Contacts of the helix formed by residues 215 - 227 (chain A) in PDB entry 6JBQ
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 GLU 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A ILE* 3.4 30.4 - - + +
212A ASP* 4.2 14.2 + - + +
214A GLU* 1.3 76.2 - - + +
216A ALA* 1.3 64.6 + - - +
217A ILE 3.3 1.8 - - - -
218A ARG* 3.5 31.7 + - + +
219A ARG* 3.2 38.0 + - + +
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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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47A LEU* 3.6 21.5 - - + +
51A MET* 5.8 2.2 - - + -
179A PRO* 6.3 0.9 - - + -
180A VAL* 4.8 9.9 - - + -
205A MET* 4.0 26.5 - - + -
207A THR* 5.0 2.0 - - + -
211A ILE* 4.5 11.2 - - + -
212A ASP 3.7 16.2 + - - +
213A PRO* 4.1 2.4 - - + -
214A GLU 3.4 1.4 - - - -
215A GLU* 1.3 78.1 - - - +
217A ILE* 1.3 63.3 + - - +
219A ARG* 3.6 16.6 + - - +
220A ALA 3.7 4.2 + - - -
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Residues in contact with ILE 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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24A ALA* 6.2 0.4 - - + -
26A VAL* 3.8 33.2 - - + -
43A LEU* 3.8 28.6 - - + +
47A LEU* 4.7 9.6 - - + -
203A ILE* 4.8 11.0 - - + -
205A MET* 3.8 29.6 - - + -
213A PRO 4.3 6.7 - - - +
214A GLU 4.9 4.7 - - - +
215A GLU* 3.3 0.6 - - - +
216A ALA* 1.3 74.2 - - - +
218A ARG* 1.3 60.9 + - + +
220A ALA* 3.3 3.5 + - - +
221A ALA* 2.9 26.7 + - - +
231B PHE* 4.1 16.4 - - + -
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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
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214A GLU* 3.6 44.1 + - - +
215A GLU* 3.5 32.0 + - + +
216A ALA 3.4 0.6 - - - -
217A ILE* 1.3 75.9 - - + +
219A ARG* 1.3 58.9 + - + +
221A ALA* 3.6 7.9 - - - +
222A THR* 2.9 32.1 + - - +
231B PHE* 4.6 19.3 - - + +
232B VAL* 4.2 15.5 - - + +
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Residues in contact with ARG 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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51A MET* 4.1 28.2 - - + +
52A PRO* 4.4 15.9 + - - -
179A PRO* 4.5 5.9 - - - +
211A ILE* 3.5 44.7 - - - +
215A GLU* 3.2 28.9 + - + +
216A ALA* 3.8 12.3 - - - +
217A ILE 3.2 0.2 - - - -
218A ARG* 1.3 76.5 - - - +
220A ALA* 1.3 57.3 + - - +
222A THR* 3.3 10.1 - - + +
223A ILE* 2.9 38.5 + - + +
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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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43A LEU* 4.7 13.9 - - + +
46A ILE* 3.8 28.9 - - + +
47A LEU* 3.8 29.6 - - + -
51A MET* 5.0 2.3 - - - -
216A ALA 3.7 2.2 + - - +
217A ILE* 3.3 7.9 + - - +
219A ARG* 1.3 79.3 - - - +
221A ALA* 1.3 57.0 + - - +
223A ILE* 3.7 5.5 - - - +
224A LEU* 2.9 30.8 + - - +
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Residues in contact with ALA 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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43A LEU* 5.6 2.9 - - + +
217A ILE 2.9 17.9 + - - +
218A ARG* 3.6 6.5 - - - +
219A ARG 3.2 0.2 - - - -
220A ALA* 1.3 77.1 - - - +
222A THR* 1.3 57.6 + - - +
224A LEU 3.4 0.2 + - - -
225A ALA* 2.9 29.6 + - - +
228B LEU* 3.5 18.5 - - + +
231B PHE* 4.0 22.0 - - + -
232B VAL* 3.8 25.5 - - + +
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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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218A ARG 2.9 18.4 + - - +
219A ARG* 3.3 18.4 - - + +
221A ALA* 1.3 73.0 - - - +
223A ILE* 1.3 62.7 + - + +
225A ALA* 3.8 8.3 - - - +
226A GLU* 2.9 31.0 + - - +
232B VAL* 4.4 10.5 - - - +
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Residues in contact with ILE 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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46A ILE* 4.0 11.9 - - + -
50A SER 4.7 6.1 - - - +
51A MET* 4.5 19.1 - - - -
52A PRO* 4.7 14.1 - - + -
150A ARG* 5.8 1.3 - - - +
219A ARG* 2.9 27.7 + - + +
220A ALA* 3.7 5.6 - - - +
221A ALA 3.3 0.2 - - - -
222A THR* 1.3 79.5 - - + +
224A LEU* 1.3 64.0 + - - +
226A GLU* 3.3 7.0 + - - +
227A GLN* 3.1 26.0 + - + +
8B PHE 5.9 2.2 - - - +
35B PHE* 3.8 30.5 - - + -
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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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39A LEU* 5.8 1.1 - - + -
42A ALA* 4.2 20.6 - - + -
43A LEU* 5.0 9.0 - - + -
46A ILE* 3.7 26.7 - - + -
220A ALA 2.9 17.3 + - - +
223A ILE* 1.3 78.3 - - - +
225A ALA* 1.3 61.3 + - - +
227A GLN* 3.5 13.7 + - + +
228A LEU* 3.5 17.7 - - + +
35B PHE* 6.1 1.8 - - + -
38B THR* 5.3 2.9 - - + -
39B LEU* 3.8 32.1 - - + -
224B LEU* 5.0 17.3 - - + -
228B LEU* 3.7 24.5 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.7 + - - +
222A THR* 4.1 7.6 - - - +
224A LEU* 1.3 75.7 - - - +
226A GLU* 1.3 61.5 + - - +
228A LEU* 3.5 18.0 + - - +
229A GLU* 4.6 1.2 + - - +
232A VAL* 6.0 0.9 - - - +
225B ALA* 6.3 6.1 - - + +
228B LEU* 4.1 10.7 - - + +
229B GLU* 5.7 9.0 - - + +
232B VAL* 5.5 7.9 - - + -
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Residues in contact with GLU 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* 2.9 22.1 + - - +
223A ILE* 3.3 7.5 + - - +
225A ALA* 1.3 74.3 - - - +
227A GLN* 1.3 77.3 + - - +
228A LEU 3.2 2.0 + - - -
229A GLU* 4.1 10.5 + - - +
8B PHE* 4.1 10.6 + - - +
10B LYS* 3.3 41.6 + - - +
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Residues in contact with GLN 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 ILE* 3.1 20.8 + - + +
224A LEU* 3.7 16.6 - - + +
225A ALA 3.3 0.6 - - - -
226A GLU* 1.3 85.3 - - - +
228A LEU* 1.3 66.6 + - + +
229A GLU 3.6 2.0 + - - -
231A PHE* 5.6 0.9 - - - -
8B PHE 3.0 23.2 + - - -
9B LEU 3.0 28.6 + - - +
10B LYS* 4.8 2.0 - - - +
11B PRO* 3.4 44.7 - - - +
31B LEU* 4.3 11.3 - - - +
32B GLU* 5.7 0.6 - - - +
35B PHE* 4.1 31.0 - - + -
39B LEU* 4.6 6.1 - - + +
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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