Contacts of the helix formed by residues 486 - 501 (chain A) in PDB entry 1QQW
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 HIS 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A ARG* 4.5 8.1 - - + +
447A TYR* 4.0 16.1 - + + -
448A VAL* 4.1 25.3 - - + +
482A PHE 3.1 4.8 + - - +
483A THR* 3.4 6.5 + - - -
485A VAL* 1.3 86.1 + - + +
487A PRO* 1.3 87.1 - - + +
488A ASP* 2.9 54.4 + - + +
489A TYR* 2.9 24.3 + - + -
490A GLY 3.1 10.0 + - - -
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Residues in contact with PRO 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ARG* 6.1 1.1 - - - +
483A THR* 3.6 22.3 - - + +
486A HIS* 1.3 99.0 - - + +
488A ASP* 1.3 64.1 + - - +
490A GLY* 3.5 0.9 + - - -
491A SER* 2.9 27.3 + - - -
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Residues in contact with ASP 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A TYR* 4.0 11.7 - - + +
486A HIS* 2.9 27.0 + - + +
487A PRO* 1.3 78.2 - - - +
489A TYR* 1.3 66.7 + - - +
491A SER* 3.1 8.3 + - - -
492A HIS* 2.9 30.4 + - + +
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Residues in contact with TYR 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A SER* 3.3 28.3 + - - -
443A VAL* 4.9 0.4 - - + -
447A TYR* 3.7 31.0 + + + -
459A LEU* 3.4 19.5 - - + +
460A CYS* 3.7 17.0 - - - -
463A ILE* 3.2 24.8 - - + +
482A PHE* 3.6 26.3 - + + +
485A VAL* 3.9 30.3 - - + -
486A HIS* 2.9 20.1 + - + +
488A ASP* 1.3 80.3 - - - +
490A GLY* 1.3 63.1 + - - +
493A ILE* 3.5 34.1 + - + +
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Residues in contact with GLY 490 (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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479A VAL* 3.8 9.4 - - - +
482A PHE* 3.8 9.5 + - - -
483A THR* 3.6 30.5 - - - -
486A HIS 3.1 8.3 + - - -
487A PRO 4.0 0.2 - - - -
489A TYR* 1.3 77.8 - - - +
491A SER* 1.3 59.1 + - - +
493A ILE* 3.2 6.3 + - - +
494A GLN* 2.9 26.5 + - - +
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Residues in contact with SER 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A THR* 4.6 1.6 + - - +
487A PRO 2.9 20.5 + - - -
488A ASP* 3.1 13.3 + - - -
490A GLY* 1.3 70.3 - - - +
492A HIS* 1.3 60.8 + - - +
494A GLN* 2.9 10.9 + - - +
495A ALA* 2.7 36.4 + - - +
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Residues in contact with HIS 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A TYR* 4.7 5.9 + - - +
456A ARG* 4.1 2.4 + - + +
457A LYS* 3.6 41.6 - - + +
460A CYS* 3.4 26.7 - - + -
461A GLU* 4.6 2.4 + - - -
488A ASP* 2.9 20.0 + - + +
491A SER* 1.3 77.4 + - - +
493A ILE* 1.3 62.8 + - - +
495A ALA* 3.4 8.5 + - + +
496A LEU* 3.2 35.4 + - + +
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Residues in contact with ILE 493 (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 CYS* 4.0 22.0 - - + +
463A ILE* 4.0 13.5 - - + -
464A ALA* 4.8 3.4 - - + +
467A LEU* 4.1 11.0 - - + -
479A VAL* 4.0 13.9 - - + -
482A PHE* 3.6 34.1 - - + -
489A TYR* 3.5 32.2 + - + +
490A GLY 3.2 6.4 + - - +
491A SER 3.1 0.4 - - - -
492A HIS* 1.3 75.1 - - - +
494A GLN* 1.3 69.0 + - - +
496A LEU* 2.9 11.9 + - - +
497A LEU* 2.8 43.6 + - + +
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Residues in contact with GLN 494 (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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475A GLN* 5.8 0.7 - - - +
476A LYS* 5.8 1.4 - - - -
479A VAL* 3.8 21.9 - - + +
490A GLY 2.9 13.8 + - - +
491A SER* 3.1 14.6 - - - +
493A ILE* 1.3 79.0 - - - +
495A ALA* 1.3 62.8 + - - +
497A LEU* 3.2 20.0 + - - +
498A ASP* 2.8 52.7 + - - +
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Residues in contact with ALA 495 (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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491A SER 2.7 14.6 + - - +
492A HIS* 3.5 15.7 - - + +
494A GLN* 1.3 76.1 - - - +
496A LEU* 1.3 62.1 - - + +
498A ASP* 3.4 16.0 + - - +
499A LYS* 3.5 11.4 + - - +
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Residues in contact with LEU 496 (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 CYS* 3.8 9.2 - - + +
461A GLU* 3.7 48.7 - - + +
464A ALA* 3.6 12.1 - - + -
492A HIS* 3.2 31.1 + - + +
493A ILE* 2.9 7.4 + - - +
495A ALA* 1.3 79.9 - - + +
497A LEU* 1.3 64.5 + - - +
499A LYS* 3.3 31.7 - - - +
500A TYR* 3.4 34.0 - - + +
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Residues in contact with LEU 497 (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 ALA* 3.9 22.0 - - + +
467A LEU* 4.0 11.7 - - + -
468A LYS* 3.8 24.6 - - + +
475A GLN* 3.5 35.0 - - + +
479A VAL* 3.9 10.8 - - + -
493A ILE* 2.8 30.7 + - + +
494A GLN* 3.2 26.2 + - - +
496A LEU* 1.3 71.7 - - - +
498A ASP* 1.3 64.7 + - - +
499A LYS 2.8 5.7 + - - -
500A TYR* 2.9 6.3 + - - +
501A ASN* 2.7 30.0 + - - +
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Residues in contact with ASP 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLN* 2.8 38.4 + - - +
495A ALA* 3.7 11.1 - - - +
497A LEU* 1.3 77.7 - - - +
499A LYS* 1.3 61.6 + - - +
501A ASN* 3.9 11.9 + - - +
502A ALA* 3.1 21.8 + - - +
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Residues in contact with LYS 499 (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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495A ALA 3.5 6.5 + - - +
496A LEU* 3.3 27.3 + - - +
497A LEU 2.8 1.8 + - - -
498A ASP* 1.3 76.7 - - - +
500A TYR* 1.3 82.0 + - + +
502A ALA* 3.1 21.3 - - - +
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Residues in contact with TYR 500 (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 GLU* 5.0 8.1 + - - +
464A ALA* 4.0 26.5 - - + +
465A GLY* 4.0 8.4 + - - -
468A LYS* 3.4 48.2 - - + -
496A LEU* 3.4 41.8 - - + +
497A LEU* 2.9 3.7 + - - +
499A LYS* 1.3 88.0 + - + +
501A ASN* 1.3 58.0 + - - +
502A ALA 2.9 22.5 - - - +
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Residues in contact with ASN 501 (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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468A LYS* 4.3 8.9 - - - +
472A ILE* 4.0 21.7 - - - +
475A GLN* 3.0 41.0 + - - +
497A LEU* 2.7 25.2 + - - +
498A ASP* 3.9 13.6 + - - +
500A TYR* 1.3 71.5 - - - +
502A ALA* 1.3 61.3 + - - +
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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