Contacts of the helix formed by residues 223 - 235 (chain A) in PDB entry 2C56
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 GLN 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A CYS* 3.7 12.6 - - - -
208A PHE* 5.1 1.8 - - - -
221A THR 3.2 16.1 + - - +
222A CYS* 1.3 74.1 - - - +
224A HIS* 1.3 69.6 + - - +
225A PHE 3.2 3.4 - - - -
226A LEU* 3.0 25.9 + - + +
227A VAL* 3.0 29.5 + - + +
230A ARG* 5.1 5.0 + - - +
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Residues in contact with HIS 224 (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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186A MET* 3.6 22.9 - - + +
188A TRP* 3.0 26.4 + - + +
206A LEU* 3.3 41.3 - - + +
207A LYS 2.9 39.9 + - - -
208A PHE* 3.6 11.1 - + + +
222A CYS* 3.5 18.2 - - - -
223A GLN* 1.3 78.9 - - - +
225A PHE* 1.3 55.0 + - + +
227A VAL* 4.3 5.8 - - + -
228A ALA* 2.7 37.6 + - - +
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Residues in contact with PHE 225 (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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84A ILE* 4.9 0.4 - - + -
116A VAL* 4.2 7.4 - - + -
119A ALA* 4.0 20.9 - - + -
120A VAL* 3.8 30.7 - - + -
123A CYS* 3.9 18.6 - - - -
124A TYR* 3.4 13.9 + - + -
138A TRP* 4.4 4.7 - + - -
186A MET* 4.0 8.3 - - + -
188A TRP* 3.8 37.0 - + - -
219A PHE* 4.7 1.8 - + - -
222A CYS* 4.3 10.8 - - - -
223A GLN 3.1 0.8 + - - -
224A HIS* 1.3 75.0 - - - +
226A LEU* 1.3 59.7 + - - +
228A ALA* 3.8 0.9 + - - +
229A ASN* 3.4 15.2 + - - -
242A TRP* 3.2 70.7 + + + +
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Residues in contact with LEU 226 (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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123A CYS* 3.8 39.9 - - + +
124A TYR* 3.6 28.5 - - + +
223A GLN* 3.0 28.9 + - + +
225A PHE* 1.3 76.3 - - - +
227A VAL* 1.3 66.9 + - - +
229A ASN* 3.3 4.8 + - - +
230A ARG* 3.2 48.5 + - - +
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Residues in contact with VAL 227 (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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204A CYS* 4.9 4.5 - - - -
206A LEU* 3.6 30.3 - - + -
223A GLN* 3.0 25.7 + - + +
224A HIS* 3.8 9.0 - - + +
226A LEU* 1.3 77.0 - - - +
228A ALA* 1.3 62.0 + - - +
230A ARG* 3.3 28.7 + - + +
231A TYR* 3.0 21.1 + - + +
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Residues in contact with ALA 228 (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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82A VAL* 4.8 4.5 - - + -
184A VAL* 3.8 23.0 - - + +
186A MET* 3.5 21.5 - - + -
204A CYS* 5.4 0.2 - - - -
206A LEU* 4.0 5.8 - - + +
224A HIS 2.7 21.5 + - - +
225A PHE* 3.8 4.0 - - - +
227A VAL* 1.3 74.0 - - - +
229A ASN* 1.3 59.5 + - - +
231A TYR* 3.1 6.1 + - - +
232A LEU* 2.9 31.5 + - - +
242A TRP* 4.5 7.9 - - + -
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Residues in contact with ASN 229 (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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124A TYR* 3.5 15.5 + - - +
225A PHE 3.4 8.2 + - - +
226A LEU* 3.3 6.2 + - - +
228A ALA* 1.3 72.9 - - - +
230A ARG* 1.3 66.9 + - - +
232A LEU* 3.3 10.7 + - - +
233A GLU* 3.0 31.8 + - + +
239A PRO* 3.4 21.3 - - + +
240A ILE* 2.8 47.7 + - - +
242A TRP* 3.4 13.0 + - - +
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Residues in contact with ARG 230 (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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223A GLN* 5.1 4.9 + - - -
226A LEU* 3.2 44.2 + - - +
227A VAL* 3.3 35.2 + - + +
229A ASN* 1.3 75.7 - - - +
231A TYR* 1.3 66.9 + - - +
233A GLU* 3.3 11.1 + - - +
234A THR* 3.2 25.3 + - + +
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Residues in contact with TYR 231 (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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182A GLY* 3.4 41.0 - - - -
183A LEU 4.2 0.7 - - - -
184A VAL* 3.6 11.0 - - + -
202A VAL 3.7 11.1 + - - -
203A HIS 4.1 1.8 - - - -
204A CYS* 3.5 47.3 + - + -
227A VAL* 3.0 13.9 + - + +
228A ALA 3.4 7.4 - - - +
230A ARG* 1.3 76.9 - - - +
232A LEU* 1.3 67.3 - - - +
234A THR* 2.6 25.6 + - - -
235A ARG* 3.2 53.8 + - + -
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Residues in contact with LEU 232 (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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81A ARG* 4.0 16.6 - - + +
82A VAL* 4.4 11.0 - - + -
182A GLY 4.3 6.3 - - - +
184A VAL* 4.0 18.6 - - + -
228A ALA* 2.9 20.8 + - + +
229A ASN* 3.7 24.9 - - - +
231A TYR* 1.3 74.2 - - + +
233A GLU* 1.3 57.1 + - - +
235A ARG* 2.8 19.9 + - - +
236A SER 3.1 0.2 + - - -
237A ILE* 2.9 60.0 + - + +
238A SER 3.7 16.4 - - - +
239A PRO* 4.2 1.3 - - + -
240A ILE* 4.3 14.1 - - + -
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Residues in contact with GLU 233 (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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229A ASN* 3.0 20.5 + - - +
230A ARG* 3.6 9.7 - - - +
231A TYR 3.2 0.2 - - - -
232A LEU* 1.3 76.4 - - - +
234A THR* 1.3 57.7 + - + +
235A ARG 3.0 0.2 - - - -
236A SER* 3.0 19.4 + - - +
237A ILE 3.9 11.0 - - - +
239A PRO* 4.1 26.0 - - + +
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Residues in contact with THR 234 (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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230A ARG* 3.2 15.8 + - + +
231A TYR* 2.6 22.5 + - - -
233A GLU* 1.3 75.9 - - + +
235A ARG* 1.3 89.5 + - - +
236A SER* 3.3 2.9 + - - -
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Residues in contact with ARG 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A GLY* 4.8 7.4 - - - -
201A ARG 5.3 6.1 + - - -
231A TYR* 3.2 52.2 + - + +
232A LEU* 2.8 10.4 + - - +
234A THR* 1.3 110.1 + - - +
236A SER* 1.3 73.3 + - - +
237A ILE* 3.1 25.2 + - + +
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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