Contacts of the helix formed by residues 447 - 457 (chain D) in PDB entry 6NR8
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 GLU 447 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D ILE* 4.3 16.4 - - + -
135D GLU* 6.3 1.6 - - + -
136D SER* 2.5 44.4 + - - +
139D LYS* 2.5 36.0 + - - +
443D LEU* 4.0 3.5 - - - +
444D SER 4.0 13.3 - - - +
445D GLY* 4.5 4.4 - - - -
446D MET* 1.3 81.6 - - + +
448D SER* 1.3 58.2 + - - +
449D TYR 3.2 2.5 - - - -
450D CYS* 3.0 23.7 + - - -
451D VAL* 3.2 19.0 + - - +
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Residues in contact with SER 448 (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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440D SER* 2.7 26.4 + - - -
444D SER 3.3 21.1 - - - -
445D GLY* 2.5 27.8 + - - -
446D MET 3.3 0.4 - - - -
447D GLU* 1.3 76.7 - - - +
449D TYR* 1.3 63.1 + - - +
451D VAL* 3.5 0.4 + - - -
452D ARG* 2.7 57.2 + - - +
478M ARG* 5.7 2.5 - - - +
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Residues in contact with TYR 449 (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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123D LEU* 4.3 16.1 - - + +
126D LYS* 3.6 26.7 - - + -
128D ILE* 5.0 2.7 - - + -
446D MET* 4.4 13.4 + - - +
447D GLU* 3.2 0.6 - - - +
448D SER* 1.3 80.6 + - - +
450D CYS* 1.3 52.5 + - - +
452D ARG* 3.2 33.2 + - + +
453D ALA* 2.6 37.0 + - - +
453M ASP* 6.1 4.7 - - + -
456M GLU* 3.2 28.6 + - + +
471M ILE* 5.6 2.2 - - + -
474M MET* 2.6 52.4 - - + +
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Residues in contact with CYS 450 (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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123D LEU* 3.7 27.1 - - + -
128D ILE* 4.2 18.6 - - - -
132D ILE* 5.0 0.4 - - - -
133D ILE* 4.0 24.7 - - + -
136D SER* 3.3 21.8 - - - +
137D PHE* 3.2 14.6 - - + -
447D GLU* 3.0 19.8 + - - +
449D TYR* 1.3 79.2 - - - +
451D VAL* 1.3 52.3 + - - +
453D ALA* 3.3 1.6 + - - +
454D PHE* 2.6 34.5 + - - +
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Residues in contact with VAL 451 (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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136D SER* 3.3 21.5 - - - +
139D LYS* 4.9 1.1 - - - -
140D ALA* 3.9 20.2 - - + -
143D LYS* 3.4 36.1 - - - +
436D LEU* 3.9 13.5 - - + +
440D SER* 3.4 23.1 - - - +
443D LEU* 5.9 0.4 - - + -
447D GLU* 3.2 16.9 + - - +
450D CYS* 1.3 75.2 - - - +
452D ARG* 1.3 59.2 + - - +
454D PHE* 3.2 7.5 - - + +
455D ALA* 2.8 28.4 + - - +
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Residues in contact with ARG 452 (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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437D THR* 4.0 16.2 - - + +
440D SER* 3.0 46.5 + - - +
441D ARG* 3.2 45.9 - - - +
448D SER* 2.7 44.8 + - - +
449D TYR* 3.2 36.5 - - + +
451D VAL* 1.3 76.4 - - - +
453D ALA* 1.3 56.7 + - - +
455D ALA* 3.9 6.2 + - - +
456D ASP* 2.9 31.3 + - - +
456M GLU* 6.0 1.6 - - - +
478M ARG* 5.3 6.8 - - - +
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Residues in contact with ALA 453 (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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119D SER* 2.4 44.1 + - - +
122D LYS* 5.8 3.4 - - + -
123D LEU* 4.1 16.8 - - + -
449D TYR 2.6 21.4 + - - +
450D CYS 3.7 3.8 - - - +
452D ARG* 1.3 71.2 - - - +
454D PHE* 1.3 63.5 + - - +
455D ALA 3.3 0.4 - - - -
456D ASP* 3.3 10.7 + - + +
457D ALA 3.1 10.7 + - - -
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Residues in contact with PHE 454 (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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116D LEU* 3.6 25.3 - - + +
119D SER* 4.4 2.2 - - - -
137D PHE* 3.5 36.1 - + + -
140D ALA* 3.7 29.4 - - + -
141D LEU* 4.3 12.1 - - + -
144D GLY* 5.7 0.4 - - - -
432D LEU* 6.3 0.4 - - + -
436D LEU* 4.1 20.4 - - + -
450D CYS 2.6 21.4 + - - +
451D VAL* 3.1 11.0 + - + +
453D ALA* 1.3 73.8 - - - +
455D ALA* 1.3 62.0 + - - +
457D ALA* 3.2 15.3 + - - +
458D MET* 3.4 21.9 - - + +
519D LEU* 4.7 16.2 - - + -
523D THR* 3.9 27.6 - - + -
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Residues in contact with ALA 455 (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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433D ALA* 3.2 30.3 - - - +
436D LEU* 3.9 17.7 - - + -
437D THR* 3.7 27.8 - - + +
451D VAL 2.8 15.8 + - - +
452D ARG 4.2 0.4 - - - +
454D PHE* 1.3 75.7 - - - +
456D ASP* 1.3 65.4 + - - +
458D MET* 3.1 19.0 + - - +
459D GLU* 3.9 2.9 + - - +
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Residues in contact with ASP 456 (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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119D SER* 4.8 1.3 - - - +
437D THR* 4.6 3.8 - - - +
452D ARG* 2.9 21.2 + - - +
453D ALA* 3.3 11.6 + - - +
454D PHE 3.3 0.6 - - - -
455D ALA* 1.3 79.4 - - - +
457D ALA* 1.3 59.9 + - - +
458D MET 3.5 0.3 + - - -
459D GLU 4.0 3.5 + - - -
460D VAL* 3.4 15.6 - - - +
122M GLN* 5.8 4.2 + - - +
126M ARG* 4.1 20.1 + - - +
449M ARG* 3.0 40.1 + - - +
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Residues in contact with ALA 457 (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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112D ILE* 4.7 0.8 - - - +
115D SER* 3.3 48.7 - - - +
116D LEU* 3.7 16.4 - - + +
119D SER* 3.5 12.3 + - - +
453D ALA 3.1 5.4 + - - +
454D PHE 3.5 11.2 - - - +
455D ALA 3.2 0.6 - - - -
456D ASP* 1.3 76.7 - - - +
458D MET* 1.3 64.0 + - - +
459D GLU 3.4 0.2 - - - -
460D VAL* 3.5 11.9 + - - -
461D ILE* 3.3 7.8 - - - +
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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