Contacts of the helix formed by residues 216 - 231 (chain A) in PDB entry 2XRI
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 SER 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A VAL* 3.7 1.8 - - - -
189A GLN* 4.1 13.9 - - - +
191A VAL* 5.3 10.3 - - - -
214A GLN 3.9 0.4 + - - -
215A PRO* 1.3 73.9 - - - +
217A LEU* 1.3 65.0 + - - +
218A GLN* 3.5 8.2 + - - +
219A GLN* 3.0 32.1 + - - +
220A VAL* 3.0 19.6 + - - +
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Residues in contact with LEU 217 (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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165A ILE* 4.2 22.0 - - + +
168A PHE* 3.9 34.1 - - + -
188A VAL* 3.4 18.2 - - + +
189A GLN 4.8 0.8 + - - -
216A SER* 1.3 74.0 - - - +
218A GLN* 1.3 57.5 + - - +
220A VAL* 3.1 2.6 + - + -
221A LEU* 2.8 46.4 + - + +
254A LEU* 4.7 0.9 - - + -
257A GLN* 3.5 45.5 - - + +
258A CYS* 4.7 9.2 - - - -
261A LEU* 4.1 14.3 - - + +
263A LEU* 4.8 0.2 - - + -
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Residues in contact with GLN 218 (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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216A SER* 3.3 8.8 + - - +
217A LEU* 1.3 78.6 - - - +
219A GLN* 1.3 63.7 + - + +
221A LEU* 3.3 5.1 + - - +
222A GLU* 3.1 41.7 + - + +
261A LEU* 5.1 3.2 - - + +
263A LEU* 3.5 44.4 - - + +
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Residues in contact with GLN 219 (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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215A PRO* 3.3 20.2 - - + +
216A SER* 3.0 37.5 + - - +
218A GLN* 1.3 77.3 - - + +
220A VAL* 1.3 57.4 + - - +
222A GLU* 3.2 17.6 + - - +
223A ARG* 3.0 35.9 + - - +
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Residues in contact with VAL 220 (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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168A PHE* 3.7 39.9 - - + -
184A PHE* 4.2 13.9 - - + -
186A MET* 4.1 12.1 - - + -
187A TYR 4.5 0.7 - - - +
188A VAL* 3.8 19.1 - - + -
215A PRO* 4.0 23.3 - - + +
216A SER 3.0 17.6 + - - +
217A LEU* 3.1 10.1 + - - +
219A GLN* 1.3 76.4 - - - +
221A LEU* 1.3 58.5 + - - +
223A ARG* 3.2 9.5 + - - +
224A VAL* 2.8 26.4 + - + +
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Residues in contact with LEU 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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168A PHE* 3.7 31.0 - - + -
217A LEU* 2.8 28.9 + - + +
218A GLN* 3.6 5.4 - - - +
220A VAL* 1.3 74.5 - - - +
222A GLU* 1.3 56.1 + - - +
224A VAL* 3.3 6.3 + - + +
225A ASP* 3.0 27.0 + - - +
254A LEU* 4.0 8.3 - - + -
258A CYS* 3.9 19.7 - - - -
263A LEU* 3.8 30.5 - - + -
264A PRO 4.9 5.4 - - - +
268A TYR* 4.7 1.2 + - - -
269A PHE* 4.0 22.4 - - + -
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Residues in contact with GLU 222 (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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218A GLN* 3.1 41.2 + - + +
219A GLN* 3.5 18.5 - - - +
221A LEU* 1.3 75.0 - - + +
223A ARG* 1.3 59.1 + - + +
225A ASP* 3.2 7.6 + - - +
226A GLU* 3.0 40.7 + - - +
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Residues in contact with ARG 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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184A PHE* 3.6 7.4 - - + -
186A MET* 3.3 43.1 - - - +
215A PRO* 4.3 11.9 - - - +
219A GLN* 3.0 23.2 + - - +
220A VAL 3.2 6.9 + - - +
222A GLU* 1.3 73.9 - - + +
224A VAL* 1.3 64.9 + - - +
226A GLU* 3.4 18.9 + - - +
227A TRP* 2.9 23.6 + - - +
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Residues in contact with VAL 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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168A PHE* 3.8 23.8 - - + -
170A ILE* 3.8 18.6 - - + -
184A PHE* 3.4 32.5 - - + -
220A VAL 2.8 23.1 + - - +
221A LEU* 3.3 9.8 + - - +
223A ARG* 1.3 71.9 - - - +
225A ASP* 1.3 59.5 + - - +
227A TRP* 3.0 5.6 + - - +
228A MET* 2.8 36.2 + - + +
268A TYR* 4.2 9.0 - - + +
269A PHE* 3.9 21.3 - - + -
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Residues in contact with ASP 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 LEU 3.0 12.1 + - - +
222A GLU* 3.2 11.4 + - - +
224A VAL* 1.3 78.0 - - - +
226A GLU* 1.3 56.1 + - + +
228A MET* 3.3 3.9 + - - +
229A ALA* 3.0 28.2 + - - +
234A LEU* 3.7 13.0 - - - +
266A ALA* 4.9 2.1 - - - +
268A TYR* 2.5 39.3 + - - +
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Residues in contact with GLU 226 (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 GLU* 3.0 27.5 + - - +
223A ARG* 3.6 21.1 - - - +
225A ASP* 1.3 74.8 - - - +
227A TRP* 1.3 57.2 - - - +
229A ALA* 3.3 7.4 + - - +
230A LYS* 2.9 31.1 + - - +
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Residues in contact with TRP 227 (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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147A LEU* 4.7 1.1 - - + -
170A ILE* 3.8 37.7 - - + -
172A LYS* 3.8 26.5 - - + -
182A SER* 3.2 29.0 + - - -
183A THR 3.9 10.5 + - - -
184A PHE* 3.7 41.1 - + + -
223A ARG 2.9 15.0 + - - +
224A VAL 3.3 8.7 - - - +
226A GLU* 1.3 75.3 - - - +
228A MET* 1.3 92.6 + - - +
230A LYS* 3.4 9.9 + - + +
231A GLU* 2.8 48.6 + - + +
233A LEU* 4.0 9.0 - - + -
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Residues in contact with MET 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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147A LEU* 3.7 25.8 - - + -
224A VAL* 2.8 25.7 + - + +
225A ASP* 3.6 7.0 - - - +
227A TRP* 1.3 84.9 - - + +
229A ALA* 1.3 61.5 + - - +
232A GLY 3.3 3.1 + - - -
233A LEU* 2.8 62.8 + - + +
234A LEU* 3.6 19.7 + - + -
240A SER* 4.6 3.6 - - - +
242A PHE* 4.6 7.0 - - - -
268A TYR* 3.7 51.6 - - + -
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Residues in contact with ALA 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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225A ASP 3.0 13.7 + - - +
226A GLU* 3.5 11.4 - - - +
227A TRP 3.2 0.2 - - - -
228A MET* 1.3 77.1 - - - +
230A LYS* 1.3 63.1 + - - +
232A GLY* 3.0 15.9 + - - -
234A LEU* 3.6 20.5 + - + +
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Residues in contact with LYS 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 GLU 2.9 20.0 + - - +
227A TRP* 3.8 10.1 - - + +
229A ALA* 1.3 72.8 - - - +
231A GLU* 1.3 71.4 + - + +
232A GLY 3.2 1.1 + - - -
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Residues in contact with GLU 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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145A TYR* 5.2 2.3 - - - -
172A LYS* 2.8 51.8 + - + +
181A GLU 5.2 0.2 - - - +
182A SER* 2.9 26.7 + - - -
227A TRP* 2.8 47.6 + - + +
229A ALA 3.2 0.2 - - - -
230A LYS* 1.3 86.2 - - + +
232A GLY* 1.3 61.4 + - - +
233A LEU* 3.2 19.2 + - + +
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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