Contacts of the helix formed by residues 364 - 367 (chain D) in PDB entry 2CX9
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 LEU 364 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346C GLY* 6.0 1.8 - - - -
349C TYR* 3.6 45.8 - - + -
87D LEU* 3.9 21.8 - - + -
207D LYS* 6.1 1.3 - - + -
210D LEU* 3.2 31.4 - - + -
255D MET* 5.7 0.4 - - + -
361D ASP 3.5 2.3 + - - +
362D ALA 3.0 1.2 + - - -
363D ARG* 1.3 73.6 - - - +
365D THR* 1.3 57.2 + - + +
366D ARG 3.1 5.6 - - - -
367D ILE* 3.0 15.7 + - + +
368D GLY* 2.9 44.3 + - - +
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Residues in contact with THR 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D ILE* 4.0 17.5 - - + -
255D MET* 4.2 30.1 - - + -
256D ALA* 3.9 25.3 - - + +
259D LEU* 4.9 0.2 - - + -
326D LYS* 2.8 26.0 + - - -
330D SER* 3.2 34.0 + - - -
333D ALA* 5.2 0.2 - - - +
334D VAL* 4.2 0.5 - - - +
362D ALA* 2.8 25.4 + - - +
364D LEU* 1.3 76.5 - - - +
366D ARG* 1.3 56.4 + - - +
367D ILE 3.3 0.9 - - - -
368D GLY* 4.6 0.9 - - - +
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Residues in contact with ARG 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C LYS* 5.7 0.8 - - - +
338C ASP* 2.8 30.1 + - - -
339C GLU* 4.7 9.9 + - - -
342C GLN* 3.1 29.2 + - - +
326D LYS* 3.9 3.4 - - - +
330D SER* 3.6 26.2 - - - +
331D GLU* 2.9 32.1 + - - +
334D VAL* 3.4 33.5 - - + +
363D ARG* 3.2 38.7 + - - +
364D LEU 3.1 1.4 - - - -
365D THR* 1.3 76.9 - - - +
367D ILE* 1.3 58.7 + - - +
371D THR* 3.4 0.2 - - - -
372D SER* 3.1 32.3 + - - +
373D GLU* 5.6 1.0 + - - -
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Residues in contact with ILE 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C ILE* 4.4 15.7 - - + +
342C GLN* 3.8 16.2 - - - +
345C GLY* 3.5 24.2 - - - +
346C GLY* 3.6 28.0 - - - +
349C TYR* 4.7 14.6 - - + -
363D ARG* 3.8 23.6 - - - +
364D LEU* 3.0 13.8 + - + +
366D ARG* 1.3 84.1 - - - +
368D GLY* 1.3 69.7 + - - +
370D GLY 3.3 18.0 + - - -
371D THR* 3.3 15.4 + - + +
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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