Contacts of the helix formed by residues 214 - 231 (chain A) in PDB entry 2B7O
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 TYR 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A PHE* 4.0 20.6 - + + -
205A VAL* 4.0 9.6 - - + -
208A SER* 5.2 1.8 - - - -
209A PRO 5.7 0.2 - - - -
210A ALA* 3.6 22.6 - - + +
211A GLY* 2.7 9.7 + - - +
213A ARG* 1.3 101.4 - - + +
215A GLU* 1.3 66.3 + - - +
216A ALA 3.3 3.3 + - - -
217A LEU* 3.3 6.2 + - + +
218A ALA* 3.0 22.2 + - - +
451A GLU* 2.8 48.3 + - + +
454A PHE* 3.6 44.7 - + + -
455A LEU* 3.9 24.5 - - + +
458A GLU* 6.5 1.3 - - + -
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Residues in contact with GLU 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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205A VAL* 4.0 18.4 - - + -
211A GLY 3.1 10.4 + - - +
212A ALA* 4.1 17.3 - - - +
213A ARG 3.6 1.0 - - - -
214A TYR* 1.3 76.5 - - - +
216A ALA* 1.3 62.8 + - - +
218A ALA* 3.2 2.9 + - - +
219A THR* 2.7 62.5 + - - +
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Residues in contact with ALA 216 (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 ALA 5.1 1.0 + - - +
213A ARG 5.1 2.8 + - - +
214A TYR 3.3 0.8 - - - -
215A GLU* 1.3 89.3 + - - +
217A LEU* 1.3 56.4 + - - +
219A THR* 3.8 3.5 - - - -
220A GLU* 2.9 32.3 + - - +
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Residues in contact with LEU 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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112A VAL* 4.3 4.3 - - + -
115A TYR* 3.7 32.3 - - + -
116A GLY 5.6 0.2 - - - +
213A ARG 5.7 0.4 + - - -
214A TYR* 3.3 8.7 + - - +
216A ALA* 1.3 78.0 - - - +
218A ALA* 1.3 58.2 + - - +
220A GLU* 3.2 7.1 + - + +
221A ILE* 2.8 42.1 + - + +
454A PHE* 3.6 31.6 - - + +
457A ALA* 3.9 28.0 - - + -
458A GLU* 3.5 27.6 - - + +
461A ARG* 4.0 14.8 - - - +
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Residues in contact with ALA 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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198A HIS* 2.9 36.0 + - + +
201A ASN 5.0 1.1 - - - +
202A ARG* 4.6 12.1 - - + +
205A VAL* 3.9 22.7 - - + -
214A TYR 3.0 18.5 + - - +
215A GLU* 3.5 4.5 - - - +
217A LEU* 1.3 78.2 - - - +
219A THR* 1.3 56.5 + - - +
222A ASP* 3.0 15.5 + - - +
454A PHE* 3.9 11.8 - - + -
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Residues in contact with THR 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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202A ARG* 5.7 3.1 - - - +
215A GLU* 2.7 45.5 + - - +
216A ALA* 3.8 4.5 - - - +
218A ALA* 1.3 69.3 - - - +
220A GLU* 1.3 66.4 + - - +
222A ASP* 3.2 9.2 + - + +
223A ARG* 3.0 58.5 + - - +
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Residues in contact with GLU 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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115A TYR* 2.5 28.9 + - + +
216A ALA* 2.9 22.3 + - - +
217A LEU* 3.3 8.9 - - - +
219A THR* 1.3 78.4 - - - +
221A ILE* 1.3 55.7 + - - +
223A ARG* 3.2 10.6 + - - +
224A GLY* 3.0 23.9 + - - -
461A ARG* 2.4 43.7 + - - -
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Residues in contact with ILE 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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111A VAL* 4.3 14.1 - - + -
112A VAL* 3.9 34.8 - - + +
115A TYR* 3.7 37.2 - - + -
198A HIS* 3.5 37.7 - - + +
217A LEU* 2.8 38.7 + - + +
218A ALA* 4.6 0.9 - - - -
220A GLU* 1.3 69.7 - - - +
222A ASP* 1.3 66.6 + - - +
224A GLY* 3.1 3.3 + - - -
225A LEU* 3.0 30.0 + - + +
454A PHE* 4.6 1.1 - - + -
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Residues in contact with ASP 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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198A HIS* 3.7 10.3 + - + -
199A ASP* 5.1 1.0 - - - +
202A ARG* 3.4 38.3 + - - -
218A ALA 3.0 14.7 + - - +
219A THR* 3.4 13.2 - - + +
221A ILE* 1.3 75.6 - - - +
223A ARG* 1.3 56.9 + - - +
225A LEU* 3.1 8.9 + - - +
226A ARG* 2.9 63.2 + - - +
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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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219A THR* 3.0 40.1 + - - +
220A GLU* 3.2 10.7 + - - +
222A ASP* 1.3 73.9 - - - +
224A GLY* 1.3 61.2 + - - +
226A ARG* 4.1 24.3 - - - +
227A PHE* 2.9 30.3 + - - +
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Residues in contact with GLY 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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115A TYR* 4.7 13.0 - - - -
220A GLU 3.0 14.4 + - - -
221A ILE 3.1 5.1 + - - -
223A ARG* 1.3 75.5 - - - +
225A LEU* 1.3 56.7 + - - +
227A PHE* 3.4 11.2 - - - +
228A MSE 3.0 28.4 + - - +
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Residues in contact with LEU 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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111A VAL* 4.7 8.5 - - + -
194A LEU* 3.9 40.6 - - + +
195A HIS* 3.5 29.8 - - + +
198A HIS* 3.6 37.5 - - + -
221A ILE* 3.0 25.1 + - + +
222A ASP* 3.6 8.7 - - - +
224A GLY* 1.3 75.1 - - - +
226A ARG* 1.3 61.5 + - + +
228A MSE 3.4 12.1 + - - +
229A SER* 3.0 27.9 + - - -
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Residues in contact with ARG 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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195A HIS* 5.7 0.9 - - - +
222A ASP* 2.9 48.6 + - - +
223A ARG* 4.1 26.6 - - - +
225A LEU* 1.3 76.2 - - + +
227A PHE* 1.3 52.6 + - - +
229A SER* 3.4 6.7 + - - -
230A ALA* 2.8 35.3 + - - +
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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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223A ARG 2.9 21.5 + - - +
224A GLY* 3.4 9.9 - - - +
226A ARG* 1.3 76.5 - - - +
228A MSE 1.3 65.5 + - + +
230A ALA* 3.1 10.5 + - + +
231A CYS* 3.0 48.6 + - - -
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Residues in contact with MSE 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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194A LEU* 4.7 6.7 - - + -
195A HIS* 4.6 8.5 - - + +
224A GLY 3.0 16.6 + - - +
225A LEU* 3.4 27.6 + - - +
227A PHE* 1.3 79.5 - - + +
229A SER* 1.3 64.4 + - - +
231A CYS* 3.2 12.5 + - - +
233A VAL* 3.1 62.8 + - + +
238A LEU* 3.6 28.9 - - + -
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Residues in contact with SER 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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195A HIS* 4.3 13.2 - - - -
225A LEU 3.0 18.1 + - - -
226A ARG* 3.6 7.2 - - - -
228A MSE 1.3 78.4 - - - +
230A ALA* 1.3 57.0 + - - +
232A GLY* 3.1 19.6 + - - -
233A VAL 3.7 13.5 + - - +
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Residues in contact with ALA 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 ARG 2.8 21.0 + - - +
227A PHE* 3.1 12.1 + - + +
229A SER* 1.3 73.3 - - - +
231A CYS* 1.3 58.4 + - - +
232A GLY 3.1 4.0 + - - -
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Residues in contact with CYS 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 PHE* 3.0 47.9 + - - -
228A MSE 3.6 11.0 - - - +
229A SER 3.2 1.0 - - - -
230A ALA* 1.3 75.8 - - - +
232A GLY* 1.3 59.1 + - - +
233A VAL* 3.3 10.0 + - + +
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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