Contacts of the helix formed by residues 461 - 481 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457C THR* 3.2 7.3 + - + +
458C ILE 3.3 14.2 - - - +
459C LEU 3.5 0.4 - - - -
460C ALA* 1.3 77.9 - - + +
462C GLU* 1.3 57.3 + - - +
463C GLU* 3.2 20.0 + - - +
464C VAL* 2.9 48.7 + - + +
465C LEU 3.3 2.8 + - - -
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Residues in contact with GLU 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C ARG* 5.9 3.3 - - - -
458C ILE 4.8 0.7 - - - -
459C LEU 5.2 2.8 + - - +
460C ALA 4.1 2.8 + - - -
461C ASP* 1.3 72.2 + - - +
463C GLU* 1.3 57.0 + - - +
465C LEU* 3.4 19.7 + - + +
466C LEU* 3.0 30.0 + - - +
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Residues in contact with GLU 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C ASP* 3.1 16.6 + - - +
462C GLU* 1.3 74.9 - - - +
464C VAL* 1.3 65.9 + - + +
466C LEU* 3.6 17.4 + - - +
467C GLN* 3.1 24.1 + - - +
470C ARG* 3.3 23.4 + - - -
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Residues in contact with VAL 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C THR* 4.1 21.1 - - + +
458C ILE* 3.8 31.0 - - + +
461C ASP* 2.9 34.9 + - + +
463C GLU* 1.3 77.4 - - + +
465C LEU* 1.3 60.7 + - - +
467C GLN* 3.3 8.9 + - - +
468C LEU* 3.1 20.1 + - - +
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Residues in contact with LEU 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LYS* 4.1 32.5 - - + +
363C VAL* 4.5 7.6 - - + +
364C ARG* 3.7 39.0 - - + -
458C ILE* 3.8 37.0 + - + +
459C LEU* 5.4 3.1 - - + -
461C ASP 3.3 3.7 + - - +
462C GLU* 3.6 22.7 - - + +
464C VAL* 1.3 76.1 - - - +
466C LEU* 1.3 71.4 + - + +
468C LEU* 3.0 17.6 + - - +
469C VAL* 3.0 15.0 + - + +
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Residues in contact with LEU 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C SER* 3.5 24.7 - - - +
356C LEU* 4.4 10.5 - - + -
360C LYS* 3.9 31.2 - - + -
462C GLU 3.0 17.9 + - - +
463C GLU* 3.8 16.6 - - - +
465C LEU* 1.3 81.1 - - + +
467C GLN* 1.3 56.1 + - - +
469C VAL* 3.3 7.4 + - + +
470C ARG* 3.0 57.6 + - - +
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Residues in contact with GLN 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C GLU* 3.1 17.9 + - - +
464C VAL* 3.4 11.9 - - - +
465C LEU 3.2 0.2 - - - -
466C LEU* 1.3 72.4 - - - +
468C LEU* 1.3 56.2 + - - +
470C ARG* 3.1 35.1 + - - +
471C ASP* 2.7 75.5 + - - +
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Residues in contact with LEU 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C VAL* 3.8 16.6 - - + -
366C ARG* 3.7 18.4 - - - +
367C THR* 4.6 2.0 - - - +
458C ILE* 3.8 32.8 - - + -
464C VAL 3.1 11.3 + - - +
465C LEU* 3.0 13.9 + - - +
467C GLN* 1.3 72.5 - - - +
469C VAL* 1.3 61.3 + - - +
471C ASP* 3.3 10.6 + - + +
472C GLU* 3.0 52.2 + - + +
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Residues in contact with VAL 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C ARG* 5.1 2.5 + - - +
356C LEU* 4.0 16.6 - - + -
359C GLN* 4.0 29.8 - - + +
360C LYS* 4.2 10.1 - - + -
363C VAL* 3.9 30.7 - - + -
465C LEU* 3.0 19.8 + - + +
466C LEU* 3.3 11.6 + - + +
468C LEU* 1.3 76.2 - - - +
470C ARG* 1.3 57.6 + - + +
472C GLU* 3.3 3.5 + - - +
473C LEU* 3.0 49.4 + - + +
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Residues in contact with ARG 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C LEU* 3.7 20.8 - - + +
199C SER* 2.9 51.5 + - - +
200C LYS* 3.7 23.9 - - - +
463C GLU* 3.3 23.2 + - - -
466C LEU* 3.0 29.6 + - + +
467C GLN* 3.1 49.6 + - - +
469C VAL* 1.3 77.0 - - + +
471C ASP* 1.3 58.8 - - - +
473C LEU* 3.5 4.6 + - - +
474C THR* 2.9 34.0 + - - -
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Residues in contact with ASP 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C GLN* 2.7 52.9 + - - +
468C LEU* 3.3 12.9 + - + +
470C ARG* 1.3 76.6 - - - +
472C GLU* 1.3 59.9 + - + +
474C THR* 3.3 8.3 + - - +
475C GLU* 3.1 26.5 + - - +
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Residues in contact with GLU 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ARG* 2.8 41.1 + - - +
363C VAL* 4.1 2.3 - - - +
366C ARG* 2.9 34.5 + - - -
468C LEU* 3.0 36.5 + - + +
469C VAL 3.9 1.1 - - - +
471C ASP* 1.3 72.9 - - + +
473C LEU* 1.3 65.1 + - - +
475C GLU* 3.4 9.1 + - - +
476C ILE* 3.2 29.4 + - + +
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Residues in contact with LEU 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C ARG* 3.8 21.7 - - - +
165C PRO* 4.5 2.2 - - + -
192C ILE* 3.6 37.2 - - + +
195C VAL* 3.7 29.8 - - + -
196C LEU* 4.6 9.4 - - + -
355C TYR* 4.0 21.8 - - + +
356C LEU* 5.0 0.9 - - + -
359C GLN* 5.1 4.7 - - + +
469C VAL* 3.0 36.6 + - + +
470C ARG* 3.6 5.2 - - - +
472C GLU* 1.3 74.6 - - - +
474C THR* 1.3 52.0 + - - +
476C ILE* 3.2 9.2 + - + +
477C ARG* 2.9 33.1 + - - +
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Residues in contact with THR 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C ILE* 4.6 1.5 - - - +
196C LEU* 3.7 19.8 - - - +
470C ARG 2.9 22.0 + - - -
471C ASP* 3.5 9.1 - - - +
472C GLU 3.3 0.2 - - - -
473C LEU* 1.3 72.8 - - - +
475C GLU* 1.3 59.5 + - - +
477C ARG* 3.3 29.6 + - - +
478C ASP* 3.0 38.3 + - - +
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Residues in contact with GLU 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471C ASP 3.1 13.8 + - - +
472C GLU* 3.5 12.6 - - - +
473C LEU 3.3 0.2 - - - -
474C THR* 1.3 73.8 - - - +
476C ILE* 1.3 58.9 + - + +
478C ASP* 3.4 7.8 + - - +
479C ARG* 3.1 35.4 + - - +
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Residues in contact with ILE 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ILE* 5.9 0.2 - - + -
134C GLU* 3.6 34.5 - - + +
163C ARG* 3.2 39.9 - - + +
164C PHE* 4.0 17.5 - - + -
188C LEU* 4.6 5.4 - - + -
192C ILE* 3.9 16.4 - - + -
472C GLU* 3.2 21.7 + - + +
473C LEU* 3.2 7.1 + - - +
475C GLU* 1.3 72.5 - - + +
477C ARG* 1.3 61.1 + - - +
479C ARG* 3.3 7.4 + - - +
480C PHE* 2.9 45.1 + - + +
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Residues in contact with ARG 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LEU* 5.3 0.7 - - - -
189C THR* 3.9 37.2 + - + +
192C ILE* 3.7 24.9 - - + -
193C ASN* 2.7 37.0 + - - -
196C LEU* 3.7 18.4 - - - +
473C LEU 2.9 13.4 + - - +
474C THR* 3.3 28.6 + - - +
476C ILE* 1.3 76.2 - - - +
478C ASP* 1.3 79.8 + - - +
481C GLY* 2.8 32.0 + - - +
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Residues in contact with ASP 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C THR* 3.0 30.4 + - - +
475C GLU* 3.4 6.9 + - - +
476C ILE 3.2 0.2 - - - -
477C ARG* 1.3 101.3 + - - +
479C ARG* 1.3 59.6 + - - +
481C GLY 4.9 1.9 + - - +
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Residues in contact with ARG 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LYS* 5.3 2.4 + - - +
134C GLU* 3.3 28.5 + - - -
475C GLU* 3.1 19.7 + - - +
476C ILE* 3.3 10.8 + - - +
478C ASP* 1.3 79.1 - - - +
480C PHE* 1.3 95.5 + - + +
481C GLY 3.9 1.7 - - - +
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Residues in contact with PHE 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TYR* 4.1 13.2 - - - -
130C LYS* 3.8 21.8 - - + -
131C ILE* 3.7 48.0 - - + -
134C GLU* 3.7 18.4 - - + -
188C LEU* 3.8 21.7 - - + +
476C ILE* 2.9 25.7 + - + +
479C ARG* 1.3 118.9 - - + +
481C GLY* 1.3 70.9 + - - +
482C ASP* 3.6 3.6 + - - +
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Residues in contact with GLY 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LEU* 4.1 6.7 - - - +
189C THR* 3.1 22.9 - - - -
476C ILE 3.9 0.6 + - - -
477C ARG* 2.8 24.8 + - - +
478C ASP 5.2 1.9 - - - +
479C ARG 5.0 1.7 - - - +
480C PHE* 1.3 81.7 + - - +
482C ASP* 1.3 58.5 + - - +
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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
------------------------------------------------------------
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