Contacts of the helix formed by residues 214 - 232 (chain B) in PDB entry 4LOU
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 214 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ASP* 5.3 0.2 + - - -
31B THR* 2.5 40.3 + - - +
35B ILE* 5.4 0.2 - - - -
172B GLU* 4.7 7.4 - - - -
176B THR* 2.9 16.1 + - - +
212B LEU 3.5 2.0 + - - -
213B ILE* 1.3 69.3 - - - +
215B ILE* 1.3 57.9 + - - +
216B LYS* 3.8 3.5 + - - +
217B ALA* 2.9 35.6 + - - +
218B VAL* 3.0 16.0 + - - +
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Residues in contact with ILE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE 5.1 8.7 - - - +
202A GLU* 4.6 26.0 - - + +
207A GLN* 5.4 7.4 - - - +
406A LEU* 4.8 7.4 - - + -
197B ILE* 4.7 10.4 - - + +
201B ILE* 4.1 33.0 - - + -
213B ILE* 3.2 9.8 + - + +
214B SER* 1.3 70.6 + - - +
216B LYS* 1.3 62.0 + - - +
218B VAL* 3.4 10.5 + - + +
219B PHE* 3.1 29.0 + - + +
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Residues in contact with LYS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PRO* 6.0 4.0 - - + -
430A LEU* 4.4 4.2 - - + +
433A THR* 3.0 46.3 + - + -
434A LEU* 3.8 26.7 - - + +
437A GLN* 2.5 34.5 + - - +
29B ASP* 3.1 36.3 + - - +
31B THR* 5.1 1.1 - - - +
36B LEU* 4.2 9.9 - - + -
214B SER* 3.2 6.1 + - - +
215B ILE* 1.3 80.2 - - - +
217B ALA* 1.3 60.1 + - - +
219B PHE* 3.3 21.8 - - - +
220B ILE* 3.3 12.2 + - + +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B THR* 4.4 3.1 - - + -
35B ILE* 4.6 3.6 - - + -
36B LEU* 3.8 21.1 - - + +
39B ALA* 3.3 23.5 - - + +
176B THR* 3.7 16.4 - - + -
180B THR* 3.6 3.8 - - - +
214B SER* 2.9 27.3 + - - +
216B LYS* 1.3 78.5 - - - +
218B VAL* 1.3 63.3 + - - +
220B ILE* 3.5 2.1 + - - +
221B GLY 3.3 15.4 + - - -
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ALA 4.6 1.1 - - - +
180B THR* 3.5 26.3 - - + +
183B ALA* 3.6 28.5 - - + -
197B ILE* 4.6 15.0 - - + -
200B ILE* 4.7 13.9 - - + -
213B ILE* 4.0 21.3 - - + -
214B SER 3.0 17.0 + - - +
215B ILE* 3.4 10.3 + - - +
217B ALA* 1.3 73.6 - - - +
219B PHE* 1.3 65.9 + - - +
221B GLY* 3.2 2.9 + - - -
222B VAL* 3.0 30.0 + - + +
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Residues in contact with PHE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PRO* 4.4 9.6 - - + -
406A LEU* 3.7 42.6 - - + -
409A ILE* 3.8 20.2 - - + -
426A ILE* 3.4 36.8 - - + -
430A LEU* 3.4 29.6 - - + -
194B LEU* 5.1 2.0 - - + -
197B ILE* 3.2 31.8 - - + +
215B ILE* 3.1 17.2 + - + +
216B LYS* 3.3 16.4 - - - +
218B VAL* 1.3 79.1 - - - +
220B ILE* 1.3 62.9 + - - +
222B VAL* 3.0 5.9 + - + +
223B ILE* 3.0 26.2 + - - +
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Residues in contact with ILE 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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430A LEU* 3.4 19.7 - - + +
434A LEU* 3.6 28.3 - - + -
36B LEU* 4.0 33.0 - - + +
39B ALA* 4.4 1.3 - - + -
40B ALA* 3.8 33.0 - - + +
216B LYS 3.3 12.9 + - - +
217B ALA 3.7 6.7 - - - +
218B VAL 3.3 0.2 - - - -
219B PHE* 1.3 76.0 - - - +
221B GLY* 1.3 61.8 + - - +
223B ILE* 3.6 3.6 + - + +
224B MET* 3.2 29.0 + - + +
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Residues in contact with GLY 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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39B ALA 3.7 19.5 + - - -
43B GLY* 3.3 17.3 - - - -
180B THR* 4.3 10.8 - - - -
184B ALA* 3.6 4.8 - - - +
217B ALA 3.3 7.6 + - - -
218B VAL 3.2 8.6 + - - -
220B ILE* 1.3 79.5 - - - +
222B VAL* 1.3 59.0 + - - +
225B SER* 3.1 24.4 + - - -
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Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ILE* 6.0 0.2 - - + -
180B THR 5.0 0.2 - - - +
183B ALA* 3.7 29.8 - - + +
184B ALA* 3.9 8.7 - - - +
187B ALA* 3.6 11.0 - - + -
193B PRO* 3.2 42.8 - - + +
197B ILE* 4.0 17.5 - - + +
218B VAL 3.1 13.9 - - - +
219B PHE* 3.0 8.4 + - + +
221B GLY* 1.3 77.1 - - - +
223B ILE* 1.3 60.2 + - - +
225B SER* 3.9 3.7 - - - -
226B THR* 2.8 34.1 + - - -
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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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423A LEU* 5.7 4.7 - - + -
426A ILE* 3.4 34.3 - - + -
427A ILE* 3.7 30.7 - - + -
430A LEU* 3.4 29.4 - - + -
193B PRO* 5.8 2.0 - - - -
219B PHE* 3.0 15.7 + - + +
220B ILE* 4.0 4.5 - - - +
221B GLY 3.5 0.2 - - - -
222B VAL* 1.3 76.6 - - + +
224B MET* 1.3 61.4 + - + +
226B THR* 3.2 4.0 + - - -
227B ILE* 2.8 50.0 + - + +
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Residues in contact with MET 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ALA* 3.8 28.0 - - + +
43B GLY* 4.2 2.2 - - - -
44B THR* 3.2 30.3 - - + +
220B ILE* 3.2 21.9 + - + +
221B GLY 4.2 1.6 - - - +
223B ILE* 1.3 77.9 - - + +
225B SER* 1.3 64.9 + - - +
227B ILE* 3.6 10.6 + - + +
228B MET* 3.1 43.9 + - + +
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY 3.2 17.9 + - - -
47B GLY* 3.5 13.2 + - - -
184B ALA* 2.8 35.3 + - - -
187B ALA* 5.0 0.2 - - - -
188B ALA* 3.4 11.5 - - - +
221B GLY 3.1 20.5 + - - -
222B VAL 3.9 2.5 - - - -
224B MET* 1.3 80.0 - - - +
226B THR* 1.3 65.4 + - - +
228B MET* 3.3 3.6 + - - +
229B TYR* 3.2 20.3 + - - +
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Residues in contact with THR 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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423A LEU* 3.5 29.8 - - + -
187B ALA* 3.3 28.4 + - - +
188B ALA* 5.1 2.9 - - - +
191B ASN* 4.0 7.4 - - - +
193B PRO* 3.9 17.9 - - + +
222B VAL 2.8 20.8 + - - -
223B ILE* 3.9 3.1 - - - -
225B SER* 1.3 77.2 - - - +
227B ILE* 1.3 61.1 + - - +
229B TYR* 3.4 7.3 + - - +
230B ARG* 3.0 39.9 + - - +
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Residues in contact with ILE 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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249A LEU* 5.6 2.9 - - + -
252A LEU* 4.2 13.5 - - + -
423A LEU* 4.0 16.6 - - + -
427A ILE* 3.8 18.4 - - + -
223B ILE* 2.8 43.4 + - + +
224B MET* 3.9 13.2 - - + +
226B THR* 1.3 69.4 - - - +
228B MET* 1.3 72.9 + - + +
230B ARG* 2.9 19.6 + - + +
231B ILE* 3.1 29.5 + - + +
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Residues in contact with MET 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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44B THR* 3.6 40.4 - - + +
47B GLY* 4.0 8.5 - - - -
48B LEU* 3.5 28.9 - - + +
51B VAL* 4.3 0.9 - - - -
224B MET* 3.1 33.1 + - + +
225B SER 3.5 7.6 - - - +
227B ILE* 1.3 86.9 - - + +
229B TYR* 1.3 62.1 + - - +
230B ARG 3.3 0.2 + - - -
231B ILE* 3.3 17.3 + - + +
232B PHE* 3.0 29.9 - - - -
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Residues in contact with TYR 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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47B GLY 5.0 0.7 - - - +
50B ALA* 5.4 1.8 - - + -
51B VAL* 3.7 26.5 - - + -
54B ASP* 4.3 14.8 + - + -
188B ALA* 3.7 42.2 - - + -
189B ALA* 5.4 4.0 - - - -
191B ASN* 3.9 35.3 - - + +
225B SER 3.2 12.1 + - - +
226B THR* 4.0 3.6 - - - +
228B MET* 1.3 79.9 - - - +
230B ARG* 1.3 65.9 + - - +
232B PHE 3.4 4.4 + - - -
233B ASN* 3.4 51.7 + - + +
236B VAL 5.5 3.0 + - - -
237B ALA* 6.1 0.5 - - - -
238B LEU* 3.9 26.0 - - - +
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Residues in contact with ARG 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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249A LEU* 3.9 22.3 - - + +
419A TYR* 5.9 0.6 + - - -
420A GLN* 5.2 6.5 + - - +
422A ILE* 4.3 12.1 - - - +
423A LEU* 3.3 49.2 - - + +
191B ASN* 2.6 51.9 + - - +
193B PRO* 5.2 3.0 - - - +
226B THR* 3.0 27.7 + - - +
227B ILE* 2.9 10.3 + - - +
229B TYR* 1.3 74.2 - - - +
231B ILE* 1.3 59.3 + - - +
232B PHE 2.9 10.8 + - - -
233B ASN 4.6 0.2 - - - +
234B HIS* 3.0 42.9 + - + +
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Residues in contact with ILE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 3.8 23.3 - - + -
227B ILE* 3.1 26.9 + - + +
228B MET* 3.3 24.4 + - + +
230B ARG* 1.3 75.0 - - - +
232B PHE* 1.3 80.3 + - + +
233B ASN 3.7 0.4 + - - -
234B HIS* 4.2 2.0 + - - -
103C TYR* 3.1 37.6 + - + +
52D LYS* 5.7 0.5 - - - -
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Residues in contact with PHE 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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48B LEU* 4.6 18.4 - - + -
51B VAL* 3.7 33.2 - - + -
55B LYS* 3.9 9.2 + - - -
228B MET* 3.0 27.8 - - - -
229B TYR 3.4 4.6 + - - +
230B ARG 2.9 1.0 - - - -
231B ILE* 1.3 100.5 - - + +
233B ASN* 1.3 74.0 + - - +
103C TYR* 5.7 2.0 - - - -
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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
------------------------------------------------------------
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