Contacts of the helix formed by residues 211 - 227 (chain B) in PDB entry 4NH1
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 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 3.7 12.6 - - + -
11B VAL 3.4 18.2 - - - -
12B TYR* 2.7 30.6 + + + -
13B THR 4.9 0.2 + - - -
15B VAL* 4.7 1.6 - - - +
16B ASN* 5.1 0.2 + - - -
148B HIS* 3.2 72.5 + + + +
151B GLY* 3.3 32.1 - - - -
152B ILE 3.9 0.2 - - - -
153B MET* 3.9 15.3 - - + -
182B TYR* 3.2 36.0 + + + -
210B ASP* 1.3 79.1 - - + +
212B SER* 1.3 57.3 + - - +
213B LEU 3.0 6.8 + - - -
214B ASP* 3.1 12.6 + - - +
215B MET* 3.9 0.9 + - - -
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Residues in contact with SER 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLU* 4.7 0.5 + - - -
210B ASP* 2.9 24.4 + - - -
211B TYR* 1.3 74.4 - - - +
213B LEU* 1.3 65.2 + - - +
214B ASP 3.3 0.4 - - - -
215B MET* 3.1 22.5 + - - +
216B TRP 3.3 0.7 + - - -
309B HIS* 3.2 43.7 + - - +
312B ARG* 3.2 26.2 + - - -
313B LEU 5.8 0.7 - - - -
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ARG* 4.1 26.0 - - + -
192B VAL* 4.4 2.0 - - + -
193B ALA* 5.4 3.1 - - + -
197B PHE 5.3 0.7 - - - +
199B GLY* 3.8 16.4 - - - +
201B GLU* 3.6 22.9 - - + +
202B LEU* 3.7 38.4 - - + -
209B TYR* 3.7 30.1 - - + -
210B ASP 3.3 14.5 + - - +
211B TYR 3.0 0.6 + - - -
212B SER* 1.3 81.0 + - - +
214B ASP* 1.3 66.0 + - - +
216B TRP* 3.3 13.0 + - - +
217B SER* 3.3 16.4 + - - +
312B ARG* 3.9 0.7 - - - +
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Residues in contact with ASP 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 4.4 8.7 - - + +
148B HIS* 2.9 26.5 + - + +
153B MET* 3.8 4.7 - - - +
154B HIS* 2.8 31.7 + - - +
155B ARG* 2.7 32.6 + - - +
156B ASP 4.1 0.2 + - - -
157B VAL* 3.8 19.2 + - + +
211B TYR 3.1 8.1 + - - +
213B LEU* 1.3 78.5 - - - +
215B MET* 1.3 59.1 + - - +
217B SER* 3.3 7.1 + - - -
218B LEU* 2.9 28.1 + - - +
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Residues in contact with MET 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.8 22.4 - - + -
144B LEU* 4.7 7.9 - - - -
148B HIS* 4.3 12.6 - - + +
211B TYR 4.2 3.1 - - - +
212B SER* 3.1 23.5 + - - +
214B ASP* 1.3 77.6 - - - +
216B TRP* 1.3 62.0 + - - +
218B LEU* 3.5 5.1 + - + +
219B GLY* 3.2 15.4 + - - -
304B LEU* 3.6 38.2 - - + +
312B ARG* 4.8 7.4 - - + +
313B LEU 3.3 29.8 - - - +
314B THR* 3.8 15.9 - - - +
315B ALA* 3.9 19.1 - - - -
318B ALA* 4.2 1.3 - - + -
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Residues in contact with TRP 216 (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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196B TYR 5.3 0.2 + - - -
197B PHE 3.6 12.1 - - - -
198B LYS 3.1 13.9 + - - -
199B GLY* 3.5 17.5 - - - -
200B PRO* 3.6 20.2 - - + -
212B SER 3.3 2.6 + - - -
213B LEU 3.3 10.0 + - - +
214B ASP 3.2 0.6 - - - -
215B MET* 1.3 75.7 - - - +
217B SER* 1.3 65.3 + - - +
219B GLY 3.0 10.7 + - - -
220B CYS* 3.1 26.5 + - - -
233B PHE* 3.8 13.9 - + - -
241B GLN* 6.2 0.2 - - - +
245B ILE* 3.6 43.7 - - + +
249B LEU* 3.6 12.1 - - + -
304B LEU 4.3 5.4 - - - -
305B LEU* 3.4 28.9 - - + +
306B ARG 3.5 42.6 - - - -
312B ARG* 3.8 18.0 - - - +
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Residues in contact with SER 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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155B ARG* 5.9 0.5 - - - -
156B ASP 5.6 0.5 + - - -
157B VAL* 3.5 33.2 + - - +
193B ALA* 5.1 4.3 - - - +
197B PHE* 2.9 33.6 + - - +
213B LEU* 3.3 14.0 + - - +
214B ASP* 3.3 11.5 + - - -
216B TRP* 1.3 78.1 - - - +
218B LEU* 1.3 61.1 + - - +
220B CYS* 3.4 4.2 + - - +
221B MET* 3.2 27.3 + - - +
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B MET* 3.6 29.6 - - + -
140B ILE* 3.7 30.5 - - + -
141B LEU* 3.6 39.3 - - + -
144B LEU* 4.3 10.5 - - + -
157B VAL* 4.4 3.5 - - + +
214B ASP 2.9 16.8 + - - +
215B MET* 3.7 17.0 - - + +
216B TRP 3.2 0.2 - - - -
217B SER* 1.3 74.4 - - - +
219B GLY* 1.3 60.7 + - - +
221B MET* 3.3 12.7 + - - +
222B LEU* 2.9 27.2 + - - +
300B PHE* 5.0 0.2 - - + -
304B LEU* 4.3 11.9 - - + -
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Residues in contact with GLY 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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215B MET 3.2 7.3 + - - -
216B TRP 3.0 8.6 + - - -
218B LEU* 1.3 76.6 - - - +
220B CYS* 1.3 55.9 + - - +
222B LEU* 3.3 1.0 + - - -
223B ALA* 2.9 26.5 + - - +
301B LEU* 3.2 14.7 - - - +
304B LEU* 3.7 22.4 - - - +
305B LEU* 3.8 16.4 - - - -
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Residues in contact with CYS 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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196B TYR 3.8 17.3 - - - +
197B PHE* 3.5 26.3 - - + -
216B TRP* 3.1 47.3 + - - -
217B SER 3.6 1.3 - - - +
218B LEU 3.3 0.2 - - - -
219B GLY* 1.3 75.3 - - - +
221B MET* 1.3 58.1 + - - +
223B ALA* 3.6 6.3 + - - +
224B SER* 3.0 29.3 + - - -
232B PHE* 4.3 8.1 + - + +
233B PHE* 4.2 15.5 - - + +
305B LEU* 4.0 6.7 - - - -
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Residues in contact with MET 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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125B TYR* 3.9 20.6 - - + +
137B MET* 5.0 3.1 - - + -
140B ILE* 4.1 16.6 - - + -
157B VAL* 3.6 27.6 - - - -
158B LYS* 3.9 10.8 - - - -
159B PRO* 3.8 21.3 - - + -
162B VAL* 3.9 11.4 - - + -
197B PHE* 3.8 17.7 - - + -
217B SER 3.2 13.8 + - - +
218B LEU* 3.5 16.4 - - + +
219B GLY 3.2 0.2 - - - -
220B CYS* 1.3 74.1 - - - +
222B LEU* 1.3 65.6 + - - +
224B SER* 2.6 23.6 + - - -
225B MET* 3.1 23.9 + - - +
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Residues in contact with LEU 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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133B ILE* 4.3 0.4 - - + -
137B MET* 3.8 29.1 - - + +
218B LEU 2.9 17.0 + - - +
219B GLY* 3.6 3.6 - - - +
221B MET* 1.3 75.2 - - - +
223B ALA* 1.3 59.0 + - - +
225B MET* 3.3 1.5 + - - +
226B ILE* 3.0 55.2 + - + +
297B ALA 4.3 4.7 - - - +
300B PHE* 3.5 30.3 - - + -
301B LEU* 3.7 31.4 - - + +
304B LEU* 4.1 4.0 - - + -
323B TYR* 3.8 24.5 - - + +
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Residues in contact with ALA 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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219B GLY 2.9 17.2 + - - +
220B CYS* 3.9 4.5 - - - +
222B LEU* 1.3 77.5 - - - +
224B SER* 1.3 61.9 + - - +
227B PHE* 3.2 37.4 + - - +
232B PHE* 3.6 33.1 - - + -
301B LEU* 3.7 22.0 - - + +
305B LEU* 4.6 4.0 - - + -
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Residues in contact with SER 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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125B TYR* 5.3 6.6 - - - -
159B PRO* 5.6 1.9 - - - +
197B PHE* 5.5 2.4 - - - -
220B CYS 3.0 15.0 + - - -
221B MET* 2.6 23.9 + - - -
223B ALA* 1.3 77.2 - - - +
225B MET* 1.3 61.6 + - - +
228B ARG* 3.5 3.5 + - - -
229B LYS 3.1 45.9 + - - +
230B GLU* 3.9 23.2 + - - +
232B PHE* 4.2 8.7 - - - +
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Residues in contact with MET 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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125B TYR* 4.0 42.8 - - + +
128B LEU* 3.8 22.2 - - + -
133B ILE* 3.7 44.5 - - + +
136B TYR* 5.7 5.8 - - + -
137B MET* 3.8 20.2 - - + -
164B ILE* 6.4 0.7 - - + -
221B MET* 3.1 24.7 + - - +
222B LEU 3.8 3.4 - - - +
223B ALA 3.2 0.2 - - - -
224B SER* 1.3 81.9 - - - +
226B ILE* 1.3 63.7 + - - +
227B PHE 3.3 1.9 + - - -
228B ARG* 3.6 11.1 + - - +
292B LEU* 3.3 18.4 - - - +
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Residues in contact with ILE 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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133B ILE* 4.1 10.3 - - + -
222B LEU* 3.0 42.1 + - + +
225B MET* 1.3 77.2 - - - +
227B PHE* 1.3 90.7 - - + +
289B ASN* 3.2 19.6 - - - +
292B LEU* 3.6 26.4 - - - +
293B VAL* 3.4 14.6 - - + +
297B ALA* 4.5 19.1 - - + +
298B LEU* 4.6 6.5 - - + -
301B LEU* 4.0 13.5 - - + -
323B TYR* 4.0 13.2 - - + +
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Residues in contact with PHE 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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223B ALA* 3.2 25.5 + - - +
226B ILE* 1.3 90.0 - - + +
228B ARG* 1.3 70.7 + - - +
229B LYS* 3.4 5.1 + - + +
232B PHE* 3.6 28.7 - + + -
281B TRP* 3.4 34.8 - + + -
284B PHE* 3.2 28.2 - - + +
285B VAL* 3.6 16.6 - - + -
286B HIS* 3.9 5.2 + - - -
289B ASN* 2.9 24.9 + - - +
293B VAL* 4.0 7.6 - - + -
298B LEU* 3.5 17.9 - - + -
301B LEU* 3.6 26.2 - - + -
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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