Contacts of the helix formed by residues 461 - 481 (chain t) 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 t).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457t THR* 3.3 7.7 + - + +
458t ILE 3.3 6.9 - - - +
459t LEU 5.0 0.2 - - - -
460t ALA* 1.3 78.5 - - + +
462t GLU* 1.3 58.8 + - - +
463t GLU* 3.2 20.4 + - - +
464t VAL* 2.9 53.5 + - + +
465t LEU 3.2 4.7 + - - -
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Residues in contact with GLU 462 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458t ILE 4.9 0.2 - - - -
459t LEU 5.1 3.5 + - - +
460t ALA 4.1 4.1 + - - +
461t ASP* 1.3 72.4 + - - +
463t GLU* 1.3 57.1 + - - +
465t LEU* 3.4 16.4 + - + +
466t LEU* 3.0 30.5 + - - +
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Residues in contact with GLU 463 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461t ASP* 3.1 16.5 + - - +
462t GLU* 1.3 74.7 - - - +
464t VAL* 1.3 63.8 + - - +
466t LEU* 3.6 15.9 + - - +
467t GLN* 3.1 24.6 + - - +
470t ARG* 3.3 27.1 + - - -
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Residues in contact with VAL 464 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457t THR* 4.1 17.9 - - + +
458t ILE* 3.7 31.9 - - + +
461t ASP* 2.9 36.1 + - + +
463t GLU* 1.3 77.0 - - + +
465t LEU* 1.3 56.7 + - - +
467t GLN* 3.3 8.7 + - - +
468t LEU* 3.1 25.5 + - + +
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Residues in contact with LEU 465 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360t LYS* 4.3 23.8 - - + +
363t VAL* 4.6 7.7 - - + +
364t ARG* 3.7 39.0 - - + -
458t ILE* 3.7 37.5 - - + +
459t LEU* 5.2 4.3 - - + -
461t ASP 3.2 3.3 + - - +
462t GLU* 3.6 17.5 - - + +
464t VAL* 1.3 76.8 - - - +
466t LEU* 1.3 72.1 + - + +
468t LEU* 3.0 16.4 + - - +
469t VAL* 3.0 20.7 + - + +
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Residues in contact with LEU 466 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199t SER* 3.5 23.8 - - - +
356t LEU* 4.6 7.9 - - + -
360t LYS* 3.9 32.1 - - + -
462t GLU 3.0 17.7 + - - +
463t GLU* 3.8 15.3 - - - +
465t LEU* 1.3 81.1 - - + +
467t GLN* 1.3 56.0 + - - +
469t VAL* 3.3 8.4 + - + +
470t ARG* 3.0 57.5 + - + +
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Residues in contact with GLN 467 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463t GLU* 3.1 21.7 + - - +
464t VAL* 3.5 8.7 - - - +
465t LEU 3.2 0.2 - - - -
466t LEU* 1.3 73.8 - - - +
468t LEU* 1.3 55.0 + - - +
470t ARG* 3.1 36.0 + - - +
471t ASP* 2.6 76.0 + - - +
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Residues in contact with LEU 468 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363t VAL* 3.8 16.6 - - + -
366t ARG* 3.8 18.2 - - - +
367t THR* 4.6 2.0 - - - +
458t ILE* 3.9 33.4 - - + -
464t VAL* 3.1 11.5 + - + +
465t LEU* 3.0 13.9 + - - +
467t GLN* 1.3 72.7 - - - +
469t VAL* 1.3 62.2 + - - +
471t ASP* 3.3 9.5 + - + +
472t GLU* 3.0 51.6 + - + +
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Residues in contact with VAL 469 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163t ARG* 5.1 2.5 + - - +
199t SER* 6.4 0.2 - - - -
356t LEU* 4.2 15.3 - - + -
359t GLN* 4.0 26.5 - - + +
360t LYS* 4.3 13.2 - - + -
363t VAL* 3.9 31.9 - - + -
465t LEU* 3.0 20.9 + - + +
466t LEU* 3.3 12.3 + - + +
468t LEU* 1.3 75.9 - - - +
470t ARG* 1.3 57.9 + - + +
472t GLU* 3.9 4.3 - - - +
473t LEU* 3.0 48.3 + - + +
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Residues in contact with ARG 470 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196t LEU* 3.7 21.2 - - + +
199t SER* 2.9 51.9 + - - +
200t LYS* 3.7 24.6 - - - +
463t GLU* 3.3 22.0 + - - -
466t LEU* 3.0 30.5 + - + +
467t GLN* 3.1 51.3 + - - +
469t VAL* 1.3 78.0 - - + +
471t ASP* 1.3 57.4 + - - +
473t LEU* 3.5 4.2 + - - +
474t THR* 2.9 34.0 + - - -
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Residues in contact with ASP 471 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467t GLN* 2.6 55.4 + - - +
468t LEU* 3.7 11.5 + - + +
470t ARG* 1.3 76.3 - - - +
472t GLU* 1.3 58.5 + - + +
474t THR* 3.3 7.6 + - - -
475t GLU* 3.1 26.7 + - - +
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Residues in contact with GLU 472 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163t ARG* 2.8 47.6 + - - +
363t VAL* 4.1 2.6 - - - +
366t ARG* 2.9 33.5 + - - -
468t LEU* 3.0 35.0 + - + +
469t VAL 3.9 1.3 - - - +
471t ASP* 1.3 72.6 - - + +
473t LEU* 1.3 64.8 + - - +
475t GLU* 3.4 8.7 + - - +
476t ILE* 3.2 30.3 + - + +
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Residues in contact with LEU 473 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163t ARG* 3.8 21.9 - - - +
165t PRO* 4.6 1.6 - - + -
192t ILE* 3.6 36.2 - - + +
195t VAL* 3.7 29.2 - - + -
196t LEU* 4.6 10.3 - - + -
199t SER* 6.5 0.2 - - - -
355t TYR* 4.1 20.9 - - + +
356t LEU* 5.0 0.9 - - + -
359t GLN* 5.0 4.7 - - + +
469t VAL* 3.0 37.2 + - + +
470t ARG* 3.6 5.6 - - - +
472t GLU* 1.3 73.1 - - - +
474t THR* 1.3 52.5 + - - +
476t ILE* 3.2 9.0 + - + +
477t ARG* 2.9 33.3 + - - +
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Residues in contact with THR 474 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192t ILE* 4.8 1.1 - - - -
196t LEU* 3.7 19.4 - - - +
470t ARG 2.9 21.6 + - - -
471t ASP* 3.5 9.8 + - - +
472t GLU 3.3 0.2 - - - -
473t LEU* 1.3 73.4 - - - +
475t GLU* 1.3 57.7 + - - +
477t ARG* 3.3 29.7 + - - +
478t ASP* 3.0 37.3 + - - +
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Residues in contact with GLU 475 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471t ASP 3.1 14.6 + - - +
472t GLU* 3.5 12.3 - - - +
473t LEU 3.3 0.2 - - - -
474t THR* 1.3 75.4 - - - +
476t ILE* 1.3 58.8 + - + +
478t ASP* 3.4 7.2 + - - +
479t ARG* 3.1 35.1 + - - +
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Residues in contact with ILE 476 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134t GLU* 3.6 34.3 - - + +
163t ARG* 3.2 39.7 - - + +
164t PHE* 4.0 17.9 - - + -
188t LEU* 4.6 5.1 - - + +
192t ILE* 3.9 16.8 - - + -
472t GLU* 3.2 22.2 + - + +
473t LEU* 3.2 6.7 + - - +
475t GLU* 1.3 74.5 - - + +
477t ARG* 1.3 60.2 + - - +
479t ARG* 3.3 6.5 + - - +
480t PHE* 2.9 45.2 + - + +
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Residues in contact with ARG 477 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189t THR* 3.9 35.2 - - + +
192t ILE* 3.7 25.6 - - + -
193t ASN* 2.7 37.7 + - - -
196t LEU* 3.7 18.7 - - - +
473t LEU 2.9 13.3 + - - +
474t THR* 3.5 27.5 + - - +
476t ILE* 1.3 76.4 - - - +
478t ASP* 1.3 80.0 + - - +
481t GLY* 2.8 32.3 + - - +
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Residues in contact with ASP 478 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474t THR* 3.0 31.0 + - - +
475t GLU* 3.9 7.2 - - - +
476t ILE 3.2 0.2 - - - -
477t ARG* 1.3 101.8 + - - +
479t ARG* 1.3 59.5 + - - +
481t GLY 4.9 2.8 + - - +
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Residues in contact with ARG 479 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130t LYS* 5.3 2.2 + - - +
134t GLU* 3.3 28.1 + - - -
475t GLU* 3.1 20.1 + - - +
476t ILE* 4.0 11.4 - - - +
478t ASP* 1.3 79.0 - - - +
480t PHE* 1.3 96.6 + - + +
481t GLY 4.9 1.9 - - - +
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Residues in contact with PHE 480 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101t TYR* 4.1 17.5 - - - -
130t LYS* 3.8 20.6 - - + -
131t ILE* 3.7 48.9 - - + -
134t GLU* 3.7 22.2 - - + -
188t LEU* 3.8 17.5 - - + -
476t ILE* 2.9 21.4 + - + +
479t ARG* 1.3 119.0 - - + +
481t GLY* 1.3 69.8 + - - +
482t ASP* 3.6 3.6 + - - +
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Residues in contact with GLY 481 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188t LEU* 4.1 7.1 - - - +
189t THR* 3.1 23.6 - - - -
476t ILE 3.8 0.2 + - - -
477t ARG* 2.8 24.6 + - - +
478t ASP 5.1 2.4 - - - +
479t ARG 4.9 1.7 - - - +
480t PHE* 1.3 81.3 + - - +
482t ASP* 1.3 59.2 + - - +
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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
------------------------------------------------------------
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