Contacts of the helix formed by residues 165 - 181 (chain B) in PDB entry 5LDH
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 CYS 165 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLY* 1.3 63.6 - - - -
166B ASN* 1.3 65.9 + - - -
167B LEU 2.9 1.3 - - - -
168B ASP* 2.9 18.1 + - - +
169B SER* 2.7 26.5 + - - +
190B TRP* 5.5 0.2 - - + -
191B ILE* 3.9 24.0 - - - +
192B LEU* 5.1 2.0 - - - -
193B GLY 5.9 0.2 - - - -
194B GLU 4.8 6.9 + - - -
270B PRO* 2.3 46.4 - - + -
271B VAL 3.5 1.8 - - - +
288B SER* 3.4 32.1 + - - -
289B LEU 4.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 5.2 3.7 - - + +
72A PHE* 4.9 8.7 - - + -
163B SER* 3.3 17.1 + - - +
164B GLY 2.5 21.3 + - - +
165B CYS* 1.3 76.2 - - - +
167B LEU* 1.3 79.1 + - - +
169B SER* 3.1 7.6 + - - -
170B ALA* 2.9 23.3 + - - +
190B TRP* 5.7 0.2 - - - -
253B SER* 3.2 30.7 + - - -
256B ASP* 5.0 2.9 - - - +
257B LEU* 5.0 10.3 - - - +
269B HIS* 4.0 24.1 - - + +
270B PRO* 2.8 12.5 - - + +
271B VAL* 3.6 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A HIS* 5.3 2.0 - - + -
163B SER* 5.7 2.0 - - - +
164B GLY* 3.3 10.7 + - - +
165B CYS 2.9 0.2 - - - -
166B ASN* 1.3 87.0 + - - +
168B ASP* 1.3 66.9 + - - +
170B ALA* 3.0 12.9 + - + +
171B ARG* 3.0 64.7 + - - +
195B HIS* 5.4 2.0 - - + -
249B ALA* 5.1 9.9 - - + -
250B ILE* 3.9 21.5 - - + +
253B SER* 3.8 25.1 - - - +
332B LNC 3.1 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B CYS* 2.9 18.8 + - - +
167B LEU* 1.3 78.7 - - - +
169B SER* 1.3 50.7 + - - +
171B ARG* 3.3 16.5 + - - +
172B PHE* 2.6 36.2 + - - +
191B ILE* 2.9 26.5 - - + +
194B GLU 4.9 1.9 - - - +
195B HIS* 4.2 29.1 + - - -
196B GLY 5.1 1.6 + - - -
199B SER* 4.2 21.7 + - - -
232B VAL* 6.1 0.3 - - - +
233B VAL* 5.2 5.5 - - - +
236B ALA* 5.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 6.3 0.4 - - - -
165B CYS 2.7 26.9 + - - -
166B ASN* 3.3 10.9 - - - -
168B ASP* 1.3 67.9 - - - +
170B ALA* 1.3 59.1 + - - +
172B PHE* 2.8 5.2 + - - +
173B ARG* 2.5 51.0 + - - +
189B GLY 4.9 7.6 - - - -
190B TRP* 4.0 20.3 - - - -
191B ILE* 2.8 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A HIS* 4.2 20.6 - - + +
71A LEU* 4.0 22.1 - - + +
72A PHE* 5.6 3.8 - - + -
166B ASN 2.9 12.0 + - - +
167B LEU* 3.1 18.4 - - + +
169B SER* 1.3 77.4 - - - +
171B ARG* 1.3 64.9 + - + +
173B ARG* 3.6 9.9 - - - +
174B TYR* 3.0 28.3 + - - +
253B SER* 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A HIS* 3.5 47.2 + - - -
167B LEU* 3.0 41.7 + - - +
168B ASP* 3.4 14.3 + - - +
170B ALA* 1.3 80.5 - - - +
172B PHE* 1.3 58.2 + - - +
174B TYR* 3.7 6.7 + - - +
175B LEU* 2.4 35.1 + - + +
232B VAL* 4.1 18.1 + - + +
235B SER* 5.2 10.1 - - - -
236B ALA* 3.5 21.9 - - - +
246B THR* 4.7 2.8 + - - +
249B ALA* 5.5 3.2 - - - +
332B LNC 2.1 51.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ASP 2.6 18.1 + - - +
169B SER* 2.8 11.1 + - - +
171B ARG* 1.3 75.3 - - - +
173B ARG* 1.3 57.5 + - + +
175B LEU* 3.2 8.9 - - + +
176B MET* 3.2 35.4 - - + +
189B GLY* 3.4 25.1 - - - -
190B TRP 4.1 10.5 - - - -
191B ILE* 4.1 12.1 - - + -
201B ALA* 3.9 24.5 - - + -
202B VAL 4.4 4.5 - - - -
203B TRP* 6.1 2.2 - + + -
206B VAL* 4.3 23.3 - - + -
228B VAL* 4.3 23.8 - - + -
229B HIS* 4.4 15.9 - + + -
232B VAL* 4.2 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.1 45.0 - - - +
169B SER* 2.5 37.1 + - - +
170B ALA* 3.1 6.7 + - - +
172B PHE* 1.3 71.9 - - + +
174B TYR* 1.3 57.0 + - - +
176B MET* 3.9 11.2 - - + +
177B GLY* 2.8 32.7 + - - -
184B PRO 3.9 10.4 + - - -
185B SER* 3.5 12.5 + - - +
186B SER 3.2 24.9 + - - -
187B CYS* 3.6 25.5 + - - -
188B HIS* 5.1 2.0 - - - +
189B GLY 4.5 17.2 - - - +
333B CIT 3.7 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 2.3 48.0 + - + +
68A HIS* 5.0 18.8 - + - +
70A SER* 4.7 21.3 - - - -
170B ALA 3.0 14.7 + - - +
171B ARG* 4.8 4.3 - - - -
173B ARG* 1.3 74.4 - - - +
175B LEU* 1.3 90.5 + - + +
177B GLY* 3.4 0.6 - - - -
178B GLU* 2.6 62.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ARG* 2.4 34.1 - - - +
172B PHE* 3.2 11.0 - - + +
174B TYR* 1.3 100.4 - - + +
176B MET* 1.3 81.8 + - + +
178B GLU* 2.8 6.0 + - - +
179B LYS* 2.6 25.1 + - + +
228B VAL* 4.2 27.6 - - + +
231B MET* 5.3 10.8 - - + -
232B VAL* 3.3 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PHE* 3.2 33.9 - - + +
173B ARG* 4.4 8.3 - - + +
174B TYR 3.3 0.4 - - - -
175B LEU* 1.3 85.9 - - + +
177B GLY* 1.3 59.3 + - - +
179B LYS* 2.8 16.8 + - + +
180B LEU* 2.5 52.1 + - + +
187B CYS* 4.3 24.2 - - + -
188B HIS 4.9 4.9 - - - +
189B GLY* 6.4 0.2 - - - -
206B VAL* 4.2 27.6 - - + -
207B ASN 4.5 12.1 - - - +
210B GLN* 5.0 5.8 - - - +
228B VAL* 5.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG 2.8 19.1 + - - -
174B TYR 3.4 0.7 - - - -
176B MET* 1.3 85.0 - - - +
178B GLU* 1.3 52.7 + - - +
180B LEU* 2.8 7.4 + - - +
181B GLY 2.5 34.1 + - - -
182B VAL* 3.4 27.1 + - - -
183B HIS 5.7 0.4 - - - -
187B CYS* 5.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 5.5 0.2 + - - -
77A LYS* 5.4 16.3 + - - +
174B TYR* 2.6 53.0 + - + +
175B LEU* 2.8 12.7 + - - +
177B GLY* 1.3 70.3 - - - -
179B LYS* 1.3 64.6 + - - +
181B GLY* 3.2 12.7 + - - +
182B VAL 4.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 2.6 17.1 + - + +
176B MET* 3.2 13.9 - - + +
178B GLU* 1.3 73.0 - - - +
180B LEU* 1.3 76.5 + - + +
181B GLY* 4.0 0.7 - - - -
223B GLU* 4.5 8.9 + - - +
224B ASN 5.0 1.0 + - - -
225B TRP* 3.3 38.1 - - - -
228B VAL* 4.0 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 2.5 63.1 + - + +
5A GLU* 5.8 1.6 - - + +
176B MET* 2.5 35.9 + - + +
177B GLY* 3.0 9.9 - - - +
179B LYS* 1.3 80.1 - - + +
181B GLY* 1.3 53.6 + - - +
182B VAL* 4.4 9.4 - - + -
208B VAL* 3.5 41.3 - - + -
210B GLN* 4.4 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 4.2 11.2 + - - -
177B GLY 2.5 11.9 + - - -
178B GLU* 3.5 10.8 - - - -
179B LYS 3.2 1.5 + - - -
180B LEU* 1.3 75.1 - - - +
182B VAL* 1.3 69.1 + - - +
----------------------------------------------------------
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