Contacts of the helix formed by residues 461 - 481 (chain r) 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 r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457r THR* 3.2 7.7 + - + +
458r ILE 3.3 8.3 - - - +
460r ALA* 1.3 77.3 - - + +
462r GLU* 1.3 55.4 + - - +
463r GLU* 3.2 22.1 + - - +
464r VAL* 2.9 50.1 + - + +
465r LEU 3.3 8.1 + - - -
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Residues in contact with GLU 462 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360r LYS* 4.7 13.9 + - - -
364r ARG* 3.7 22.7 + - - +
458r ILE 4.9 0.2 - - - -
459r LEU 5.1 2.1 + - - +
460r ALA 4.1 2.4 + - - -
461r ASP* 1.3 71.3 + - - +
463r GLU* 1.3 56.5 + - - +
465r LEU* 3.4 16.6 + - + +
466r LEU* 3.0 30.7 + - - +
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Residues in contact with GLU 463 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461r ASP* 3.1 17.2 + - - +
462r GLU* 1.3 75.2 - - - +
464r VAL* 1.3 64.9 + - + +
466r LEU* 3.6 15.8 + - - +
467r GLN* 3.1 24.8 + - - +
470r ARG* 3.3 24.1 + - - -
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Residues in contact with VAL 464 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457r THR* 4.1 18.2 - - + +
458r ILE* 3.7 32.1 - - + +
461r ASP* 2.9 35.4 + - + +
463r GLU* 1.3 76.7 - - + +
465r LEU* 1.3 56.9 + - - +
467r GLN* 3.3 8.7 + - - +
468r LEU* 3.1 25.3 + - + +
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Residues in contact with LEU 465 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360r LYS* 4.3 9.9 - - + +
363r VAL* 3.4 32.8 - - + -
364r ARG* 3.6 56.8 - - + +
458r ILE* 3.6 36.7 + - + +
459r LEU* 5.9 1.8 - - + -
461r ASP 3.3 3.3 + - - +
462r GLU* 3.6 17.7 - - + +
463r GLU 3.3 0.2 - - - -
464r VAL* 1.3 75.1 - - - +
466r LEU* 1.3 65.6 + - - +
468r LEU* 3.0 16.8 + - - +
469r VAL* 3.0 15.1 + - + +
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Residues in contact with LEU 466 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199r SER* 3.5 25.1 - - - +
356r LEU* 4.6 8.3 - - + -
360r LYS* 3.9 38.8 - - + -
462r GLU 3.0 17.5 + - - +
463r GLU* 3.8 16.4 - - - +
465r LEU* 1.3 77.3 - - - +
467r GLN* 1.3 56.2 + - - +
469r VAL* 3.3 10.7 + - + +
470r ARG* 3.0 56.4 + - + +
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Residues in contact with GLN 467 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463r GLU* 3.1 17.6 + - - +
464r VAL* 3.5 12.1 - - - +
465r LEU 3.2 0.2 - - - -
466r LEU* 1.3 72.5 - - - +
468r LEU* 1.3 54.9 + - - +
470r ARG* 3.1 35.7 + - - +
471r ASP* 2.7 75.9 + - - +
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Residues in contact with LEU 468 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363r VAL* 3.8 16.2 - - + -
366r ARG* 3.8 18.2 - - - +
367r THR* 4.6 2.0 - - - +
458r ILE* 3.8 32.8 - - + -
464r VAL* 3.1 11.7 + - + +
465r LEU* 3.0 14.3 + - - +
467r GLN* 1.3 73.0 - - - +
469r VAL* 1.3 63.1 + - - +
471r ASP* 3.3 10.2 + - + +
472r GLU* 3.0 52.2 + - + +
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Residues in contact with VAL 469 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163r ARG* 5.1 2.9 + - - +
356r LEU* 4.1 16.4 - - + -
359r GLN* 4.0 26.7 - - + +
360r LYS* 4.2 17.3 - - + -
363r VAL* 3.9 31.2 - - + -
465r LEU* 3.0 17.8 + - + +
466r LEU* 3.3 12.8 + - + +
468r LEU* 1.3 74.9 - - - +
470r ARG* 1.3 65.5 + - + +
472r GLU* 3.3 3.4 + - - +
473r LEU* 3.0 43.0 + - + +
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Residues in contact with ARG 470 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196r LEU* 3.7 19.0 - - + +
199r SER* 2.9 51.7 + - - +
200r LYS* 3.7 31.6 - - - +
463r GLU* 3.3 22.4 + - - -
466r LEU* 3.0 30.7 + - + +
467r GLN* 3.1 50.9 + - - +
469r VAL* 1.3 77.8 - - + +
471r ASP* 1.3 59.2 + - - +
473r LEU* 3.5 4.0 + - + +
474r THR* 2.9 33.8 + - - -
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Residues in contact with ASP 471 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467r GLN* 2.7 53.8 + - - +
468r LEU* 3.7 12.3 + - + +
470r ARG* 1.3 76.3 - - - +
472r GLU* 1.3 58.5 + - + +
474r THR* 3.3 8.5 + - - +
475r GLU* 3.1 26.5 + - - +
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Residues in contact with GLU 472 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137r ARG* 3.6 19.1 + - - +
163r ARG* 2.8 47.0 + - - +
363r VAL* 4.1 1.9 - - - +
366r ARG* 2.9 30.3 + - - -
468r LEU* 3.0 36.8 + - + +
469r VAL 3.9 1.3 - - - +
471r ASP* 1.3 72.6 - - + +
473r LEU* 1.3 64.8 + - - +
475r GLU* 3.4 10.4 + - - +
476r ILE* 3.2 28.5 + - + +
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Residues in contact with LEU 473 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163r ARG* 3.8 21.5 - - - +
165r PRO* 4.5 2.0 - - + -
192r ILE* 3.6 36.7 - - + +
195r VAL* 3.7 29.4 - - + -
196r LEU* 4.6 11.0 - - + -
355r TYR* 4.1 21.1 - - + +
356r LEU* 5.0 0.9 - - + -
359r GLN* 5.2 4.5 - - + +
469r VAL* 3.0 37.4 + - + +
470r ARG* 3.6 5.2 - - - +
472r GLU* 1.3 74.3 - - - +
474r THR* 1.3 51.7 + - - +
476r ILE* 3.2 8.5 + - + +
477r ARG* 2.9 33.4 + - - +
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Residues in contact with THR 474 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192r ILE* 4.8 1.1 - - - -
196r LEU* 3.6 19.9 - - - +
470r ARG 2.9 21.9 + - - -
471r ASP* 3.5 8.7 - - - +
472r GLU 3.3 0.4 - - - -
473r LEU* 1.3 74.7 - - - +
475r GLU* 1.3 59.8 + - - +
477r ARG* 3.3 29.6 + - - +
478r ASP* 3.0 39.5 + - - +
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Residues in contact with GLU 475 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137r ARG* 4.5 7.1 + - - -
471r ASP 3.1 13.3 + - - +
472r GLU* 3.5 11.9 - - - +
473r LEU 3.3 0.2 - - - -
474r THR* 1.3 75.6 - - - +
476r ILE* 1.3 63.4 + - - +
478r ASP* 3.4 7.4 + - - +
479r ARG* 2.9 64.1 + - - +
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Residues in contact with ILE 476 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134r GLU* 3.6 33.7 - - + +
137r ARG* 4.0 6.3 - - - +
163r ARG* 3.2 38.8 - - + +
164r PHE* 3.9 17.9 - - + -
188r LEU* 4.6 4.9 - - + -
192r ILE* 3.9 17.3 - - + -
472r GLU* 3.2 20.4 + - + +
473r LEU* 3.5 6.5 - - - +
475r GLU* 1.3 80.4 - - - +
477r ARG* 1.3 61.1 + - - +
479r ARG* 3.3 2.3 + - - +
480r PHE* 2.9 44.7 + - + +
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Residues in contact with ARG 477 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188r LEU* 5.4 0.2 - - - -
189r THR* 3.9 37.2 + - + +
192r ILE* 3.7 24.7 - - + -
193r ASN* 2.7 37.7 + - - +
196r LEU* 3.7 18.6 - - - +
473r LEU 2.9 13.6 + - - +
474r THR* 3.3 28.0 + - - +
476r ILE* 1.3 76.7 - - - +
478r ASP* 1.3 81.3 + - - +
481r GLY* 2.8 31.8 + - - +
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Residues in contact with ASP 478 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474r THR* 3.0 32.0 + - - +
475r GLU* 3.9 6.3 - - - +
477r ARG* 1.3 102.9 + - - +
479r ARG* 1.3 60.7 + - - +
481r GLY 5.0 2.6 + - - +
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Residues in contact with ARG 479 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130r LYS* 5.3 2.4 + - - +
134r GLU* 3.3 27.5 + - - -
137r ARG* 4.9 1.8 - - - +
475r GLU* 2.9 48.4 + - - +
476r ILE* 3.3 4.2 + - - +
478r ASP* 1.3 79.3 - - - +
480r PHE* 1.3 96.0 + - + +
481r GLY 4.9 1.8 - - - +
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Residues in contact with PHE 480 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101r TYR* 3.9 16.5 - - - -
130r LYS* 3.8 18.4 - - + -
131r ILE* 3.7 50.3 - - + -
134r GLU* 3.7 21.3 - - + -
188r LEU* 3.8 17.0 - - + -
476r ILE* 2.9 22.1 + - + +
479r ARG* 1.3 119.1 - - + +
481r GLY* 1.3 70.9 + - - +
482r ASP* 3.6 4.2 + - - +
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Residues in contact with GLY 481 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188r LEU* 4.1 7.6 - - - +
189r THR* 3.2 23.8 - - - -
476r ILE 3.8 0.4 + - - -
477r ARG* 2.8 23.6 + - - +
478r ASP 5.1 2.1 - - - +
479r ARG 4.9 1.6 - - - +
480r PHE* 1.3 82.0 + - - +
482r ASP* 1.3 60.6 + - - +
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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
------------------------------------------------------------
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