Contacts of the helix formed by residues 474 - 484 (chain A) in PDB entry 4R2G
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 ASP 474 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A GLN* 5.1 2.4 + - - +
472A GLY* 3.5 4.2 - - - -
473A GLY* 1.3 74.8 + - - +
475A MET* 1.3 58.4 + - - +
476A ARG* 3.0 61.5 + - - +
477A ASP* 3.1 22.3 + - - +
478A ASN* 3.8 3.6 - - - +
480A ARG* 5.4 0.7 + - - -
25L GLN* 3.2 20.2 + - - +
40L GLN* 3.3 24.6 + - - +
41L GLY* 3.5 26.0 + - - +
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Residues in contact with MET 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLN* 3.9 10.4 + - - +
255A VAL* 3.5 33.4 - - + -
256A SER 3.3 28.7 - - - +
257A THR* 3.7 10.5 - - + -
427A TRP* 4.0 26.0 - - + -
473A GLY* 3.1 33.6 + - - +
474A ASP* 1.3 70.2 + - - +
476A ARG* 1.3 64.5 + - - +
477A ASP 3.2 0.4 - - - -
478A ASN* 2.9 31.9 + - + +
479A TRP* 3.0 34.6 + - + -
43L PHE* 4.1 3.6 - - + -
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Residues in contact with ARG 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A VAL* 4.3 5.6 - - + +
102A GLU* 3.6 37.6 + - - +
105A GLN* 3.8 28.8 + - + +
474A ASP* 3.0 31.0 + - - +
475A MET* 1.3 77.7 - - - +
477A ASP* 1.3 56.4 + - - +
479A TRP* 2.8 27.2 + - + +
480A ARG* 2.8 37.7 + - - +
22L LYS* 5.6 3.0 - - - +
23L SER 5.6 2.0 + - - -
24L ILE* 3.2 36.0 - - - +
25L GLN* 4.9 7.5 - - - +
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Residues in contact with ASP 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A TRP* 4.4 8.3 - - - -
283A THR* 3.8 24.0 - - - +
285A ILE* 3.5 20.5 - - + +
453A LEU* 4.2 16.0 - - + +
472A GLY* 5.9 2.7 - - - -
474A ASP* 3.1 15.4 + - - +
476A ARG* 1.3 75.9 - - - +
478A ASN* 1.3 58.4 + - - +
480A ARG* 3.3 28.4 + - - -
481A SER* 3.0 26.9 + - - -
25L GLN* 4.5 7.8 + - - -
40L GLN* 3.8 14.6 - - - +
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Residues in contact with ASN 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A VAL 3.8 15.3 + - - +
256A SER* 3.5 20.7 + - - +
260A LEU* 2.9 31.5 - - + +
453A LEU* 4.1 8.9 - - - +
473A GLY 4.8 1.0 + - - -
474A ASP 3.8 3.3 - - - +
475A MET* 2.9 40.0 + - + +
477A ASP* 1.3 78.4 - - - +
479A TRP* 1.3 73.9 + - + +
481A SER* 2.4 27.4 + - - -
482A GLU* 4.0 4.7 + - - +
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Residues in contact with TRP 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A VAL* 3.6 33.0 - - + -
104A MET* 3.6 31.0 - - - -
105A GLN* 2.9 30.7 + - - +
108A VAL* 3.6 27.1 - - + -
251A ILE* 5.7 3.8 - - + -
253A PRO* 3.4 40.4 - - + -
254A VAL 4.1 16.8 - - - -
255A VAL* 4.4 6.7 - - + -
427A TRP* 5.0 1.8 - + - -
475A MET* 3.0 30.9 + - + -
476A ARG* 2.8 17.2 + - - +
478A ASN* 1.3 82.6 - - + +
480A ARG* 1.3 64.5 + - - +
482A GLU* 2.9 15.8 + - + +
483A LEU* 3.0 16.7 + - + +
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Residues in contact with ARG 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A MET* 3.1 39.3 + - + +
96A TRP* 3.1 44.6 + - - +
97A LYS* 5.0 0.2 - - - +
98A ASN 4.5 2.6 + - - -
101A VAL* 3.7 35.4 - - + +
102A GLU* 4.0 12.1 + - - -
285A ILE* 4.2 2.0 - - + -
474A ASP* 5.4 1.0 + - - -
476A ARG* 2.8 43.5 + - - +
477A ASP* 3.3 32.6 + - - +
479A TRP* 1.3 74.3 - - - +
481A SER* 1.3 55.8 + - - +
482A GLU 2.8 11.1 + - - -
483A LEU* 4.3 2.5 - - - +
484A TYR* 2.9 28.2 + - - +
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Residues in contact with SER 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A MET* 4.9 1.3 - - - -
260A LEU* 3.9 27.7 - - - +
263A GLY* 5.9 0.2 - - - -
273A ARG* 5.1 3.5 + - - +
285A ILE* 4.1 18.3 - - - +
287A GLN* 4.7 10.2 + - - +
477A ASP 3.0 13.8 + - - -
478A ASN* 2.4 25.8 + - - -
480A ARG* 1.3 75.2 - - - +
482A GLU* 1.3 74.4 + - - +
484A TYR* 3.9 14.2 - - - -
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Residues in contact with GLU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A HIS* 4.3 9.3 + - + -
251A ILE* 2.8 59.9 - - + +
263A GLY* 3.3 8.1 - - - -
264A SER* 3.0 42.3 + - - +
287A GLN* 4.9 0.9 + - - -
478A ASN 4.4 4.0 - - - +
479A TRP* 2.9 6.9 + - + +
480A ARG 2.9 0.4 - - - -
481A SER* 1.3 99.2 + - - +
483A LEU* 1.3 65.8 + - + +
484A TYR* 3.4 14.4 + - - -
485A LYS* 4.2 4.3 - - - +
486A TYR* 4.2 12.8 - - - -
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Residues in contact with LEU 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A MET* 5.4 0.4 - - - -
98A ASN* 3.8 7.4 + - - +
100A MET* 3.8 32.1 - - + +
101A VAL* 3.7 31.4 - - + -
104A MET* 3.9 33.0 - - + -
217A TYR* 5.8 1.1 - - + -
248A THR* 4.3 21.5 - - + +
251A ILE* 5.0 0.9 - - + -
479A TRP 3.0 15.4 + - - +
480A ARG* 3.8 1.1 - - - +
482A GLU* 1.3 81.9 - - + +
484A TYR* 1.3 63.2 + - - +
485A LYS 3.0 3.8 - - - -
486A TYR* 2.8 43.1 + - + +
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Residues in contact with TYR 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PHE* 5.1 4.7 - - - +
94A ASN 5.8 0.2 + - - -
95A MET* 3.7 42.2 + - + +
230A ASN 5.2 4.2 + - - -
231A LYS 5.0 6.8 + - - -
233A PHE* 3.7 42.5 - + + -
235A GLY* 4.7 2.4 - - - -
266A ALA* 5.6 2.6 - - - -
271A VAL* 5.8 0.2 - - - +
273A ARG* 3.1 36.9 + - - +
287A GLN* 3.7 25.3 + - - -
480A ARG 2.9 13.3 + - - +
481A SER* 3.9 10.5 - - - -
482A GLU 3.6 14.8 - - - -
483A LEU* 1.3 76.5 - - - +
485A LYS* 1.3 86.0 + - + +
486A TYR 3.3 6.2 + - - +
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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