Contacts of the helix formed by residues 213 - 232 (chain B) in PDB entry 3IYD
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 PRO 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 5.4 1.9 - - - +
18B GLN* 4.1 17.7 - - - +
21B SER 3.6 15.0 - - - +
22B THR* 3.2 37.7 - - - +
23B HIS 4.3 0.2 - - - +
24B ALA* 3.8 21.9 - - + +
26B VAL* 5.2 1.9 - - - +
205B MET* 3.8 18.0 - - + +
207B THR* 4.4 2.5 - - + +
211B ILE* 3.9 3.5 - - - +
212B ASP* 1.3 85.6 - - + +
214B GLU* 1.3 59.7 + - - +
216B ALA* 3.9 3.6 - - + -
217B ILE* 3.3 26.5 + - - +
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Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.6 25.6 - - + +
18B GLN* 3.8 19.6 + - - +
212B ASP* 3.0 7.0 - - + -
213B PRO* 1.3 82.1 - - - +
215B GLU* 1.3 63.2 + - + +
216B ALA 3.6 0.3 + - - -
217B ILE* 3.8 9.1 + - - +
218B ARG* 3.3 45.6 + - - +
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLN* 5.7 3.0 - - - +
91B ARG* 4.3 9.0 + - - -
211B ILE* 4.0 15.8 - - + +
212B ASP* 3.3 44.8 + - + +
214B GLU* 1.3 77.4 - - + +
216B ALA* 1.3 59.2 + - - +
217B ILE 3.3 1.1 - - - -
218B ARG* 4.0 9.8 - - - +
219B ARG* 3.0 31.0 + - - +
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.6 4.1 - - + +
51B MET* 5.0 11.2 - - + +
205B MET* 4.3 14.6 - - + -
207B THR* 5.0 0.2 - - + -
211B ILE* 3.6 24.7 - - + -
212B ASP 2.9 17.3 + - - +
213B PRO* 4.0 9.6 - - + +
214B GLU 3.3 0.4 - - - -
215B GLU* 1.3 77.3 - - - +
217B ILE* 1.3 65.2 + - - +
219B ARG* 3.9 4.6 - - - +
220B ALA* 3.2 25.1 + - - +
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PHE* 3.5 28.9 - - + -
13B LEU* 6.3 1.3 - - + -
26B VAL* 3.7 37.0 - - + -
43B LEU* 6.1 4.4 - - + +
47B LEU* 5.4 6.3 - - + -
203B ILE* 4.8 11.9 - - + -
205B MET* 3.7 28.0 - - + -
213B PRO 3.3 16.6 + - - +
214B GLU* 3.8 6.7 + - - +
215B GLU 3.3 0.4 - - - -
216B ALA* 1.3 76.4 - - - +
218B ARG* 1.3 64.8 + - + +
220B ALA* 4.1 3.3 - - - +
221B ALA* 3.2 22.4 + - + +
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Residues in contact with ARG 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ALA 4.4 11.7 + - - -
231A PHE* 3.4 40.3 - - + +
233A ASP* 5.3 12.2 - - - +
13B LEU* 4.2 24.2 - - - +
16B ILE* 4.9 3.0 - - - +
214B GLU* 3.3 53.3 + - - +
215B GLU* 3.7 9.5 + - - +
217B ILE* 1.3 76.5 - - + +
219B ARG* 1.3 54.1 + - - +
221B ALA* 3.7 0.5 - - - +
222B THR* 2.7 42.9 + - - +
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Residues in contact with ARG 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GLN* 3.9 23.0 + - + +
4A SER* 3.1 42.8 + - - +
7A GLU* 6.2 1.6 - - - -
51B MET* 6.4 2.2 - - + -
52B PRO* 5.8 4.3 - - + -
215B GLU 3.0 20.6 + - - +
216B ALA* 3.9 6.1 - - - +
218B ARG* 1.3 77.2 - - - +
220B ALA* 1.3 62.4 + - - +
222B THR* 3.4 35.1 - - - +
223B ILE* 3.1 57.5 + - + +
226B GLU* 5.1 3.0 - - - +
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 4.5 4.7 - - - +
46B ILE* 3.7 32.4 - - + +
47B LEU* 3.7 24.9 - - + -
51B MET* 4.3 7.8 - - - +
216B ALA 3.2 15.6 + - - +
217B ILE* 4.2 2.7 - - - +
219B ARG* 1.3 81.2 - - - +
221B ALA* 1.3 61.0 + - - +
223B ILE* 3.8 11.1 - - - +
224B LEU* 3.8 14.4 + - - +
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 3.3 28.8 - - + +
231A PHE* 3.6 33.9 - - + -
43B LEU* 4.4 14.3 - - + +
217B ILE* 3.2 19.4 + - + +
218B ARG 3.7 0.4 - - - +
219B ARG 3.2 0.6 - - - -
220B ALA* 1.3 76.3 - - - +
222B THR* 1.3 65.3 + - - +
223B ILE 3.2 0.2 - - - -
224B LEU* 3.2 3.3 + - - +
225B ALA 3.1 15.2 + - - -
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Residues in contact with THR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 4.7 2.2 - - - -
231A PHE 3.8 13.9 + - - -
232A VAL* 4.6 13.3 - - + +
218B ARG* 2.7 28.6 + - - +
219B ARG* 3.3 23.7 + - - +
221B ALA* 1.3 69.1 - - - +
223B ILE* 1.3 60.5 + - - +
225B ALA* 2.9 11.0 + - + +
226B GLU* 2.8 45.8 + - + +
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Residues in contact with ILE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 4.0 37.2 - - + -
35A PHE* 4.2 19.1 - - + -
46B ILE* 5.4 4.0 - - + -
50B SER* 4.6 17.3 - - - +
51B MET* 6.2 0.2 - - - -
52B PRO* 5.9 4.5 - - + -
150B ARG* 5.7 1.6 - - - +
219B ARG* 3.1 45.5 - - + +
220B ALA* 3.8 15.3 - - - +
221B ALA 3.2 0.2 - - - -
222B THR* 1.3 78.0 - - - +
224B LEU* 1.3 60.7 + - - +
226B GLU* 3.2 18.4 + - + +
227B GLN* 3.3 16.0 + - - +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 5.1 7.4 - - + -
38A THR* 5.1 1.8 - - + +
39A LEU* 3.8 26.7 - - + -
224A LEU* 3.6 29.2 - - + -
228A LEU* 4.4 8.3 - - + -
42B ALA* 3.3 38.8 - - + +
43B LEU* 3.9 15.0 - - + -
46B ILE* 5.0 7.4 - - + +
220B ALA 3.8 6.0 + - - +
221B ALA* 3.2 12.7 + - - +
223B ILE* 1.3 79.4 - - - +
225B ALA* 1.3 59.1 + - - +
227B GLN* 3.0 29.2 + - - +
228B LEU* 4.0 6.3 - - + +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ALA* 6.4 1.6 - - - -
228A LEU* 3.9 17.9 - - + +
232A VAL* 5.7 9.0 - - + -
221B ALA 3.1 11.3 + - - +
222B THR* 2.9 16.3 + - + +
224B LEU* 1.3 73.3 - - - +
226B GLU* 1.3 56.7 + - + +
227B GLN 3.0 10.0 + - - -
228B LEU* 3.4 16.9 + - - +
229B GLU* 2.8 18.4 - - - +
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 3.3 44.1 - - - +
11A PRO* 3.5 3.3 - - - +
219B ARG* 5.1 2.7 - - - +
222B THR* 2.8 35.6 + - + +
223B ILE* 3.4 12.6 - - - +
224B LEU 3.1 0.8 - - - -
225B ALA* 1.3 75.8 - - - +
227B GLN* 1.3 68.2 + - - +
229B GLU* 2.9 26.9 - - - +
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Residues in contact with GLN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.9 21.6 - - - +
9A LEU 3.5 14.4 + - - +
10A LYS* 5.4 0.4 - - - +
11A PRO* 3.2 39.5 - - + +
30A PRO 4.4 2.6 - - - +
31A LEU* 4.6 6.6 - - - +
32A GLU* 5.6 2.2 + - - +
35A PHE* 4.2 27.2 - - + -
39A LEU* 3.9 21.6 - - + +
223B ILE* 3.3 21.5 + - - +
224B LEU* 3.3 13.0 - - - +
225B ALA 3.0 1.2 - - - -
226B GLU* 1.3 88.2 + - - +
228B LEU* 1.3 69.5 + - - +
229B GLU 3.7 2.2 - - - -
231B PHE* 3.7 8.8 - - - -
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Residues in contact with LEU 228 (chain B).
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* 4.7 15.7 - - + -
221A ALA* 3.7 42.6 - - + +
224A LEU* 3.7 28.0 - - + -
225A ALA* 4.1 12.6 - - + +
224B LEU* 4.0 14.1 - - + +
225B ALA* 3.4 11.4 + - - +
227B GLN* 1.3 89.9 - - - +
229B GLU* 1.3 66.4 + - - +
230B ALA 3.2 2.5 - - - -
231B PHE* 3.5 14.6 + - + +
232B VAL* 3.3 32.0 + - + +
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Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS* 4.7 9.1 - - + +
11A PRO* 4.6 9.8 + - - +
225B ALA 2.8 19.2 - - - +
226B GLU* 2.9 48.3 - - - +
227B GLN* 3.7 1.0 - - - -
228B LEU* 1.3 79.2 + - - +
230B ALA* 1.3 56.5 + - - +
231B PHE 3.1 5.8 + - - -
232B VAL* 4.4 6.1 - - + -
233B ASP* 3.8 6.8 + - - +
234B LEU* 3.5 26.0 + - + +
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO* 3.2 30.5 + - + +
12A ARG* 3.8 7.0 - - - -
13A LEU* 3.9 4.9 - - - +
28A LEU* 3.8 21.7 - - + +
218A ARG* 2.9 22.2 + - - -
228B LEU 3.2 0.8 - - - -
229B GLU* 1.3 77.5 - - - +
231B PHE* 1.3 73.9 + - + +
234B LEU* 3.7 12.8 - - + -
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Residues in contact with PHE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO* 4.9 3.8 - - + -
28A LEU* 3.6 37.2 - - + -
39A LEU* 6.1 1.8 - - + -
43A LEU* 5.7 2.5 - - + -
201A LEU* 4.8 15.0 - - + -
217A ILE* 4.4 16.6 - - + -
218A ARG* 3.3 51.0 - - + +
221A ALA* 3.5 30.3 - - + -
222A THR* 4.1 0.9 + - - -
227B GLN 3.7 16.6 - - - -
228B LEU* 3.6 30.1 - - + +
229B GLU 3.1 2.4 + - - -
230B ALA* 1.3 88.7 - - + +
232B VAL* 1.3 66.5 + - + +
233B ASP 3.3 4.2 + - - +
235B ARG* 4.9 1.6 + - - -
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Residues in contact with VAL 232 (chain B).
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 4.6 1.8 - - - +
222A THR* 3.6 42.6 - - + +
225A ALA* 3.7 20.2 - - + -
228B LEU* 3.3 19.5 - - + +
229B GLU* 4.4 6.3 - - + -
231B PHE* 1.3 79.3 - - - +
233B ASP* 1.3 83.3 + - + +
235B ARG* 3.0 16.6 + - - -
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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