Contacts of the helix formed by residues 413 - 422 (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 HIS 413 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350X GLU* 2.9 27.1 + - - -
386X VAL* 3.6 24.4 - - + +
398X LEU* 3.6 43.8 + - + +
399X GLY* 4.4 6.4 + - - -
400X ARG 4.8 0.4 + - - -
404X MET* 3.6 38.5 - - + +
411X ASN* 4.4 3.5 - - - +
412X ILE* 1.3 80.5 - - - +
414X PRO* 1.3 64.5 - - + +
415X SER* 3.3 2.9 - - - +
416X GLU* 2.9 35.9 + - + +
417X ILE* 3.8 5.2 + - - +
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Residues in contact with PRO 414 (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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403X ASP* 3.0 46.4 - - + +
404X MET* 4.3 0.2 - - - -
405X ILE* 4.2 5.8 - - + +
412X ILE 3.3 8.7 - - - +
413X HIS* 1.3 84.0 - - + +
415X SER* 1.3 59.2 + - - +
417X ILE* 3.2 8.1 + - + +
418X GLU* 2.8 39.8 + - - +
432X VAL* 3.1 43.0 - - + +
495X ARG* 3.7 3.4 - - - +
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Residues in contact with SER 415 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283X THR* 6.5 1.6 - - - -
398X LEU 3.1 24.4 + - - -
399X GLY* 4.0 9.1 - - - -
413X HIS* 4.3 2.4 - - - +
414X PRO* 1.3 78.0 - - - +
416X GLU* 1.3 61.1 + - - +
418X GLU* 3.4 17.6 + - - +
419X ARG* 3.0 45.7 + - - +
495X ARG* 5.1 2.8 - - - +
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Residues in contact with GLU 416 (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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398X LEU 5.2 0.6 + - - +
413X HIS* 2.9 23.5 + - + +
415X SER* 1.3 78.1 + - - +
417X ILE* 1.3 65.1 + - + +
419X ARG* 3.1 29.3 + - + +
420X VAL* 3.2 16.8 + - + +
469X GLU 6.0 0.3 - - - -
470X LEU* 3.6 15.4 - - + +
474X LYS* 2.7 43.6 + - - +
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Residues in contact with ILE 417 (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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405X ILE* 5.7 0.2 - - + -
412X ILE* 3.6 26.0 - - + -
413X HIS 4.1 9.4 - - - +
414X PRO* 3.6 5.6 - - + +
416X GLU* 1.3 72.6 - - + +
418X GLU* 1.3 55.4 + - - +
420X VAL* 3.1 3.7 + - - +
421X LEU* 2.8 46.1 + - + +
432X VAL* 3.8 24.7 - - + -
444X VAL* 3.9 13.2 - - + -
470X LEU* 4.1 28.9 - - + -
474X LYS* 3.3 24.2 - - + +
476X PRO* 4.0 18.4 - - + -
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Residues in contact with GLU 418 (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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414X PRO* 2.8 24.3 + - - +
415X SER* 3.4 16.6 - - - +
417X ILE* 1.3 72.7 - - - +
419X ARG* 1.3 56.3 + - + +
421X LEU* 4.6 1.3 - - - -
422X GLY* 2.8 27.7 + - - -
430X VAL* 3.4 34.8 - - + +
431X VAL* 3.6 1.5 - - - -
432X VAL* 2.8 27.1 + - + +
495X ARG* 2.6 44.7 + - - -
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Residues in contact with ARG 419 (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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282X ALA 3.9 16.6 + - - -
283X THR* 4.2 15.5 + - - +
284X MET 4.7 4.0 + - - -
285X PRO* 4.2 31.9 - - + -
286X ASP* 5.0 5.4 - - - +
322X THR* 4.0 22.8 - - - +
397X ILE 5.2 1.8 + - - -
398X LEU 4.7 6.5 + - - -
415X SER* 3.0 41.3 + - - +
416X GLU* 3.1 18.9 + - - +
418X GLU* 1.3 73.8 - - + +
420X VAL* 1.3 68.9 + - + +
422X GLY* 3.7 3.1 + - - -
423X THR* 3.4 19.4 + - - +
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Residues in contact with VAL 420 (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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416X GLU* 3.2 14.6 + - + +
417X ILE 3.1 7.6 + - - +
419X ARG* 1.3 74.9 - - + +
421X LEU* 1.3 58.6 + - - +
423X THR* 2.8 33.0 + - - +
464X PHE* 3.6 17.4 - - + -
465X CYS* 5.1 4.7 - - - -
468X SER* 3.6 32.5 - - - +
469X GLU* 5.6 4.9 - - + +
470X LEU* 4.0 29.8 - - + +
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Residues in contact with LEU 421 (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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417X ILE* 2.8 36.8 + - + +
420X VAL* 1.3 74.1 - - + +
422X GLY* 1.3 62.0 + - - +
424X ALA* 3.0 20.9 + - - +
427X VAL* 3.7 11.8 - - - +
430X VAL* 3.7 25.6 - - + -
432X VAL* 4.1 1.8 - - + -
446X ALA* 3.6 30.5 - - + -
448X VAL* 4.8 3.6 - - + -
461X LEU* 4.3 19.3 - - + +
464X PHE* 4.7 6.1 - - + -
465X CYS* 3.7 27.4 - - - -
476X PRO* 4.2 3.4 - - + -
479X TYR* 4.1 13.9 - - + +
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Residues in contact with GLY 422 (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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418X GLU 2.8 22.8 + - - -
419X ARG* 4.2 2.2 - - - -
420X VAL 3.2 0.6 + - - -
421X LEU* 1.3 72.3 - - - +
423X THR* 1.3 60.0 + - - +
424X ALA 3.3 1.5 + - - +
427X VAL* 4.2 19.0 - - - +
430X VAL* 3.8 11.1 - - - +
451X ARG* 5.4 1.9 + - - -
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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