Contacts of the helix formed by residues 233 - 240 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5P PRO* 4.5 5.8 - - - +
231P ARG 3.7 1.2 - - - -
232P THR* 1.3 80.8 - - - +
234P LYS* 1.3 66.3 + - - +
235P ALA* 2.8 13.4 + - - +
236P GLU* 3.1 32.5 + - - +
237P ALA* 3.0 21.9 + - - +
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Residues in contact with LYS 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5P PRO* 4.1 31.3 - - + +
6P HIS* 3.8 23.6 - - - -
7P ASP* 3.5 30.3 + - - +
233P SER* 1.3 71.1 - - - +
235P ALA* 1.3 62.7 + - - +
237P ALA* 3.7 4.5 - - - +
238P GLN* 3.0 44.6 + - + +
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Residues in contact with ALA 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233P SER* 2.8 14.5 + - - +
234P LYS* 1.3 83.5 - - - +
236P GLU* 1.3 61.3 + - + +
238P GLN* 3.5 18.5 + - - +
239P LYS* 3.7 13.0 + - + +
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Residues in contact with GLU 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230P ARG* 3.3 47.8 + - + +
232P THR* 2.5 33.0 + - - +
233P SER* 3.2 23.0 + - - +
235P ALA* 1.3 76.5 - - + +
237P ALA* 1.3 68.3 + - - +
238P GLN 3.2 0.4 - - - -
239P LYS* 2.9 34.2 + - - +
240P ASP* 3.2 12.8 + - - +
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Residues in contact with ALA 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P ILE* 3.7 25.6 - - + -
5P PRO* 4.4 3.6 - - + +
229P VAL* 4.4 5.4 - - + -
230P ARG 3.5 21.5 - - - +
233P SER 3.0 18.3 + - - +
234P LYS* 3.7 8.1 - - - +
236P GLU* 1.3 77.9 - - - +
238P GLN* 1.3 58.8 + - + +
240P ASP* 2.9 18.3 + - - +
241P THR* 2.9 21.5 + - - +
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Residues in contact with GLN 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P ARG* 3.1 10.8 + - - -
234P LYS* 3.0 41.2 + - + +
235P ALA* 3.6 9.4 - - - +
236P GLU 3.2 0.2 - - - -
237P ALA* 1.3 76.2 - - + +
239P LYS* 1.3 57.9 + - + +
241P THR* 2.6 32.1 - - - +
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Residues in contact with LYS 239 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P ARG* 2.8 23.9 + - - +
230P ARG* 3.3 23.7 - - - +
235P ALA* 3.8 7.9 - - + +
236P GLU* 2.9 30.2 + - - +
238P GLN* 1.3 77.7 - - + +
240P ASP* 1.3 56.5 + - - +
425P GLU* 2.9 58.2 + - - +
428P PHE* 5.0 0.3 - - - -
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Residues in contact with ASP 240 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38P PRO* 3.6 5.7 - - - +
39P ARG* 3.1 26.6 + - - +
228P GLU 4.9 0.2 - - - +
229P VAL* 3.6 15.5 - - + -
230P ARG* 2.9 54.4 + - - +
236P GLU 3.2 4.7 + - - +
237P ALA 2.9 7.9 + - - +
239P LYS* 1.3 79.6 - - - +
241P THR* 1.3 56.4 + - - +
423P THR* 4.8 0.2 - - - -
424P ILE* 3.2 28.1 + - + +
425P GLU 2.8 31.6 + - - +
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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