Contacts of the helix formed by residues 281 - 289 (chain A) in PDB entry 2CXQ
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 281 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A MET* 4.0 6.5 - - - -
164A PRO* 4.9 0.2 - - - -
276A LEU* 3.2 22.7 + - - -
278A SER 2.9 10.4 + - - -
280A ILE* 1.3 76.5 - - - +
282A LEU* 1.3 62.7 + - - +
283A SER 3.2 2.7 - - - -
284A ILE* 2.9 29.8 + - - +
285A ALA* 3.1 10.0 + - - +
293A PHE* 3.9 6.2 - - - -
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A MET* 3.7 37.8 - - + +
132A PHE* 4.0 24.2 - - + -
133A CYS* 4.1 16.2 - - - -
207A ILE* 4.7 4.3 - - + -
244A VAL* 4.2 8.5 - - + -
246A LEU* 3.7 25.8 - - + -
264A PHE* 3.8 22.0 - - + -
279A ALA 2.9 17.8 + - - +
280A ILE 3.1 1.8 - - - -
281A GLY* 1.3 76.0 - - - +
283A SER* 1.3 56.5 + - - +
285A ALA* 3.2 2.0 + - - +
286A LEU* 2.8 37.5 + - + +
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Residues in contact with SER 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 3.8 17.8 - - - +
154A ASN* 4.1 13.7 + - - -
164A PRO* 3.3 26.7 - - - +
168A THR* 4.0 2.8 - - - +
181A VAL* 4.2 12.1 - - - +
183A PHE* 3.7 8.0 - - - -
207A ILE* 4.1 19.5 - - - +
246A LEU* 5.4 0.6 - - - +
280A ILE 4.4 1.5 + - - -
282A LEU* 1.3 76.6 - - - +
284A ILE* 1.3 67.3 + - - +
287A HIS* 3.1 25.6 + - - +
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PRO* 3.8 31.2 - - + +
167A VAL* 3.8 43.3 - - + -
168A THR* 3.8 10.1 - - + -
171A LEU* 5.0 1.6 - - + -
276A LEU* 4.1 18.2 - - + +
281A GLY* 2.9 23.5 + - - +
283A SER* 1.3 78.0 + - - +
285A ALA* 1.3 57.9 + - - +
287A HIS* 3.1 2.9 + - - +
288A VAL* 2.9 49.7 + - + +
293A PHE* 3.9 20.0 - - + -
296A LEU* 4.5 2.9 - - + -
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A MET* 4.8 3.8 - - + -
133A CYS* 3.5 21.7 - - - -
137A ARG* 3.9 0.9 - - - -
281A GLY 3.1 6.1 + - - +
282A LEU* 3.7 8.7 - - - +
284A ILE* 1.3 77.9 - - - +
286A LEU* 1.3 57.7 + - - +
289A GLY* 2.8 39.9 + - - -
290A PHE* 3.5 13.4 + - + -
293A PHE* 3.8 26.9 - - + -
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE* 4.1 13.7 - - + -
133A CYS* 3.9 25.8 - - - +
136A VAL* 3.7 38.6 - - + -
137A ARG* 2.9 27.9 + - + +
152A ILE* 3.6 22.2 - - + -
179A PRO* 3.4 15.2 - - + +
205A LEU* 4.5 1.1 - - + -
207A ILE* 3.7 28.9 - - + -
282A LEU* 2.8 31.5 + - + +
285A ALA* 1.3 76.9 - - - +
287A HIS* 1.3 58.3 + - - +
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Residues in contact with HIS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG* 3.1 11.4 + - - -
152A ILE* 4.8 1.3 - - + -
168A THR* 3.8 24.5 - - + -
172A LYS* 3.0 24.7 + - + +
175A SER* 3.3 49.7 + - - -
178A GLY* 3.6 6.5 - - - -
179A PRO* 2.9 30.7 + - - -
180A ARG* 4.5 2.7 - - - -
181A VAL* 3.6 32.5 - - + +
283A SER 3.1 19.6 + - - +
284A ILE 3.6 1.8 - - - +
286A LEU* 1.3 78.1 - - - +
288A VAL* 1.3 65.2 + - + +
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG* 3.6 8.4 + - - -
168A THR* 5.4 3.6 - - + +
171A LEU* 3.5 39.3 - - + +
174A TYR* 3.4 26.7 - - + +
175A SER* 4.1 6.1 - - - +
284A ILE* 2.9 38.7 + - + +
287A HIS* 1.3 83.4 - - + +
289A GLY* 1.3 62.4 + - - +
292A HIS* 2.8 45.0 + - + -
293A PHE 4.6 2.0 - - - +
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Residues in contact with GLY 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG* 3.3 25.8 - - - +
285A ALA 2.8 18.4 + - - +
288A VAL* 1.3 82.2 - - - +
290A PHE* 1.3 65.3 + - - -
291A ASP* 3.3 3.6 - - - -
292A HIS* 3.3 3.7 + - - +
293A PHE* 3.1 18.9 + - - +
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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