Contacts of the helix formed by residues 461 - 481 (chain J) in PDB entry 6QX2
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 461 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457J THR* 3.3 7.5 + - + +
458J ILE 3.2 14.6 - - - +
459J LEU 5.0 0.2 - - - -
460J ALA* 1.3 80.0 - - + +
462J GLU* 1.3 54.7 + - - +
463J GLU* 3.2 20.1 + - - +
464J VAL* 2.9 52.5 + - + +
465J LEU 3.3 1.0 + - - -
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Residues in contact with GLU 462 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360J LYS* 6.1 1.2 - - - -
364J ARG* 4.8 14.1 + - - +
458J ILE 4.9 0.2 - - - -
459J LEU 5.1 2.6 + - - +
460J ALA 4.1 2.2 + - - -
461J ASP* 1.3 72.5 + - - +
463J GLU* 1.3 56.5 + - - +
465J LEU* 3.4 18.9 + - + +
466J LEU* 3.0 30.0 + - - +
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Residues in contact with GLU 463 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461J ASP* 3.1 16.6 + - - +
462J GLU* 1.3 75.1 - - - +
464J VAL* 1.3 64.9 + - + +
466J LEU* 3.6 16.1 + - - +
467J GLN* 3.1 23.7 + - - +
470J ARG* 3.3 24.5 + - - -
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Residues in contact with VAL 464 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457J THR* 4.1 17.9 - - + +
458J ILE* 3.7 32.3 - - + +
461J ASP* 2.9 35.4 + - + +
463J GLU* 1.3 77.4 - - + +
465J LEU* 1.3 57.2 + - - +
467J GLN* 3.3 8.4 + - - +
468J LEU* 3.1 25.0 + - + +
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Residues in contact with LEU 465 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360J LYS* 4.2 10.8 - - + +
363J VAL* 3.4 31.9 - - + -
364J ARG* 3.6 57.0 - - + +
367J THR* 5.3 0.2 - - - -
458J ILE* 3.6 36.1 + - + +
459J LEU* 5.9 1.6 - - + -
461J ASP 3.3 2.9 + - - +
462J GLU* 3.6 17.5 - - + +
463J GLU 3.3 0.2 - - - -
464J VAL* 1.3 76.4 - - - +
466J LEU* 1.3 66.0 + - - +
468J LEU* 3.0 16.6 + - - +
469J VAL* 3.0 15.5 + - + +
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Residues in contact with LEU 466 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199J SER* 3.5 23.3 - - - +
356J LEU* 4.6 8.7 - - + -
360J LYS* 3.9 39.3 - - + -
462J GLU 3.0 17.7 + - - +
463J GLU* 3.8 17.0 - - - +
465J LEU* 1.3 75.9 - - - +
467J GLN* 1.3 55.6 + - - +
469J VAL* 3.3 10.5 + - + +
470J ARG* 3.0 57.0 + - - +
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Residues in contact with GLN 467 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463J GLU* 3.1 18.1 + - - +
464J VAL* 3.5 11.9 - - - +
465J LEU 3.2 0.4 - - - -
466J LEU* 1.3 73.1 - - - +
468J LEU* 1.3 56.0 + - - +
470J ARG* 3.1 35.8 + - - +
471J ASP* 2.7 74.5 + - - +
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Residues in contact with LEU 468 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363J VAL* 3.8 16.2 - - + -
366J ARG* 3.8 17.7 - - - +
367J THR* 4.6 2.0 - - - +
458J ILE* 3.9 33.0 - - + -
464J VAL* 3.1 12.7 + - + +
465J LEU* 3.0 13.8 + - - +
467J GLN* 1.3 73.2 - - - +
469J VAL* 1.3 62.0 + - - +
471J ASP* 3.3 9.6 + - + +
472J GLU* 3.0 51.8 + - + +
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Residues in contact with VAL 469 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163J ARG* 5.1 2.9 + - - +
356J LEU* 4.1 17.0 - - + -
359J GLN* 4.0 25.8 - - + +
360J LYS* 4.2 14.6 - - + -
363J VAL* 3.9 31.0 - - + -
465J LEU* 3.0 16.7 + - + +
466J LEU* 3.3 14.3 + - + +
468J LEU* 1.3 76.5 - - - +
470J ARG* 1.3 58.6 + - + +
472J GLU* 3.3 4.0 + - - +
473J LEU* 3.0 48.2 + - + +
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Residues in contact with ARG 470 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196J LEU* 3.7 17.6 - - + +
199J SER* 2.8 52.3 + - - +
200J LYS* 3.7 33.0 - - - +
463J GLU* 3.3 22.6 + - - -
466J LEU* 3.0 31.3 + - + +
467J GLN* 3.1 49.2 + - - +
469J VAL* 1.3 75.7 - - + +
471J ASP* 1.3 58.0 + - - +
473J LEU* 3.5 4.8 + - - +
474J THR* 2.9 34.0 + - - -
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Residues in contact with ASP 471 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467J GLN* 2.7 53.7 + - - +
468J LEU* 3.3 12.8 + - + +
470J ARG* 1.3 75.2 - - - +
472J GLU* 1.3 58.5 + - + +
474J THR* 3.3 8.8 + - - -
475J GLU* 3.1 26.3 + - - +
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Residues in contact with GLU 472 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J ARG* 3.5 19.4 + - - +
163J ARG* 2.8 47.1 + - - +
363J VAL* 4.1 2.5 - - - +
366J ARG* 2.9 32.0 + - - -
468J LEU* 3.0 34.5 + - + +
469J VAL 3.9 1.3 - - - +
471J ASP* 1.3 72.8 - - + +
473J LEU* 1.3 64.1 + - - +
475J GLU* 3.4 10.3 + - - +
476J ILE* 3.2 29.0 + - + +
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Residues in contact with LEU 473 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163J ARG* 3.8 22.1 - - - +
165J PRO* 4.6 2.2 - - + -
192J ILE* 3.7 35.9 - - + +
195J VAL* 3.7 29.8 - - + -
196J LEU* 4.6 9.4 - - + -
199J SER* 6.5 0.2 - - - -
355J TYR* 4.1 21.1 - - + +
356J LEU* 5.0 1.1 - - + -
359J GLN* 5.2 4.7 - - + +
469J VAL* 3.0 37.0 + - + +
470J ARG* 3.6 5.4 - - - +
472J GLU* 1.3 73.2 - - - +
474J THR* 1.3 54.3 + - - +
476J ILE* 3.2 8.3 + - + +
477J ARG* 2.9 33.1 + - - +
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Residues in contact with THR 474 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192J ILE* 4.8 1.1 - - - -
196J LEU* 3.6 19.2 - - - +
470J ARG 2.9 21.4 + - - -
471J ASP* 3.5 8.7 - - - +
472J GLU 3.3 0.2 - - - -
473J LEU* 1.3 73.6 - - - +
475J GLU* 1.3 58.7 - - - +
477J ARG* 3.3 29.9 + - - +
478J ASP* 3.0 38.7 + - - +
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Residues in contact with GLU 475 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J ARG* 4.4 7.1 + - - -
471J ASP 3.1 12.7 + - - +
472J GLU* 3.5 11.7 - - - +
474J THR* 1.3 76.0 - - - +
476J ILE* 1.3 63.4 + - - +
478J ASP* 3.4 7.2 + - - +
479J ARG* 2.9 67.5 + - - +
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Residues in contact with ILE 476 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J GLU* 3.6 33.7 - - + +
137J ARG* 4.0 5.4 - - - +
163J ARG* 3.2 39.0 - - + +
164J PHE* 4.0 17.7 - - + -
188J LEU* 4.6 4.9 - - + -
192J ILE* 3.8 16.8 - - + -
472J GLU* 3.2 20.0 + - + +
473J LEU* 3.2 7.4 + - - +
475J GLU* 1.3 82.4 - - - +
477J ARG* 1.3 60.6 + - - +
479J ARG* 3.3 2.1 + - - +
480J PHE* 2.9 44.1 + - + +
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Residues in contact with ARG 477 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189J THR* 3.9 36.4 - - + +
192J ILE* 3.7 24.7 - - + -
193J ASN* 2.7 36.6 + - - -
196J LEU* 3.7 19.5 - - - +
473J LEU 2.9 14.2 + - - +
474J THR* 3.5 26.4 - - - +
476J ILE* 1.3 76.2 - - - +
478J ASP* 1.3 81.3 + - - +
481J GLY* 2.8 31.9 + - - +
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Residues in contact with ASP 478 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474J THR* 3.0 31.5 + - - +
475J GLU* 3.8 6.8 - - - +
476J ILE 3.2 0.2 - - - -
477J ARG* 1.3 102.4 + - - +
479J ARG* 1.3 59.7 + - - +
481J GLY 5.0 2.3 + - - +
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Residues in contact with ARG 479 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J LYS* 5.3 3.0 + - - +
134J GLU* 3.3 27.1 + - - -
137J ARG* 4.9 1.6 - - - +
475J GLU* 2.9 49.4 + - - +
476J ILE* 4.0 4.1 - - - +
478J ASP* 1.3 78.4 - - - +
480J PHE* 1.3 97.2 + - + +
481J GLY 5.0 1.6 - - - +
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Residues in contact with PHE 480 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J TYR* 4.1 9.9 - - - -
130J LYS* 3.8 19.7 - - + -
131J ILE* 3.7 48.7 - - + -
134J GLU* 3.7 22.4 - - + -
188J LEU* 3.8 21.0 - - + +
476J ILE* 2.9 23.2 + - + +
479J ARG* 1.3 117.4 - - + +
481J GLY* 1.3 72.2 + - - +
482J ASP* 3.6 6.4 + - - +
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Residues in contact with GLY 481 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188J LEU* 4.2 6.5 - - - +
189J THR* 3.1 24.9 - - - -
476J ILE 3.9 0.6 + - - -
477J ARG* 2.8 22.9 + - - +
478J ASP 5.2 2.1 - - - +
479J ARG 5.0 1.6 - - - +
480J PHE* 1.3 82.4 + - - +
482J ASP* 1.3 58.7 + - - +
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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
------------------------------------------------------------
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