Contacts of the helix formed by residues 239 - 244 (chain C) in PDB entry 1CX2
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 ASP 239 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237C THR* 3.9 7.6 - - - +
238C LEU* 1.3 86.4 - - + +
240C ARG* 1.3 57.9 + - - +
242C HIS* 3.3 16.6 + - - +
243C LYS* 3.3 30.7 + - - +
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Residues in contact with ARG 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C GLY* 3.6 13.7 - - - -
236C GLU* 2.9 42.5 + - - +
237C THR* 2.9 17.6 + - - +
239C ASP* 1.3 72.4 + - - +
241C GLN* 1.3 66.5 + - - +
242C HIS 3.1 1.8 - - - -
243C LYS* 3.1 25.1 + - - +
244C LEU* 3.4 15.0 - - + +
271C VAL* 3.3 25.9 - - + +
272C GLU* 2.7 32.7 + - - +
273C MET* 3.5 20.2 - - - -
286C ALA 3.8 2.4 + - - -
288C GLY* 2.9 24.0 + - - -
290C GLU* 3.6 17.4 + - - +
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Residues in contact with GLN 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C TYR* 3.1 31.8 + - + +
237C THR 3.3 16.2 + - - +
238C LEU* 3.3 16.7 - - - +
240C ARG* 1.3 80.7 - - - +
242C HIS* 1.3 92.9 + - - +
244C LEU* 3.4 5.8 + - - +
245C ARG* 2.9 34.6 + - - +
252C LEU* 5.4 1.0 - - - +
329C PHE* 2.8 45.0 - - + -
330C GLN* 4.2 7.5 - - - +
333C LYS* 5.9 3.8 - - - +
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Residues in contact with HIS 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C LEU* 2.7 45.5 + - + +
239C ASP* 3.3 12.3 - - - +
240C ARG 3.1 0.2 - - - -
241C GLN* 1.3 102.7 + - - +
243C LYS* 1.3 57.7 - - + +
244C LEU 2.9 6.6 + - - -
245C ARG* 3.0 29.3 + - - +
247C PHE* 3.5 38.3 - + + -
253C LYS* 5.5 0.2 - - - -
326C GLU* 4.7 7.2 - - - -
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Residues in contact with LYS 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C ASP* 3.3 26.0 + - - +
240C ARG* 3.1 22.5 + - - +
242C HIS* 1.3 73.7 - - + +
244C LEU* 1.3 60.6 + - - +
253C LYS* 3.3 5.1 + - - -
269C THR* 3.2 26.5 - - - -
270C GLN* 3.3 32.7 + - + +
271C VAL* 3.5 26.2 - - + +
272C GLU* 3.9 6.3 - - - +
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Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C ILE 4.1 7.6 - - - +
234C TYR* 4.1 4.7 - - - +
235C GLY* 3.9 26.5 - - - +
240C ARG* 3.4 20.0 - - + +
241C GLN* 3.9 4.9 - - - +
242C HIS 3.0 1.0 - - - -
243C LYS* 1.3 77.0 - - - +
245C ARG* 1.3 52.6 + - - +
252C LEU* 3.7 13.6 - - + +
253C LYS* 2.7 48.6 + - - +
264C PRO* 4.4 5.8 - - + +
271C VAL* 3.5 32.1 - - + -
286C ALA* 3.6 23.3 - - + -
287C VAL* 4.4 3.1 - - - +
288C GLY* 4.0 14.4 - - - -
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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