Contacts of the helix formed by residues 460 - 471 (chain A) in PDB entry 2QR8
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 PRO 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453A ILE* 3.7 20.4 - - + -
455A LYS* 4.7 9.6 - - + -
458A ARG* 3.2 39.5 - - - +
459A ASP* 1.3 88.6 - - - +
461A THR* 1.3 62.7 + - - +
462A GLU 3.3 2.7 - - - -
463A GLU* 3.2 6.2 + - - +
464A ILE* 3.0 29.4 + - + +
489A VAL* 3.9 31.2 - - + -
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Residues in contact with THR 461 (chain A).
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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459A ASP* 2.5 31.9 + - - -
460A PRO* 1.3 75.4 - - - +
462A GLU* 1.3 56.8 + - - +
464A ILE* 3.4 6.9 + - - +
465A GLU* 2.9 54.6 + - + +
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Residues in contact with GLU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A ARG* 6.1 0.9 - - - +
459A ASP 4.5 4.6 + - - +
460A PRO 3.3 0.6 - - - -
461A THR* 1.3 74.5 - - - +
463A GLU* 1.3 66.0 + - - +
465A GLU* 3.5 11.8 + - - +
466A ILE* 2.9 34.1 + - + +
565A ALA 3.5 21.5 - - - +
566A LYS* 3.3 21.6 - - + +
567A GLN* 2.7 37.3 + - - +
569A ARG* 3.0 25.5 + - - -
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Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LYS* 2.7 36.6 + - - +
453A ILE* 4.2 6.7 - - - +
458A ARG* 3.1 37.5 + - - +
460A PRO* 3.2 9.4 + - + +
462A GLU* 1.3 79.3 - - - +
464A ILE* 1.3 63.1 + - + +
466A ILE* 3.3 5.1 + - - +
467A LEU* 3.1 37.4 + - + +
491A VAL* 5.5 4.4 - - - +
561A ASP* 5.0 0.9 - - - -
562A PHE* 3.5 32.0 + - + +
563A GLY* 3.4 9.3 + - - -
565A ALA 5.2 0.4 + - - -
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Residues in contact with ILE 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A PRO* 3.0 28.4 + - + +
461A THR* 3.9 5.6 - - - +
463A GLU* 1.3 75.6 - - + +
465A GLU* 1.3 64.9 + - + +
467A LEU* 3.2 9.3 + - - +
468A LEU* 3.0 43.1 + - + +
479A LEU* 4.9 1.1 - - + -
482A VAL* 3.8 31.4 - - + -
489A VAL* 3.4 34.3 - - + -
491A VAL* 4.0 17.3 - - + -
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Residues in contact with GLU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A THR* 2.9 37.8 + - + +
462A GLU* 3.6 20.2 - - - +
464A ILE* 1.3 76.9 - - + +
466A ILE* 1.3 62.0 + - - +
468A LEU* 3.2 12.9 + - + +
469A ARG* 3.0 26.2 + - - +
567A GLN* 4.5 14.2 - - + +
569A ARG* 3.9 17.7 + - - -
575A LEU* 5.4 1.6 - - - +
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Residues in contact with ILE 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A GLU* 2.9 33.5 + - + +
463A GLU* 3.6 7.4 - - - +
464A ILE 3.3 0.2 - - - -
465A GLU* 1.3 75.4 - - - +
467A LEU* 1.3 58.6 + - + +
470A TYR* 2.9 48.6 + - + +
476A ILE* 6.3 0.7 - - + -
530A LEU* 5.3 0.4 - - + -
535A VAL* 4.3 10.3 - - + -
562A PHE* 3.7 34.3 - - + +
565A ALA* 3.7 38.4 - - + +
566A LYS 4.3 2.7 - - - +
567A GLN* 3.7 24.0 - - + +
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Residues in contact with LEU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A GLU* 3.1 36.9 + - + +
464A ILE* 3.2 4.9 + - - +
466A ILE* 1.3 74.5 - - + +
468A LEU* 1.3 57.7 + - - +
470A TYR 5.1 0.2 - - - -
471A GLY* 3.0 27.5 + - - +
476A ILE* 4.6 3.8 - - + -
477A ILE* 3.8 35.9 - - + +
479A LEU* 4.3 25.9 - - + +
491A VAL* 4.1 26.7 - - + -
493A THR* 4.9 6.5 - - + -
562A PHE* 3.9 25.8 - - + +
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Residues in contact with LEU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A ILE* 3.0 37.3 + - + +
465A GLU* 3.6 10.8 - - + +
467A LEU* 1.3 75.7 - - - +
469A ARG* 1.3 66.0 + - - +
471A GLY 4.5 1.0 + - - -
472A GLN* 4.7 9.2 + - - +
479A LEU* 3.3 26.0 - - + -
482A VAL* 5.0 3.6 - - + -
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Residues in contact with ARG 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A GLU 3.0 17.6 + - - +
468A LEU* 1.3 78.8 - - - +
470A TYR* 1.3 103.6 + - + +
472A GLN* 4.5 9.9 + - - +
529A TYR* 4.9 2.6 + - - -
533A GLN* 4.8 10.1 + - - -
567A GLN* 4.1 9.4 - - - +
575A LEU* 4.6 18.3 - - - +
577A THR* 6.0 3.8 - - - +
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Residues in contact with TYR 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A ILE* 2.9 30.0 + - + +
469A ARG* 1.3 117.2 + - + +
471A GLY* 1.3 62.0 + - - +
472A GLN* 3.2 3.8 - - - -
473A HIS* 3.1 23.7 + - - +
476A ILE* 3.4 9.1 - - + +
529A TYR* 3.8 27.0 - + + -
530A LEU* 4.1 19.1 - - + -
533A GLN* 3.6 38.2 + - + +
535A VAL* 3.4 26.7 - - + -
567A GLN* 2.8 31.0 + - - -
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Residues in contact with GLY 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A ILE 4.0 0.4 + - - -
467A LEU* 3.0 22.3 + - - -
469A ARG 3.8 0.4 - - - -
470A TYR* 1.3 72.9 - - - +
472A GLN* 1.3 52.4 + - - +
473A HIS 3.0 6.3 - - - -
476A ILE* 3.7 18.1 - - - +
477A ILE 3.8 7.6 - - - -
478A THR* 3.7 13.8 + - - +
479A LEU 5.1 1.1 - - - -
1000A NA 2.3 32.4 - - - -
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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