Contacts of the helix formed by residues 220 - 232 (chain A) in PDB entry 2AG1
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 ARG 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ALA 4.6 5.5 + - - -
185A HIS* 4.4 32.7 + - - +
186A GLY 5.3 0.4 - - - +
215A ALA 4.4 0.2 + - - -
218A THR* 2.9 36.4 + - - +
219A ALA* 1.3 71.7 + - - +
221A LYS* 1.3 58.0 + - - +
222A THR 3.5 2.0 - - - -
223A ALA* 4.0 7.4 - - + -
224A LEU* 3.0 28.6 + - - +
244A MSE 3.7 7.8 - - + +
323A GLY* 3.5 28.5 + - - +
324A GLY* 5.3 0.8 - - - +
326A ILE* 3.9 15.4 - - + +
327A GLU* 2.9 49.7 + - - +
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Residues in contact with LYS 221 (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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219A ALA* 2.7 31.1 + - - +
220A ARG* 1.3 69.7 - - - +
222A THR* 1.3 71.4 + - + +
224A LEU* 3.6 3.1 - - - +
225A SER* 3.0 26.6 + - - -
243A SER 5.8 2.7 - - - -
244A MSE 3.9 26.9 - - - +
247A GLY* 6.5 0.9 - - - -
248A LEU* 5.5 0.2 - - - +
410A GLY 5.6 2.8 + - - -
440A ARG* 4.8 13.1 - - - +
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Residues in contact with THR 222 (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 ARG 3.5 0.2 - - - -
221A LYS* 1.3 80.8 - - + +
223A ALA* 1.3 63.7 + - - +
225A SER* 3.5 7.6 + - - -
226A ALA* 3.1 24.3 + - - +
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Residues in contact with ALA 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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220A ARG* 3.5 7.6 + - + +
221A LYS 3.2 0.6 - - - -
222A THR* 1.3 78.1 + - - +
224A LEU* 1.3 65.3 + - - +
226A ALA* 3.1 3.0 + - - -
227A PHE* 2.9 21.0 + - - +
326A ILE* 3.9 17.0 - - + -
327A GLU* 4.0 37.9 - - + +
330A ALA* 3.4 18.6 - - + +
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Residues in contact with LEU 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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209A ILE* 5.7 2.0 - - + -
211A LEU* 4.0 28.9 - - + -
220A ARG 3.0 18.8 + - - +
221A LYS* 3.6 4.7 - - - +
223A ALA* 1.3 74.6 - - - +
225A SER* 1.3 59.2 + - - +
227A PHE* 3.1 13.0 + - + +
228A VAL* 2.8 51.3 + - + +
235A VAL* 5.1 2.7 - - + -
244A MSE 3.4 36.8 - - + +
248A LEU* 3.9 15.5 - - + -
276A LEU* 5.6 2.0 - - + -
326A ILE* 3.4 28.7 - - + +
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Residues in contact with SER 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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221A LYS 3.0 15.8 + - - -
222A THR* 3.6 9.9 + - - -
224A LEU* 1.3 77.8 - - - +
226A ALA* 1.3 58.2 + - - +
228A VAL* 4.1 0.7 - - - +
229A ALA* 2.9 30.8 + - - +
247A GLY 4.5 12.6 - - - -
248A LEU* 3.8 24.2 - - - -
249A PRO* 5.3 5.7 - - - +
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Residues in contact with ALA 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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222A THR 3.1 17.4 + - - +
223A ALA* 3.1 4.7 + - - +
225A SER* 1.3 74.3 + - - +
227A PHE* 1.3 63.9 + - - +
229A ALA* 3.5 5.3 + - - +
230A ALA* 3.1 25.5 + - - +
330A ALA* 4.4 11.9 - - + +
333A THR* 4.0 3.2 - - + +
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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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198A LEU* 4.3 4.0 - - + -
201A LEU* 3.8 24.0 - - + -
209A ILE* 3.6 27.8 - - + -
223A ALA 2.9 13.6 + - - +
224A LEU* 3.5 15.0 - - + +
226A ALA* 1.3 74.1 - - - +
228A VAL* 1.3 69.4 + - + +
230A ALA* 3.3 2.4 + - - +
231A THR* 3.0 44.6 + - + +
274A LEU* 4.2 7.0 - - + -
276A LEU* 5.4 3.6 - - + -
326A ILE* 4.7 4.0 - - + +
329A LEU* 3.7 59.0 - - + -
330A ALA* 4.1 10.9 - - + +
333A THR* 3.8 15.5 - - - -
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Residues in contact with VAL 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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209A ILE* 4.8 3.4 - - + -
224A LEU* 2.8 39.1 + - + +
225A SER 4.1 2.5 - - - +
227A PHE* 1.3 81.7 - - + +
229A ALA* 1.3 57.4 + - - +
231A THR* 3.9 5.4 - - - -
232A GLY* 2.8 29.5 + - - -
233A VAL 3.8 12.6 - - - +
235A VAL* 3.7 20.4 - - + -
248A LEU* 4.1 15.9 - - + -
249A PRO* 4.8 2.5 - - + -
252A MSE 3.4 34.7 - - + +
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Residues in contact with ALA 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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225A SER 2.9 20.9 + - - +
226A ALA* 4.0 5.8 - - - +
227A PHE 3.3 0.2 - - - -
228A VAL* 1.3 77.1 - - - +
230A ALA* 1.3 61.2 + - - +
232A GLY* 4.2 3.3 + - - -
249A PRO* 5.4 6.0 - - + +
252A MSE 3.8 15.9 - - + +
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Residues in contact with ALA 230 (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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226A ALA 3.1 10.1 + - - +
227A PHE 3.8 0.2 - - - +
228A VAL 3.3 0.2 - - - -
229A ALA* 1.3 79.8 - - - +
231A THR* 1.3 61.1 + - - +
333A THR* 3.4 46.4 - - + +
337A ALA* 5.6 3.6 - - - +
339A TRP* 3.5 23.7 - - + +
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Residues in contact with THR 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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201A LEU* 4.3 2.0 - - + -
209A ILE* 5.3 0.2 - - - +
227A PHE* 3.0 44.1 + - + +
228A VAL* 3.7 4.5 + - - -
230A ALA* 1.3 78.6 - - - +
232A GLY* 1.3 61.9 + - - +
233A VAL* 3.3 26.6 + - - +
333A THR* 3.7 13.9 - - - +
339A TRP* 3.8 33.3 - - + +
340A PRO 4.1 10.4 - - - +
341A ASP 5.6 0.2 - - - -
342A ARG* 3.9 17.3 + - - +
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Residues in contact with GLY 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 VAL 2.8 16.3 + - - -
229A ALA 4.2 2.6 + - - -
230A ALA 3.6 2.0 - - - -
231A THR* 1.3 76.8 - - - +
233A VAL* 1.3 57.7 + - - -
234A PRO* 3.7 0.2 - - - +
252A MSE 4.2 17.0 - - - -
341A ASP 4.9 4.3 - - - -
342A ARG* 3.5 15.2 - - - +
346A CYS* 3.3 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