Contacts of the helix formed by residues 171 - 192 (chain B) in PDB entry 3NDM
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 171 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASP 3.2 5.4 - - - +
170B VAL* 1.3 87.5 - - - +
172B GLU* 1.3 68.8 + - - +
173B LYS* 4.4 5.6 - - + +
174B TRP* 2.8 60.4 + - + +
175B ALA 2.9 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL 4.0 1.2 + - - -
171B PRO* 1.3 70.4 - - - +
173B LYS* 1.3 65.3 + - - +
175B ALA* 2.9 11.1 + - + +
176B ARG* 2.8 33.3 + - - +
272B LEU* 4.3 11.4 - - + +
304B ASP 5.0 1.2 - - - +
305B ILE* 4.3 7.4 - - - +
306B SER* 2.6 49.7 + - - -
309B ALA* 3.3 18.0 - - - +
337B PHE* 3.5 19.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PRO* 2.9 7.1 + - + +
172B GLU* 1.3 75.3 - - - +
174B TRP* 1.3 68.0 + - + +
176B ARG* 3.2 31.0 + - - +
177B PHE* 3.0 22.7 + - - +
340B ASN* 5.1 0.2 - - - +
341B ASP* 4.6 3.4 + - - -
342B GLN* 2.7 46.8 + - + +
343B TRP* 5.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 4.9 4.0 - - + -
168B TYR* 3.3 48.2 - + + -
169B ASP 5.6 0.2 - - - -
170B VAL* 3.9 16.8 - - + -
171B PRO* 2.8 47.1 + - + +
173B LYS* 1.3 79.3 - - + +
175B ALA* 1.3 56.2 + - - +
177B PHE* 3.4 2.3 + - - +
178B TYR* 2.9 37.2 + + + +
354B PRO* 2.8 58.9 + - + +
355B VAL* 3.8 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 3.6 8.0 - - + +
171B PRO 2.9 7.7 + - - +
172B GLU* 2.9 11.9 + - - +
174B TRP* 1.3 73.1 - - - +
176B ARG* 1.3 67.7 + - - +
178B TYR* 3.1 1.7 + - - +
179B THR* 2.7 30.0 + - - -
268B LEU* 4.4 7.0 - - + -
271B MET* 4.1 10.3 - - - -
272B LEU* 3.0 36.8 - - + -
337B PHE* 4.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLU* 2.8 24.3 + - - +
173B LYS* 3.5 42.9 + - - +
175B ALA* 1.3 71.6 - - - +
177B PHE* 1.3 57.7 + - - +
179B THR* 3.8 1.0 - - - -
180B ALA* 2.9 32.2 + - - +
337B PHE* 2.9 51.4 + - + +
338B PHE* 3.3 29.3 - - + -
339B LYS 3.6 11.7 + - - -
340B ASN* 3.7 21.9 - - - +
342B GLN* 4.2 2.0 + - - +
343B TRP* 3.8 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LYS 3.0 12.5 + - - +
174B TRP 3.7 4.7 - - - +
175B ALA 3.1 0.2 - - - -
176B ARG* 1.3 77.8 - - - +
178B TYR* 1.3 88.8 + + - +
180B ALA* 3.3 1.9 + - - +
181B GLU* 3.1 31.8 + - - +
210B GLY 4.4 0.7 - - - -
211B HIS* 3.9 25.1 - + - -
343B TRP* 4.0 23.3 - + + +
348B LEU* 3.4 36.5 - - + +
351B THR* 4.2 7.6 - - - -
352B VAL 4.8 0.9 - - - -
353B ALA* 3.6 13.7 - - + -
354B PRO* 2.9 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.2 19.5 - - + -
164B LEU* 3.3 41.3 - - + +
170B VAL* 5.1 1.1 - - + -
174B TRP* 2.9 27.6 + + + +
175B ALA 3.9 2.2 - - - +
177B PHE* 1.3 105.6 - + - +
179B THR* 1.3 65.1 + - - +
181B GLU* 3.1 11.6 + - + +
182B VAL* 3.1 27.2 + - - +
206B LEU* 4.7 9.2 - - + +
210B GLY 4.3 11.8 + - - -
212B LEU* 5.6 4.4 - - + +
267B PHE* 4.4 1.6 - - + -
271B MET* 3.8 31.4 - - + -
354B PRO* 4.2 9.9 - - + -
355B VAL* 3.8 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ALA 2.7 23.0 + - - -
176B ARG 3.9 2.9 - - - -
178B TYR* 1.3 74.0 - - - +
180B ALA* 1.3 55.4 + - - +
182B VAL* 3.2 3.9 + - - +
183B VAL* 2.8 39.4 + - + +
264B VAL* 4.7 14.4 - - + -
267B PHE* 4.3 14.5 - - + -
268B LEU* 3.4 27.9 - - + +
271B MET* 4.8 1.9 - - - -
312B LEU* 4.7 7.4 - - + -
337B PHE* 4.5 6.7 - - + -
338B PHE* 3.5 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG 2.9 18.4 + - - +
177B PHE 3.7 4.5 - - - +
178B TYR 3.2 0.2 - - - -
179B THR* 1.3 73.6 - - - +
181B GLU* 1.3 66.0 + - - +
183B VAL* 3.2 6.9 + - - +
184B LEU* 2.9 27.2 + - - +
338B PHE* 4.2 7.6 - - + -
343B TRP* 3.5 25.8 - - + -
345B TRP* 3.9 16.6 - - + -
348B LEU* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TRP* 3.0 27.2 - - + -
177B PHE* 3.1 23.8 + - + +
178B TYR* 3.1 9.2 + - + +
180B ALA* 1.3 75.4 - - - +
182B VAL* 1.3 51.7 + - - +
184B LEU* 3.1 6.2 + - - +
185B ALA* 2.7 36.0 + - - +
211B HIS* 3.0 28.1 - - - -
212B LEU* 2.9 47.8 + - + +
348B LEU* 3.1 26.3 - - + +
349B ARG* 3.8 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 5.5 0.2 - - + -
178B TYR* 3.1 16.7 + - + +
179B THR* 3.6 6.3 - - - +
181B GLU* 1.3 72.5 - - - +
183B VAL* 1.3 66.3 + - - +
184B LEU 3.0 1.1 - - - -
185B ALA* 3.9 5.6 - - - +
186B LEU* 3.2 41.4 + - + +
199B VAL* 4.7 2.7 - - + -
204B MET* 3.3 37.2 - - + -
212B LEU* 3.8 16.6 - - + -
214B LEU* 4.8 7.2 - - + -
261B TRP* 5.0 0.2 - - - -
264B VAL* 4.4 14.4 - - + -
267B PHE* 3.6 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B THR* 2.8 35.6 + - + +
180B ALA* 3.2 7.8 + - - +
182B VAL* 1.3 77.3 - - - +
184B LEU* 1.3 60.4 + - - +
187B ASP* 3.6 19.4 + - - +
261B TRP* 4.0 21.4 - - + -
264B VAL* 4.7 15.0 - - + -
316B PHE* 5.4 0.2 - - + -
329B VAL* 4.3 14.6 - - + +
332B ILE* 4.1 23.3 - - + -
333B LYS* 5.0 3.3 - - + -
338B PHE* 3.9 18.4 - - + -
345B TRP* 4.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TRP* 3.6 41.1 - - + +
180B ALA 2.9 16.9 + - - +
181B GLU 3.3 6.5 - - - +
182B VAL 3.0 0.2 - - - -
183B VAL* 1.3 76.9 - - - +
185B ALA* 1.3 68.0 + - - +
186B LEU 3.0 3.1 + - - -
187B ASP* 3.1 16.3 + - + +
188B ALA 3.2 8.7 + - - -
333B LYS* 3.5 29.6 - - - +
345B TRP* 4.0 34.1 - - + +
348B LEU* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TRP* 3.5 25.6 - - + +
181B GLU 2.7 19.1 + - - +
182B VAL* 3.9 4.9 - - - +
184B LEU* 1.3 73.1 - - - +
186B LEU* 1.3 58.6 + - - +
188B ALA* 2.9 24.1 - - - +
189B ILE* 3.4 10.0 - - - +
212B LEU* 4.0 14.1 - - + -
214B LEU* 3.8 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B VAL* 3.2 33.0 + - + +
184B LEU 3.0 0.8 - - - -
185B ALA* 1.3 77.6 - - - +
187B ASP* 1.3 51.2 + - - +
188B ALA 2.9 5.2 - - - -
189B ILE* 3.0 11.1 + - + +
190B HIS* 2.7 58.3 + - + +
196B HIS* 4.8 5.4 - - + +
199B VAL* 3.7 25.4 - - + -
214B LEU* 4.4 14.8 - - + -
260B ASP* 3.2 38.8 - - + +
261B TRP* 4.1 17.3 - - + -
264B VAL* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B VAL 3.6 12.9 + - - +
184B LEU* 3.1 12.7 + - + +
186B LEU* 1.3 77.5 - - - +
188B ALA* 1.3 56.1 + - - +
190B HIS* 3.8 17.8 - - - +
191B SER* 2.7 38.3 + - - -
261B TRP* 4.5 1.8 - - + -
329B VAL* 3.0 43.4 - - + +
333B LYS* 4.3 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B SER* 4.5 17.0 - - - +
135B TRP* 4.5 9.2 - - + -
136B VAL* 5.0 1.6 - - + -
184B LEU 3.2 7.5 + - - +
185B ALA 2.9 17.9 - - - +
187B ASP* 1.3 77.7 - - - +
189B ILE* 1.3 64.3 + - + +
191B SER* 3.0 22.6 + - - -
192B MET* 3.1 25.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 4.5 5.8 - - + -
136B VAL* 3.9 18.2 - - + -
185B ALA 3.4 16.6 - - - +
186B LEU* 3.4 10.3 - - + +
188B ALA* 1.3 71.0 - - - +
190B HIS* 1.3 68.2 + - - +
192B MET* 3.2 31.4 + - + -
194B PHE* 3.0 47.8 + - + +
196B HIS* 4.8 12.6 - - + +
214B LEU* 4.3 11.9 - - + -
217B PHE* 4.0 18.6 - - + -
220B CYS* 4.5 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 2.7 36.5 + - + +
187B ASP* 3.7 14.8 - - - +
189B ILE* 1.3 73.6 - - - +
191B SER* 1.3 57.8 + - - +
193B GLY* 2.8 17.0 + - - -
194B PHE 3.3 13.4 + - - -
195B ILE* 4.4 4.6 - - - +
196B HIS 4.6 0.4 - - - -
223B MET* 3.2 20.0 - - + +
257B ARG* 4.1 36.9 + - + +
260B ASP* 3.1 35.3 - - + +
261B TRP* 3.5 35.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ASP* 2.7 27.4 + - - -
188B ALA* 3.0 9.8 + - - -
190B HIS* 1.3 72.6 - - - +
192B MET* 1.3 58.8 + - - +
193B GLY* 3.0 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 4.1 13.0 - - + -
130B PHE 5.5 0.2 - - - -
131B ALA* 3.5 44.0 - - + +
133B SER* 5.7 1.8 - - - -
136B VAL* 4.1 4.3 - - + -
188B ALA* 3.1 18.5 + - + +
189B ILE* 3.2 37.7 + - + +
190B HIS 3.2 1.0 - - - -
191B SER* 1.3 76.7 - - - +
193B GLY* 1.3 57.8 + - - +
194B PHE* 3.0 28.8 - - + -
222B LYS* 3.8 8.7 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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