Contacts of the helix formed by residues 214 - 232 (chain A) in PDB entry 2I7V
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 LYS 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A HIS 5.3 1.3 - - - +
213A GLU* 1.3 77.5 - - - +
215A ARG* 1.3 67.0 + - - +
216A GLU* 3.4 22.0 - - - +
217A GLU* 3.2 20.4 + - + +
218A ARG* 2.9 22.2 + - - +
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Residues in contact with ARG 215 (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 GLN* 3.2 29.5 + - - +
184A GLU 4.2 16.7 + - - -
185A ASP* 4.6 4.4 + - - +
186A ARG* 3.0 47.1 - - - +
214A LYS* 1.3 73.1 - - - +
216A GLU* 1.3 91.4 + - - +
218A ARG* 3.1 24.5 + - - +
219A GLU* 2.9 52.1 + - + +
248A GLU* 4.6 3.7 + - - -
393A PHE* 5.8 0.9 - - + -
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Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLN* 4.8 1.4 - - - +
214A LYS* 3.6 30.7 - - - +
215A ARG* 1.3 103.9 + - - +
217A GLU* 1.3 70.3 + - - +
219A GLU* 3.7 6.9 + - - +
220A ALA* 3.2 23.4 + - - +
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Residues in contact with GLU 217 (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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213A GLU* 3.9 22.3 - - + +
214A LYS* 3.2 30.4 + - + +
215A ARG 3.1 0.6 - - - -
216A GLU* 1.3 84.7 - - - +
218A ARG* 1.3 60.3 + - - +
220A ALA* 3.3 6.8 + - - +
221A ARG* 2.9 30.5 + - - +
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Residues in contact with ARG 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLN* 4.0 16.2 - - - +
212A HIS* 4.1 18.4 - - + +
213A GLU* 3.4 42.1 + - + +
214A LYS 2.9 13.0 + - - +
215A ARG* 3.5 31.8 - - - +
217A GLU* 1.3 77.2 - - - +
219A GLU* 1.3 56.6 + - - +
221A ARG* 3.4 0.8 + - - +
222A PHE* 2.9 29.6 + - - +
391A ILE* 3.5 12.5 - - + +
392A SER* 3.0 31.8 + - - +
393A PHE* 3.4 31.9 - - + +
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Residues in contact with GLU 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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186A ARG* 2.6 43.1 + - - +
215A ARG* 2.9 51.0 + - + +
216A GLU* 4.0 6.1 - - - +
218A ARG* 1.3 73.6 - - - +
220A ALA* 1.3 65.1 + - - +
222A PHE* 3.4 3.0 + - - +
223A CYS* 3.0 30.0 + - - -
248A GLU* 4.5 1.2 - - - +
252A ILE* 3.7 24.2 - - + +
393A PHE* 4.0 15.7 - - + -
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Residues in contact with ALA 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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216A GLU 3.2 17.1 + - - +
217A GLU* 3.7 8.1 - - - +
219A GLU* 1.3 75.3 - - - +
221A ARG* 1.3 67.5 + - - +
223A CYS* 3.4 5.0 + - - +
224A ASN* 3.0 36.8 + - - +
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Residues in contact with ARG 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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212A HIS* 4.6 7.5 + - - -
213A GLU* 3.1 36.5 + - - -
217A GLU 2.9 16.8 + - - +
218A ARG 3.8 2.0 - - - +
220A ALA* 1.3 78.0 - - - +
222A PHE* 1.3 58.6 + - - +
224A ASN* 3.8 6.3 - - + +
225A THR* 2.7 41.3 + - - +
389A ASP* 5.1 6.2 + - - -
390A TYR 3.0 25.1 + - - +
391A ILE* 3.2 38.3 - - + +
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Residues in contact with PHE 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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218A ARG 2.9 19.0 + - - +
219A GLU 3.5 3.8 - - - +
221A ARG* 1.3 78.0 - - - +
223A CYS* 1.3 66.1 + - - +
225A THR* 3.6 2.1 - - - -
226A VAL* 3.1 29.3 + - + +
238A ILE* 3.6 34.5 - - + -
249A LEU* 3.8 31.9 - - + -
252A ILE* 4.0 20.6 - - + -
253A LEU* 3.7 29.8 - - + -
353A ILE* 4.0 29.6 - - + -
355A ALA* 5.2 1.8 - - + -
391A ILE* 3.6 10.9 - - + +
393A PHE* 4.0 22.4 - + + -
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Residues in contact with CYS 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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219A GLU 3.0 18.7 + - - +
220A ALA* 3.9 4.5 - - - +
222A PHE* 1.3 84.4 - - - +
224A ASN* 1.3 58.3 + - - +
226A VAL* 3.3 6.5 + - - +
227A HIS* 2.8 31.3 + - - +
252A ILE* 3.5 27.8 - - - -
253A LEU* 4.9 4.0 - - - -
256A TYR* 3.6 51.9 - - + -
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Residues in contact with ASN 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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220A ALA* 3.0 29.5 + - - +
221A ARG* 3.8 6.8 - - + +
223A CYS* 1.3 76.6 - - - +
225A THR* 1.3 58.8 + - - +
227A HIS* 3.7 5.4 - - - +
228A ASP* 2.9 41.5 + - - +
256A TYR* 4.1 11.7 + - - -
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Residues in contact with THR 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 ARG* 2.7 29.8 + - - +
222A PHE 3.6 4.3 - - - -
224A ASN* 1.3 74.1 - - - +
226A VAL* 1.3 64.9 + - - +
228A ASP* 3.3 8.7 + - - +
229A ILE* 3.0 36.0 + - + +
353A ILE* 3.7 22.2 - - + -
389A ASP* 3.7 33.9 + - + +
391A ILE* 3.8 8.5 - - - +
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Residues in contact with VAL 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 PHE* 3.1 22.2 + - + +
223A CYS 3.7 7.0 - - - +
225A THR* 1.3 72.5 - - - +
227A HIS* 1.3 68.3 + - - +
229A ILE* 3.3 8.5 + - + +
230A VAL* 3.2 21.8 + - - +
236A GLY* 6.1 2.7 - - - -
238A ILE* 4.3 17.3 - - + -
253A LEU* 4.3 10.5 - - + -
257A TRP* 3.8 20.6 - - + -
324A VAL* 3.5 31.2 - - + -
353A ILE* 3.4 21.8 - - + -
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Residues in contact with HIS 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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223A CYS 2.8 18.6 + - - +
224A ASN* 3.7 7.4 - - - +
226A VAL* 1.3 79.5 - - - +
228A ASP* 1.3 66.8 + - - +
230A VAL* 3.4 6.4 + - - +
231A ASN* 2.9 39.9 + - + +
256A TYR* 2.7 37.4 - + + +
260A HIS* 4.8 3.5 + + - -
262A GLU* 3.6 24.8 + - + -
263A LEU* 3.5 30.5 - - + +
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Residues in contact with ASP 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 ASN* 2.9 31.2 + - - +
225A THR* 3.5 8.6 - - - +
227A HIS* 1.3 79.3 - - - +
229A ILE* 1.3 61.0 + - + +
231A ASN* 3.5 7.1 + - - +
232A ARG* 3.3 35.5 + - - +
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Residues in contact with ILE 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 THR* 3.0 33.5 + - + +
226A VAL* 3.6 8.3 - - - +
227A HIS 3.2 0.2 - - - -
228A ASP* 1.3 75.3 - - + +
230A VAL* 1.3 62.3 + - + +
232A ARG* 3.2 33.5 - - - +
234A GLY 2.9 22.0 + - - -
235A ARG 3.4 32.3 - - - +
236A GLY* 3.9 9.2 - - - +
349A ARG 3.7 11.9 - - - +
351A GLY* 3.9 27.4 - - - +
352A VAL 4.7 0.7 - - - +
353A ILE* 4.4 11.0 - - + -
387A SER* 4.4 4.0 - - - +
389A ASP* 5.5 0.4 - - - +
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Residues in contact with VAL 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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226A VAL* 3.2 10.0 + - + +
227A HIS* 3.5 11.2 - - - +
229A ILE* 1.3 77.5 - - + +
231A ASN* 1.3 65.2 + - - +
233A GLY* 3.1 14.0 + - - -
234A GLY 3.5 12.6 - - - +
236A GLY 4.7 2.9 - - - +
257A TRP* 4.4 4.9 - - + -
263A LEU* 4.0 15.0 - - + -
266A ILE* 3.6 40.0 - - + +
322A PRO* 3.7 10.5 - - + +
323A SER 3.6 24.0 - - - +
324A VAL* 3.7 20.4 - - + -
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Residues in contact with ASN 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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227A HIS* 2.9 38.9 + - + +
228A ASP* 3.8 7.5 - - - +
229A ILE 3.2 0.2 - - - -
230A VAL* 1.3 78.7 - - - +
232A ARG* 1.3 61.5 + - - +
233A GLY 3.1 2.9 + - - -
263A LEU* 6.0 0.9 - - - -
266A ILE* 5.5 2.2 - - - -
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Residues in contact with ARG 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 ASP* 3.3 16.7 + - - +
229A ILE* 3.2 26.7 - - - +
231A ASN* 1.3 80.7 - - - +
233A GLY* 1.3 56.8 + - - +
234A GLY 3.7 0.2 + - - -
348A LYS 3.5 9.4 + - - -
349A ARG* 2.7 43.4 + - + +
350A ASN 3.0 21.8 + - - -
387A SER* 3.0 31.7 + - - -
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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