Contacts of the helix formed by residues 345 - 350 (chain C) 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 GLY 345 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C ILE 3.2 4.3 + - - +
342C GLN 3.0 18.1 + - - -
343C ILE 3.0 2.1 - - - -
344C LEU* 1.3 76.4 - - - +
346C GLY* 1.3 58.3 + - - +
348C GLY* 2.9 21.0 + - - -
349C TYR 3.6 0.2 + - - -
367D ILE* 3.5 30.2 - - - +
371D THR* 5.2 6.7 - - - -
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Residues in contact with GLY 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU 3.3 1.2 + - - -
345C GLY* 1.3 70.8 - - - -
347C TYR* 1.3 63.2 + - - +
349C TYR* 3.1 21.0 + - - +
350C VAL* 3.8 4.0 + - - +
158D PHE* 3.5 31.9 - - - -
364D LEU* 6.0 1.8 - - - -
367D ILE* 3.6 14.6 - - - +
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Residues in contact with TYR 347 (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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270C TYR* 3.9 15.9 - + - -
274C ARG* 4.1 19.5 - - - -
344C LEU* 3.6 25.6 - - + +
345C GLY 3.2 1.0 - - - -
346C GLY* 1.3 75.1 - - - +
348C GLY* 1.3 60.0 + - - +
349C TYR 3.0 5.8 - - - -
350C VAL* 2.9 30.8 + - + +
353C TYR* 3.6 43.9 - + + +
129D GLU 4.3 1.8 + - - -
130D PRO* 2.6 39.5 + - - +
157D GLN* 3.4 16.7 + - - +
158D PHE* 3.9 19.5 - + - -
205D GLU* 5.7 1.6 - - - -
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Residues in contact with GLY 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ILE* 3.7 22.7 - - - +
344C LEU* 3.5 21.2 + - - +
345C GLY 2.9 10.9 + - - -
347C TYR* 1.3 78.9 - - - +
349C TYR* 1.3 58.7 + - - +
350C VAL 3.6 0.6 + - - -
355C VAL* 3.6 16.1 - - - +
356C GLU* 3.7 22.0 - - - +
208D LEU* 4.9 0.2 - - - +
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Residues in contact with TYR 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ILE* 5.6 0.9 - - + -
345C GLY 3.6 3.9 + - - +
346C GLY* 3.1 13.4 + - - +
347C TYR 3.0 1.0 - - - -
348C GLY* 1.3 79.8 - - - +
350C VAL* 1.3 58.7 + - + +
356C GLU* 5.2 0.7 - - - -
207D LYS* 3.4 19.9 - - + +
208D LEU* 2.8 54.3 + - + -
209D GLY* 3.1 39.5 - - - -
210D LEU* 3.4 12.5 - - + +
360D ARG 2.8 28.9 + - - -
361D ASP 3.8 0.2 + - - -
363D ARG* 4.2 4.9 - - + -
364D LEU* 3.6 54.5 - - + -
367D ILE* 4.7 7.2 - - + -
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Residues in contact with VAL 350 (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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346C GLY 4.0 4.7 - - - +
347C TYR* 2.9 34.1 + - + +
348C GLY 3.3 0.5 - - - +
349C TYR* 1.3 83.6 - - + +
351C LYS* 1.3 59.0 + - - +
352C ASP* 3.0 13.7 + - + +
353C TYR* 3.1 42.6 + - + +
355C VAL* 5.9 0.2 - - - +
356C GLU* 4.1 6.1 - - - +
158D PHE* 3.9 25.1 - - + -
205D GLU* 4.0 18.2 - - + +
206D GLU 3.4 10.8 - - - +
207D LYS* 4.6 10.3 - - + -
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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