Contacts of the helix formed by residues 233 - 240 (chain G) 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 SER 233 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5G PRO* 4.3 6.5 - - - +
231G ARG 3.7 1.0 - - - -
232G THR* 1.3 80.8 - - - +
234G LYS* 1.3 66.4 + - - +
235G ALA* 2.7 13.3 + - - +
236G GLU* 3.1 33.3 + - - +
237G ALA* 3.0 19.9 + - - +
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Residues in contact with LYS 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G PRO* 3.7 28.4 - - + +
6G HIS* 3.3 32.7 + - - +
7G ASP* 4.2 13.1 - - + +
233G SER* 1.3 72.0 - - - +
235G ALA* 1.3 61.4 + - - +
237G ALA* 3.8 3.2 - - - +
238G GLN* 3.0 43.0 + - + +
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Residues in contact with ALA 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233G SER* 2.7 13.8 + - - +
234G LYS* 1.3 80.7 - - - +
236G GLU* 1.3 62.9 + - + +
238G GLN* 3.5 15.0 + - - +
239G LYS* 3.4 17.6 - - + +
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Residues in contact with GLU 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230G ARG* 3.3 46.3 + - + +
232G THR* 2.5 31.3 + - - +
233G SER* 3.2 22.9 + - - +
235G ALA* 1.3 77.3 - - + +
237G ALA* 1.3 69.2 + - - +
239G LYS* 2.9 32.8 + - + +
240G ASP* 3.2 12.0 + - - +
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Residues in contact with ALA 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ILE* 4.9 3.6 - - + -
5G PRO* 4.3 19.1 - - + +
36G PRO* 6.3 1.3 - - + -
229G VAL* 4.4 10.5 - - + -
230G ARG 3.5 21.5 - - - +
233G SER 3.0 17.8 + - - +
234G LYS* 3.8 9.0 - - - +
236G GLU* 1.3 79.1 - - - +
238G GLN* 1.3 57.5 + - + +
240G ASP* 2.9 19.4 + - - +
241G THR* 2.9 20.5 + - + +
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Residues in contact with GLN 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G PRO 5.9 1.8 - - - +
7G ASP* 5.5 5.7 + - - -
39G ARG* 3.1 10.3 + - - -
234G LYS* 3.0 35.4 + - + +
235G ALA* 3.6 9.1 - - - +
236G GLU 3.2 0.2 - - - -
237G ALA* 1.3 77.0 - - + +
239G LYS* 1.3 58.2 + - + +
241G THR* 2.7 32.3 - - - +
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Residues in contact with LYS 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G ARG* 2.7 28.2 + - - +
230G ARG* 4.0 12.9 - - - +
235G ALA* 3.4 11.4 - - + +
236G GLU* 2.9 30.3 + - + +
238G GLN* 1.3 80.4 - - + +
240G ASP* 1.3 53.4 + - - +
425G GLU* 3.0 56.7 + - - +
428G PHE* 5.0 0.3 - - - -
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Residues in contact with ASP 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G PRO* 3.6 5.4 - - - +
39G ARG* 3.1 26.9 + - - +
228G GLU 4.8 0.4 - - - +
229G VAL* 3.6 15.0 - - + -
230G ARG* 3.0 49.3 + - - +
236G GLU 3.2 4.5 + - - +
237G ALA 2.9 8.5 + - - +
239G LYS* 1.3 78.9 - - - +
241G THR* 1.3 56.2 + - - +
423G THR* 3.8 0.2 - - - -
424G ILE* 3.1 28.8 + - + +
425G GLU* 2.7 37.7 + - - +
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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