Contacts of the helix formed by residues 222 - 233 (chain A) in PDB entry 3C0H
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 THR 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A GLY* 1.3 72.8 - - - -
223A LYS* 1.3 68.6 + - - +
224A GLU* 4.5 10.3 + - - -
225A ARG* 2.8 21.7 + - - +
226A LEU 2.7 19.6 + - - -
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Residues in contact with LYS 223 (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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179A ARG* 4.9 6.4 - - - +
183A PRO* 3.8 22.7 - - + +
186A MET* 5.5 1.8 - - - +
221A GLY 3.8 1.6 + - - -
222A THR* 1.3 71.1 - - - +
224A GLU* 1.3 56.1 + - - +
226A LEU* 3.6 9.3 - - + +
227A PHE* 2.9 72.9 + - + -
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A THR* 2.9 10.2 + - - +
223A LYS* 1.3 78.5 - - - +
225A ARG* 1.3 64.3 + - - +
227A PHE* 4.0 5.4 - - - +
228A GLU* 3.0 51.4 + - + +
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Residues in contact with ARG 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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220A TYR* 3.2 52.6 + - - +
221A GLY* 3.9 11.4 - - - -
222A THR* 2.8 22.7 + - - +
224A GLU* 1.3 82.4 - - - +
226A LEU* 1.3 65.9 + - - +
228A GLU* 3.5 8.3 + - + +
229A GLY* 3.1 19.9 + - - -
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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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183A PRO* 3.9 33.0 - - + -
184A HIS* 3.9 28.9 - - + +
219A PHE* 3.4 40.9 - - + +
220A TYR* 3.7 11.7 + - - +
221A GLY 3.9 9.9 - - - +
222A THR 2.7 18.9 + - - +
223A LYS* 3.6 11.0 - - + +
225A ARG* 1.3 72.7 - - - +
227A PHE* 1.3 59.1 + - + +
229A GLY* 3.2 4.0 + - - -
230A ILE* 3.0 43.7 + - + +
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Residues in contact with PHE 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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179A ARG* 3.3 40.4 - - - +
183A PRO* 3.8 34.8 - - + -
186A MET* 4.2 9.4 - - + -
191A VAL* 3.6 36.1 - - + -
223A LYS* 2.9 54.7 + - + +
224A GLU* 4.0 4.5 - - - +
226A LEU* 1.3 74.9 - - + +
228A GLU* 1.3 60.2 + - - +
230A ILE* 3.4 9.1 + - + +
231A ILE* 3.0 38.6 + - + +
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Residues in contact with GLU 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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224A GLU* 3.0 46.8 + - + +
225A ARG* 3.7 10.8 - - + +
226A LEU 3.3 0.2 - - - -
227A PHE* 1.3 76.0 - - - +
229A GLY* 1.3 57.9 + - - +
231A ILE* 3.6 6.3 + - + +
232A LYS* 3.1 41.1 + - + +
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Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A PHE* 3.2 16.9 - - - -
225A ARG 3.1 14.3 + - - -
226A LEU 3.2 4.4 + - - -
228A GLU* 1.3 74.8 - - - +
230A ILE* 1.3 58.4 + - - +
232A LYS* 4.7 3.8 - - - -
233A GLY 2.9 21.1 + - - -
234A LYS* 3.2 18.3 + - - -
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Residues in contact with ILE 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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183A PRO 3.4 25.1 - - - +
184A HIS 4.8 3.8 - - - +
186A MET 3.5 23.1 - - - +
188A PRO* 3.7 27.3 - - + +
191A VAL* 4.0 8.7 - - + -
203A TRP* 4.0 5.4 - - + +
219A PHE* 3.8 26.7 - - + -
226A LEU* 3.0 36.9 + - + +
227A PHE* 3.8 16.2 - - + +
228A GLU 3.3 0.2 - - - -
229A GLY* 1.3 74.5 - - - +
231A ILE* 1.3 60.4 + - - +
233A GLY* 3.0 15.6 + - - -
259A LEU* 3.4 11.4 - - - +
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Residues in contact with ILE 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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179A ARG* 5.8 1.1 - - - +
188A PRO* 4.6 6.3 - - + +
191A VAL* 3.8 26.9 - - + +
192A LYS* 3.8 46.1 + - + +
227A PHE* 3.0 24.5 + - + +
228A GLU* 3.9 6.3 - - + +
230A ILE* 1.3 76.7 - - - +
232A LYS* 1.3 79.1 + - + +
259A LEU* 3.3 21.5 - - - +
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Residues in contact with LYS 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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228A GLU* 3.1 28.0 + - + +
229A GLY* 4.2 2.0 - - - +
231A ILE* 1.3 92.6 - - + +
233A GLY* 1.3 62.9 + - - +
234A LYS* 3.3 28.3 + - + +
259A LEU* 3.4 15.9 - - - +
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Residues in contact with GLY 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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203A TRP* 4.8 3.8 - - - -
219A PHE* 3.9 11.9 - - - -
229A GLY 2.9 10.3 + - - -
230A ILE 3.0 13.3 + - - -
231A ILE 3.3 0.2 - - - -
232A LYS* 1.3 78.1 - - - +
234A LYS* 1.3 62.8 + - - +
235A TYR* 3.5 18.7 + - - -
257A LEU 5.3 3.1 - - - +
259A LEU* 3.8 13.9 - - - -
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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