Contacts of the helix formed by residues 457 - 467 (chain X) in PDB entry 2QW0
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 SER 457 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456X LEU* 1.3 77.9 - - - +
458X ALA* 1.3 66.0 + - - +
459X ASP* 3.7 10.4 + - - +
460X ALA* 3.6 27.9 + - - +
461X LEU* 3.1 28.0 + - - +
481X ILE* 4.3 1.3 - - - -
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Residues in contact with ALA 458 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457X SER* 1.3 72.7 + - - +
459X ASP* 1.3 59.3 + - - +
461X LEU* 3.4 1.7 + - - +
462X ASP* 3.0 31.2 + - - +
479X TYR* 3.8 40.9 - - + +
481X ILE* 4.2 8.2 - - + +
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Residues in contact with ASP 459 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457X SER* 3.8 9.6 - - - +
458X ALA* 1.3 80.2 - - - +
460X ALA* 1.3 56.4 + - - +
462X ASP* 3.3 9.7 + - - +
463X THR* 2.9 32.6 + - - +
466X ARG* 5.1 0.2 + - - -
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Residues in contact with ALA 460 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457X SER* 3.4 23.9 + - - +
459X ASP* 1.3 78.4 - - - +
461X LEU* 1.3 58.6 + - + +
463X THR* 3.3 8.5 + - - -
464X PHE* 2.8 28.6 + - - +
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Residues in contact with LEU 461 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421X LEU* 4.3 11.4 - - + +
424X ALA* 4.3 14.4 - - + -
425X PRO 5.5 0.7 - - - +
427X VAL* 3.9 27.4 - - + -
448X VAL* 3.8 22.4 - - + -
456X LEU* 4.4 15.9 - - + -
457X SER 3.1 27.1 + - - +
458X ALA* 3.8 1.3 - - - +
460X ALA* 1.3 74.4 - - + +
462X ASP* 1.3 59.9 + - - +
464X PHE* 3.2 6.6 + - - +
465X CYS* 2.9 27.5 + - - -
479X TYR* 3.6 43.9 + - + -
481X ILE* 4.8 1.1 - - + -
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Residues in contact with ASP 462 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458X ALA 3.0 14.5 + - - +
459X ASP* 3.4 13.3 - - - +
461X LEU* 1.3 72.2 - - - +
463X THR* 1.3 66.2 + - - +
465X CYS* 3.2 3.8 + - - +
466X ARG* 3.0 48.6 + - - +
475X ARG* 4.8 9.2 + - - +
476X PRO 4.9 7.8 - - - +
479X TYR* 3.8 15.9 + - + -
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Residues in contact with THR 463 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459X ASP* 2.9 18.8 + - - +
460X ALA* 3.5 10.8 - - - -
461X LEU 3.3 0.2 - - - -
462X ASP* 1.3 77.0 - - - +
464X PHE* 1.3 63.7 + - - +
466X ARG* 3.0 43.7 + - - +
467X SER* 3.3 16.2 + - - +
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Residues in contact with PHE 464 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420X VAL* 3.6 32.8 - - + -
421X LEU* 4.9 6.5 - - + -
423X THR* 3.3 22.0 - - - -
424X ALA* 3.6 33.7 - - + -
425X PRO* 3.9 15.7 - - + -
460X ALA 2.8 17.4 + - - +
461X LEU* 3.2 12.3 + - - +
463X THR* 1.3 73.3 - - - +
465X CYS* 1.3 66.5 + - - +
467X SER* 3.1 18.6 + - - -
468X SER* 3.4 11.3 + - - -
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Residues in contact with CYS 465 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420X VAL* 5.1 2.2 - - - -
421X LEU* 3.7 21.3 - - - -
461X LEU 2.9 9.9 + - - +
462X ASP* 3.5 9.4 - - - +
464X PHE* 1.3 78.3 - - - +
466X ARG* 1.3 58.9 + - - +
468X SER* 2.8 33.8 + - - +
470X LEU* 4.4 14.7 - - + +
475X ARG* 3.9 23.3 - - + -
476X PRO* 4.0 14.8 - - - -
479X TYR* 3.2 25.8 - - - +
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Residues in contact with ARG 466 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462X ASP* 3.0 36.8 + - - +
463X THR* 3.0 43.7 + - - +
465X CYS* 1.3 77.7 - - - +
467X SER* 1.3 57.9 + - - +
468X SER 3.2 5.7 + - - +
475X ARG* 3.5 39.7 + - - +
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Residues in contact with SER 467 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463X THR* 3.3 14.9 + - - +
464X PHE* 3.1 14.3 + - - -
466X ARG* 1.3 75.8 - - - +
468X SER* 1.3 59.6 + - - +
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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
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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