Contacts of the helix formed by residues 475 - 484 (chain D) in PDB entry 5DO7
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 ARG 475 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D HIS* 3.5 43.4 + - - +
155D ASN 3.9 15.2 + - - -
156D GLN* 4.0 13.7 + - + -
472D TYR 4.4 2.2 + - - +
473D SER 3.8 4.7 + - - +
474D GLU* 1.3 72.2 - - - +
476D ALA* 1.3 71.1 + - - +
477D MET* 3.0 4.3 - - - -
478D LEU* 2.8 25.4 + - + +
479D TYR* 3.8 24.9 + - - -
667D GLN* 5.4 1.6 - - - -
668D LYS* 4.9 6.3 - - - +
669D PRO* 3.8 43.8 - - + +
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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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156D GLN* 4.2 30.0 - - + +
158D LEU* 5.3 7.9 - - + -
474D GLU* 3.4 10.9 - - + +
475D ARG* 1.3 84.1 - - - +
477D MET* 1.3 66.5 + - - +
479D TYR* 2.8 20.6 + - - +
480D TYR* 2.9 31.8 + - + +
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Residues in contact with MET 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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471D CYS* 3.8 32.5 - - - +
474D GLU* 4.0 32.9 - - + +
475D ARG 2.8 5.4 + - - +
476D ALA* 1.3 76.1 - - - +
478D LEU* 1.3 51.5 + - - +
480D TYR* 2.8 14.2 + - + +
481D GLU* 2.5 38.5 + - - +
486D LEU* 4.9 1.7 - - + +
492D TYR* 3.5 46.9 - - + +
496D LYS* 4.3 2.7 - - - +
658D TYR* 4.8 3.4 - - - +
662D LEU* 4.8 12.1 - - + -
667D GLN* 4.4 22.0 - - + +
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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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121D ARG* 4.7 6.5 - - - +
475D ARG* 2.8 18.7 + - + +
477D MET* 1.3 71.9 - - - +
479D TYR* 1.3 81.4 + - + +
481D GLU* 2.8 35.6 + - - +
482D LEU* 2.8 34.1 + - + +
666D LYS* 4.6 10.3 - - + -
667D GLN* 3.2 25.8 + - - +
668D LYS* 3.7 38.4 - - + -
669D PRO* 5.7 2.7 - - + -
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Residues in contact with TYR 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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121D ARG* 4.2 19.3 + - - -
152D ARG* 3.0 51.1 + - + -
154D HIS* 3.3 18.2 - + + -
156D GLN* 3.7 35.0 - - + +
475D ARG* 4.0 26.7 - - - -
476D ALA 2.8 11.2 + - - +
478D LEU* 1.3 90.4 - - + +
480D TYR* 1.3 59.4 + - + +
482D LEU* 4.5 6.5 - - + +
483D GLU* 2.8 53.8 + - + +
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Residues in contact with TYR 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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156D GLN* 4.5 13.7 + - + -
158D LEU* 4.8 8.0 - - + +
166D THR* 6.1 1.2 - - - +
170D ILE* 4.6 19.5 - - + +
173D MET* 5.5 2.7 - - + -
225D VAL* 6.2 0.7 - - + -
405D ARG* 2.7 44.7 + - - -
476D ALA* 2.9 27.4 + - + +
477D MET* 2.8 21.7 + - + +
479D TYR* 1.3 75.9 - - + +
481D GLU* 1.3 65.9 + - - +
483D GLU* 4.8 2.9 - - + -
484D ASP* 2.8 20.8 + - - -
485D GLY* 3.2 16.3 + - - +
486D LEU* 3.1 43.2 + - + +
492D TYR* 5.6 2.0 - + - -
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Residues in contact with GLU 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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477D MET 2.5 20.6 + - - +
478D LEU* 2.8 29.3 + - - +
480D TYR* 1.3 73.9 - - - +
482D LEU* 1.3 78.6 + - - +
484D ASP* 3.3 10.7 + - - +
486D LEU* 4.6 10.1 - - - +
487D TYR* 4.8 24.0 + - + +
666D LYS* 4.9 11.8 - - - +
667D GLN 5.5 0.2 + - - -
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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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121D ARG* 3.2 49.1 - - + +
145D ARG* 4.2 21.1 - - - +
478D LEU* 2.8 36.6 + - + +
479D TYR* 4.3 7.0 - - + +
481D GLU* 1.3 93.0 - - - +
483D GLU* 1.3 72.3 + - - +
484D ASP 3.4 0.3 + - - -
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Residues in contact with GLU 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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121D ARG* 6.1 0.9 - - - -
145D ARG* 4.3 11.7 - - - +
148D VAL 5.1 5.2 - - - +
150D HIS* 4.4 23.1 + - - +
152D ARG* 5.8 0.9 - - - +
174D ARG* 2.9 26.9 + - - +
226D GLN* 4.1 26.2 - - - +
479D TYR* 2.8 48.6 + - + +
480D TYR* 4.3 4.0 - - + +
482D LEU* 1.3 78.2 - - - +
484D ASP* 1.3 77.2 + - - +
485D GLY 4.9 2.2 - - - +
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Residues in contact with ASP 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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145D ARG* 3.7 34.2 + - - +
173D MET 5.6 0.3 - - - +
174D ARG* 3.2 33.6 + - - +
398D GLN* 5.0 3.6 + - - -
480D TYR 2.8 11.5 + - - -
481D GLU 3.6 8.3 - - - +
482D LEU 3.3 3.8 - - - +
483D GLU* 1.3 85.8 - - - +
485D GLY* 1.3 64.8 + - - +
486D LEU 3.3 9.8 + - - +
487D TYR* 6.4 0.4 - - - -
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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
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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