Contacts of the helix formed by residues 474 - 484 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B GLN* 3.2 20.7 - - - +
40B GLN* 3.0 17.3 + - - +
41B GLY* 3.7 16.0 - - - +
105O GLN* 5.7 0.9 + - - -
472O GLY* 3.6 3.4 - - - -
473O GLY* 1.3 72.4 + - - +
475O MET* 1.3 63.2 + - - +
476O ARG* 3.0 56.4 + - - +
477O ASP* 3.1 33.5 + - - +
478O ASN* 3.8 4.5 - - - +
480O ARG* 5.2 1.0 + - - -
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Residues in contact with MET 475 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PHE* 4.3 2.7 - - + -
105O GLN* 3.9 16.5 + - - +
255O VAL* 3.5 27.4 - - + -
256O SER* 3.6 20.0 - - - +
257O THR* 3.8 18.4 - - + -
427O TRP* 3.6 35.7 - - + -
473O GLY* 3.3 23.2 + - - +
474O ASP* 1.3 71.4 + - - +
476O ARG* 1.3 60.3 + - - +
477O ASP 3.2 0.2 - - - -
478O ASN* 2.9 40.1 + - - +
479O TRP* 3.0 30.1 + - + -
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Residues in contact with ARG 476 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LYS* 6.3 0.6 - - - +
24B ILE* 3.9 26.3 - - - +
25B GLN* 4.0 11.7 + - - +
41B GLY* 5.9 2.2 - - - -
101O VAL* 3.2 13.4 - - + +
102O GLU* 3.4 39.9 + - - -
105O GLN* 4.2 30.3 + - + +
474O ASP* 3.0 34.9 + - - +
475O MET* 1.3 78.1 - - - +
477O ASP* 1.3 56.6 + - - +
479O TRP* 3.1 10.1 + - - -
480O ARG* 2.9 53.2 + - - +
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Residues in contact with ASP 477 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLN* 4.2 8.5 - - - +
96O TRP* 4.2 8.2 - - - -
260O LEU* 5.0 0.2 - - - +
283O THR* 3.6 28.0 + - - +
285O ILE* 3.4 15.2 - - + +
453O LEU* 4.3 22.8 - - + +
472O GLY* 5.5 1.7 - - - -
474O ASP* 3.1 21.4 + - - +
476O ARG* 1.3 71.5 - - - +
478O ASN* 1.3 66.6 + - - +
480O ARG* 3.3 26.1 + - - -
481O SER* 3.0 21.1 + - - -
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Residues in contact with ASN 478 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254O VAL 3.8 15.7 + - - +
256O SER* 3.3 25.6 + - - +
260O LEU* 3.6 28.5 - - + +
453O LEU* 4.1 8.9 - - - +
473O GLY 5.1 1.0 + - - -
474O ASP 3.8 3.6 - - - +
475O MET* 2.9 39.7 + - - +
477O ASP* 1.3 76.8 - - - +
479O TRP* 1.3 74.7 + - + +
481O SER* 2.7 26.7 + - - -
482O GLU* 3.9 5.0 + - - +
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Residues in contact with TRP 479 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O VAL* 3.8 22.0 - - + -
104O MET* 3.4 43.5 - - + -
105O GLN* 3.2 28.2 + - - +
108O VAL* 3.8 27.6 - - + -
251O ILE* 5.4 2.0 - - + -
252O ARG 5.1 1.1 - - - -
253O PRO* 3.8 38.4 - - + -
254O VAL 3.9 14.6 - - - -
255O VAL* 4.4 6.3 - - + -
427O TRP* 4.9 2.0 - + - -
475O MET* 3.0 30.3 + - + -
476O ARG* 3.1 15.0 + - - +
478O ASN* 1.3 80.2 - - + +
480O ARG* 1.3 60.5 + - - +
482O GLU* 3.1 7.2 + - + +
483O LEU* 2.9 32.8 + - + +
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Residues in contact with ARG 480 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95O MET* 3.2 41.9 + - + +
96O TRP* 3.2 48.2 + - - +
97O LYS* 5.0 0.4 - - - +
98O ASN 4.7 1.2 + - - -
101O VAL* 3.7 31.4 - - + +
102O GLU* 4.8 2.4 + - - -
285O ILE* 4.1 2.2 - - + -
474O ASP* 5.2 1.8 + - - -
476O ARG* 2.9 52.0 + - - +
477O ASP* 3.4 23.4 + - - +
479O TRP* 1.3 71.2 - - - +
481O SER* 1.3 55.2 + - - +
482O GLU 2.6 17.1 + - - -
483O LEU* 3.0 5.1 + - - +
484O TYR* 3.0 27.7 + - - +
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Residues in contact with SER 481 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95O MET* 5.1 1.6 - - - -
260O LEU* 3.2 32.5 - - - +
264O SER* 5.1 0.3 + - - +
273O ARG* 5.5 3.6 + - - +
285O ILE* 3.8 20.5 - - - +
287O GLN* 4.8 11.0 + - - +
477O ASP 3.0 10.6 + - - -
478O ASN 2.7 16.8 + - - -
480O ARG* 1.3 73.7 - - - +
482O GLU* 1.3 71.1 + - - +
484O TYR* 3.6 18.8 - - - -
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Residues in contact with GLU 482 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249O HIS* 3.2 30.6 + - - +
251O ILE* 3.6 38.2 - - + +
252O ARG 5.6 1.1 - - - +
263O GLY* 3.7 10.5 - - - -
264O SER* 2.5 45.4 + - - +
478O ASN 4.4 4.7 - - - +
479O TRP* 3.1 8.7 + - + +
480O ARG 2.6 5.9 + - - -
481O SER* 1.3 94.5 + - - +
483O LEU* 1.3 56.9 + - - +
484O TYR* 3.2 15.8 + - - -
485O LYS* 3.9 9.2 + - - +
486O TYR* 4.1 2.9 - - - -
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Residues in contact with LEU 483 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95O MET* 6.0 0.2 - - - -
98O ASN* 3.7 17.7 + - - +
100O MET* 3.7 56.8 - - + +
101O VAL* 4.1 7.6 - - + +
104O MET* 4.2 17.7 - - + -
217O TYR* 5.3 3.6 - - + -
248O THR* 4.2 6.5 - - + +
251O ILE* 3.5 27.4 - - + -
479O TRP* 2.9 21.1 + - + +
480O ARG* 3.7 3.6 - - - +
482O GLU* 1.3 74.8 - - - +
484O TYR* 1.3 61.9 + - - +
485O LYS 2.9 7.7 + - - -
486O TYR* 3.2 24.2 + - + +
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Residues in contact with TYR 484 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93O PHE* 4.5 8.8 - - - -
95O MET* 3.5 52.4 - - + +
231O LYS 5.6 2.1 + - - -
233O PHE* 3.9 20.8 - + + -
235O GLY* 4.2 12.0 - - - +
264O SER* 6.1 0.7 - - - -
266O ALA* 5.5 0.3 - - - -
273O ARG* 2.5 39.4 + - - -
287O GLN* 3.3 26.0 + - - -
480O ARG* 3.0 6.9 + - - +
481O SER* 3.6 25.8 - - - -
482O GLU* 3.7 4.9 - - - -
483O LEU* 1.3 77.2 - - - +
485O LYS* 1.3 94.6 + - + +
486O TYR 3.4 3.6 + - - +
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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