 4.3 8.7 - - + +
93A ARG* 4.1 8.3 - - - +
94A VAL* 3.9 24.2 - - + -
476D ALA* 3.7 37.0 - - + +
479D ILE* 3.8 18.2 - - + -
480D ASP* 3.7 16.8 - - - +
510D SER 3.0 13.7 + - - +
511D VAL* 2.9 9.7 + - - +
513D LEU* 1.3 75.1 - - - +
515D LEU* 1.3 57.4 + - - +
517D HIS* 3.1 9.3 - - + +
518D TYR* 2.9 61.5 + - + -
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Residues in contact with LEU 515 (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* 4.7 12.8 - - + -
471D ALA* 4.6 1.1 - - + -
479D ILE* 4.3 24.7 - - + -
489D VAL* 4.4 10.2 - - + +
499D PRO* 3.7 20.4 - - + +
500D LEU* 3.5 38.6 - - + +
503D ALA* 4.2 1.3 - - + -
511D VAL* 2.8 37.0 + - + +
512D THR 3.6 3.8 - - - +
514D LEU* 1.3 75.9 - - - +
516D LEU* 1.3 57.3 + - - +
518D TYR* 2.9 23.8 + - + +
519D LYS 3.1 0.5 + - - -
520D ALA* 3.0 28.8 + - + +
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Residues in contact with LEU 516 (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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500D LEU* 4.0 21.3 - - + -
512D THR* 3.0 32.0 + - + +
513D LEU* 3.6 12.8 - - + +
515D LEU* 1.3 74.3 - - - +
517D HIS* 1.3 58.0 + - - +
519D LYS* 2.9 21.0 + - - +
520D ALA* 4.0 20.1 - - - +
522D ALA* 4.5 4.5 - - + -
547D ALA 4.2 9.0 - - - +
548D LEU* 4.2 13.9 - - + -
551D TYR* 3.5 48.3 + - + -
552D ASP* 4.4 15.7 - - - +
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Residues in contact with HIS 517 (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* 4.6 13.9 + - + -
94A VAL* 3.8 43.0 + - + +
97A LYS* 3.9 49.1 + - + +
513D LEU 2.7 16.8 + - - +
514D LEU* 3.1 15.9 - - + +
516D LEU* 1.3 75.2 - - - +
518D TYR* 1.3 78.6 + + - +
519D LYS* 3.4 9.9 + - - +
551D TYR* 3.2 13.5 + - - +
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Residues in contact with TYR 518 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 3.6 8.5 + - - -
479D ILE* 4.2 6.1 - - + -
480D ASP* 2.5 33.7 + - - +
483D VAL* 3.6 41.1 - - + -
489D VAL* 3.6 28.1 - - + +
514D LEU* 2.9 47.9 + - + -
515D LEU* 2.9 15.8 + - + +
517D HIS* 1.3 87.6 - + - +
519D LYS* 1.3 69.6 + - - +
520D ALA 3.4 0.7 + - - -
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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