Contacts of the helix formed by residues 423 - 430 (chain M) in PDB entry 2QJK
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 THR 423 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225M THR* 5.8 0.6 - - - +
227M VAL* 4.6 7.9 - - - -
228M GLU 5.8 0.2 - - - -
230M ARG* 3.6 42.4 + - + +
240M ASP* 3.9 0.4 - - - -
421M PRO* 3.9 9.3 - - - +
422M ALA* 1.3 94.9 - - + +
424M ILE* 1.3 65.1 + - - +
425M GLU* 3.4 8.5 + - - +
426M GLU* 2.9 38.0 + - + +
427M ASP* 3.3 4.5 + - - +
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Residues in contact with ILE 424 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38M PRO* 4.3 4.9 - - + -
39M ARG* 5.3 0.2 - - - -
40M ASN* 3.1 41.7 - - + +
223M ASN* 4.0 11.0 - - - +
225M THR* 5.0 3.4 - - - -
227M VAL* 3.4 22.6 - - + +
228M GLU 3.3 21.1 - - - +
229M VAL* 3.4 29.8 - - + -
240M ASP* 3.2 27.6 + - + +
423M THR* 1.3 69.7 - - - +
425M GLU* 1.3 55.5 + - - +
427M ASP* 3.1 8.1 + - - +
428M PHE* 2.7 37.1 + - + +
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Residues in contact with GLU 425 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230M ARG* 2.9 24.7 + - - +
239M LYS* 3.0 61.2 + - - +
240M ASP* 3.0 7.0 + - - +
423M THR* 3.4 7.4 + - - +
424M ILE* 1.3 74.9 - - - +
426M GLU* 1.3 60.8 + - - +
428M PHE* 2.9 7.8 + - + +
429M ASN* 2.4 53.1 + - - +
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Residues in contact with GLU 426 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421M PRO* 3.9 13.3 - - + +
422M ALA* 2.6 40.9 + - - +
423M THR* 2.9 21.7 + - + +
425M GLU* 1.3 79.1 - - - +
427M ASP* 1.3 63.5 + - - +
429M ASN* 3.5 9.8 + - - +
430M ALA* 3.2 18.5 + - - +
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Residues in contact with ASP 427 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40M ASN* 4.5 10.9 - - - +
225M THR* 3.1 33.7 - - + +
358M ARG* 3.6 15.2 + - - -
359M TYR* 3.8 6.9 + - - -
421M PRO* 4.1 14.3 - - + +
423M THR 3.3 6.0 + - - +
424M ILE* 3.1 8.6 + - - +
426M GLU* 1.3 76.8 - - - +
428M PHE* 1.3 71.0 + - - +
430M ALA* 2.9 27.2 - - - +
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Residues in contact with PHE 428 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M ARG* 2.9 81.4 - - + -
40M ASN* 4.0 10.5 - - + +
239M LYS 5.2 0.7 - - - -
424M ILE* 2.7 16.8 + - + +
425M GLU* 3.2 13.5 - - + +
427M ASP* 1.3 76.7 + - - +
429M ASN* 1.3 63.2 + - - +
430M ALA 3.0 1.0 - - - +
252N TRP* 4.8 10.8 - + - -
255N VAL* 4.2 10.3 - - + -
256N LYS* 2.7 79.9 + - + +
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Residues in contact with ASN 429 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425M GLU* 2.4 59.6 + - - +
426M GLU* 3.5 9.4 - - - +
428M PHE* 1.3 79.8 - - - +
430M ALA* 1.3 64.5 + - - +
256N LYS* 3.7 7.8 + - - +
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Residues in contact with ALA 430 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426M GLU 3.2 9.3 + - - +
427M ASP* 2.9 22.6 + - - +
428M PHE 3.0 12.6 - - - +
429M ASN* 1.3 82.5 - - - +
256N LYS* 3.1 12.3 + - - -
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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