Contacts of the helix formed by residues 178 - 199 (chain A) in PDB entry 6DC0
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 ARG 178 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ARG* 3.5 33.0 - - - +
176A ARG 5.3 2.2 - - - +
177A LEU* 1.3 72.7 - - - +
179A GLU* 1.3 66.9 + - - +
180A GLU* 3.1 7.0 - - + +
181A GLU* 2.8 26.1 + - + +
182A ALA 3.0 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU 3.7 1.2 + - - +
178A ARG* 1.3 71.8 - - - +
180A GLU* 1.3 54.9 + - - +
182A ALA* 3.7 0.2 - - - +
183A ALA* 2.7 37.4 + - - +
278A LEU* 3.8 24.3 - - + +
306A HIS 4.9 1.2 - - - +
307A ILE* 4.1 6.2 - - + +
308A SER* 2.7 50.0 + - - -
311A ALA* 3.6 7.8 - - - +
337A TRP* 3.3 18.6 + - + -
341A VAL* 3.6 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ARG* 3.1 6.0 - - + +
179A GLU* 1.3 77.1 - - - +
181A GLU* 1.3 59.4 + - + +
183A ALA* 3.9 2.4 - - - +
184A ARG* 2.9 70.0 + - + +
341A VAL* 3.3 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TYR* 2.6 37.4 + - - -
174A ARG* 3.4 25.2 + - - -
177A LEU* 3.8 15.6 - - + +
178A ARG* 2.8 16.6 + - + +
180A GLU* 1.3 79.5 - - - +
182A ALA* 1.3 67.9 + - - +
184A ARG* 3.0 29.9 + - - +
185A LEU* 2.9 40.2 + - + +
218A ARG 5.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 4.2 21.4 - - + +
178A ARG 3.0 9.3 + - - +
179A GLU 3.7 3.8 - - - +
181A GLU* 1.3 76.6 - - - +
183A ALA* 1.3 52.7 + - - +
185A LEU* 3.8 1.0 - - - +
186A PHE* 2.7 39.1 + - - +
274A LEU* 5.4 0.7 - - + -
277A LEU* 4.4 12.9 - - + +
278A LEU* 3.4 35.0 - - + -
337A TRP* 3.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU 2.7 22.1 + - - +
180A GLU 3.9 3.4 - - - +
182A ALA* 1.3 71.3 - - - +
184A ARG* 1.3 65.2 + - - +
187A LYS* 3.0 26.2 + - - +
337A TRP* 3.4 31.6 - - + -
338A PHE* 3.7 19.2 - - + +
341A VAL* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLU* 2.9 52.2 + - + +
181A GLU* 3.0 37.8 + - - +
183A ALA* 1.3 78.6 - - - +
185A LEU* 1.3 72.0 + - + +
187A LYS* 3.7 4.0 + - - +
188A GLN* 3.5 27.6 + - - +
219A THR* 4.8 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A MET* 3.7 31.4 - - + -
170A TYR* 4.0 12.6 - - + -
177A LEU* 4.1 4.0 - - + -
181A GLU* 2.9 38.9 + - + +
182A ALA* 3.9 3.1 - - - +
184A ARG* 1.3 81.5 - - - +
186A PHE* 1.3 65.1 + - - +
187A LYS 3.1 2.0 - - - -
188A GLN* 3.1 33.9 + - - +
189A ILE* 3.1 15.6 + - - +
213A PHE* 4.1 7.4 - - + -
218A ARG 5.0 0.7 - - - +
219A THR* 3.7 18.4 - - - +
221A LEU* 3.7 23.4 - - + +
277A LEU* 5.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA 2.7 24.8 + - - +
183A ALA* 4.4 2.2 - - - +
185A LEU* 1.3 73.3 - - - +
187A LYS* 1.3 55.9 + - - +
189A ILE* 3.4 15.3 + - + +
190A VAL* 2.9 52.2 + - + +
270A LEU* 3.2 43.1 - - + -
273A MET* 4.3 4.7 - - + -
274A LEU* 3.8 42.4 - - + -
277A LEU* 4.0 19.0 - - + +
314A LEU* 4.4 1.6 - - + -
318A LEU* 4.2 7.6 - - + -
332A ILE* 4.3 7.0 - - + -
337A TRP* 4.1 0.2 - + - -
338A PHE* 3.7 22.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ALA 3.0 18.8 + - - +
184A ARG* 3.9 6.3 - - - +
185A LEU 3.1 0.2 - - - -
186A PHE* 1.3 78.4 - - - +
188A GLN* 1.3 51.1 - - + +
190A VAL* 3.3 3.2 + - - -
191A SER* 2.7 40.2 + - - +
333A LEU* 3.8 38.6 + - + +
338A PHE* 3.6 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 3.2 32.1 + - - +
184A ARG* 3.5 21.0 + - - +
185A LEU* 3.1 20.6 + - - +
187A LYS* 1.3 73.0 - - + +
189A ILE* 1.3 66.9 + - - +
191A SER* 3.3 2.1 + - - -
192A ALA* 3.0 23.0 + - - +
211A PHE* 5.5 0.4 - - - -
219A THR 3.0 24.5 + - - -
220A GLN* 3.0 19.6 - - - +
221A LEU* 2.7 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A MET* 4.5 7.4 - - + -
185A LEU 3.1 10.5 + - - +
186A PHE* 3.4 23.6 - - + +
188A GLN* 1.3 79.4 - - - +
190A VAL* 1.3 59.8 + - - +
192A ALA* 3.4 5.2 - - - +
193A VAL* 3.2 21.5 + - - +
208A LEU* 4.7 15.0 - - + -
211A PHE* 3.8 44.7 - - + -
221A LEU* 3.7 25.6 - - + -
270A LEU* 3.6 23.1 - - + -
273A MET* 4.0 9.2 - - - -
277A LEU* 4.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PHE* 2.9 56.0 + - + +
187A LYS* 3.8 5.6 - - - +
189A ILE* 1.3 74.9 - - - +
191A SER* 1.3 56.0 + - - +
193A VAL* 3.1 5.9 + - - +
194A ALA* 2.7 33.3 + - - +
270A LEU* 4.1 13.0 - - + -
329A ALA* 3.7 23.1 - - + +
332A ILE* 3.8 24.5 - - + -
333A LEU* 3.7 14.6 - - + -
338A PHE* 5.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A HIS* 3.8 21.9 + - - -
142A ASN* 3.9 5.3 + - - -
187A LYS* 2.7 26.1 + - - +
188A GLN* 3.3 6.6 + - - -
190A VAL* 1.3 76.9 - - - +
192A ALA* 1.3 63.0 + - - +
194A ALA* 3.9 0.5 - - - +
195A HIS* 3.0 26.3 + - - +
333A LEU* 3.5 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A HIS* 4.2 6.6 + - - -
142A ASN* 3.6 15.5 - - + +
143A ILE* 3.5 25.4 - - + +
188A GLN 3.0 11.5 + - - +
189A ILE 3.4 10.1 - - - +
190A VAL 3.2 0.2 - - - -
191A SER* 1.3 78.7 - - - +
193A VAL* 1.3 62.7 + - - +
195A HIS* 3.5 2.8 - - - +
196A CYS* 3.1 27.5 + - - -
211A PHE* 3.9 16.6 - - + -
223A LEU* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE 3.2 13.2 + - - +
190A VAL 3.1 6.8 + - - +
192A ALA* 1.3 73.0 - - - +
194A ALA* 1.3 66.6 + - - +
196A CYS* 3.4 1.6 + - - +
197A HIS* 3.0 51.4 + - + +
203A LEU* 3.9 13.0 - - + -
206A LEU* 3.7 37.5 - - + -
211A PHE* 4.4 4.7 - - + -
223A LEU* 6.2 0.4 - - + -
266A ASP* 4.6 1.3 - - + -
270A LEU* 4.0 23.6 - - + -
329A ALA* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A VAL 2.7 21.4 + - - +
191A SER 3.9 3.6 - - - +
193A VAL* 1.3 72.6 - - - +
195A HIS* 1.3 53.1 + - - +
197A HIS* 3.1 3.6 + - - +
198A GLN* 2.8 42.5 + - + +
329A ALA* 3.7 33.2 - - + +
330A PRO* 4.0 8.1 - - + -
333A LEU* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.8 17.9 - - + +
138A PRO* 2.7 43.9 + - + -
139A SER 3.9 5.8 - - - -
140A HIS* 3.5 39.9 + + + +
143A ILE* 4.1 7.6 - - + -
191A SER 3.0 19.5 + - - +
192A ALA 3.5 4.0 - - - +
194A ALA* 1.3 74.1 - - - +
196A CYS* 1.3 63.2 + - - +
198A GLN* 3.7 9.7 + - - +
199A SER* 3.4 23.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 3.8 30.5 - - - -
143A ILE* 3.9 10.5 - - - -
192A ALA 3.1 18.2 + - - -
193A VAL 3.5 7.6 - - - +
195A HIS* 1.3 73.1 - - - +
197A HIS* 1.3 59.7 + - - +
199A SER* 2.9 19.6 + - - -
201A ILE* 3.0 37.8 + - + +
203A LEU* 3.7 30.7 - - + -
223A LEU* 4.4 3.4 - - - -
226A LEU* 4.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A VAL* 3.0 32.3 + - + +
194A ALA* 3.5 9.0 - - - +
196A CYS* 1.3 74.6 - - - +
198A GLN* 1.3 67.3 + - - +
200A ALA* 3.1 9.6 + - - +
201A ILE 3.4 17.0 - - - -
202A VAL* 4.4 0.9 - - - -
203A LEU* 3.9 3.8 - - + -
263A LYS* 2.9 82.1 + - + +
266A ASP* 2.8 31.8 + - + +
267A VAL* 4.8 3.1 - - + +
329A ALA* 4.2 13.4 + - + +
330A PRO* 5.3 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA* 2.8 29.7 + - + +
195A HIS* 3.8 9.9 - - - +
196A CYS 3.2 0.2 - - - -
197A HIS* 1.3 75.3 - - - +
199A SER* 1.3 58.8 + - - +
200A ALA 3.3 2.2 + - - -
263A LYS* 5.5 0.7 + - - -
330A PRO* 3.3 34.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLN* 4.7 8.6 - - - +
137A LEU* 3.5 24.7 - - - -
138A PRO* 3.3 27.5 - - - +
195A HIS* 3.4 10.2 + - - -
196A CYS 2.9 2.6 + - - -
198A GLN* 1.3 76.4 - - - +
200A ALA* 1.3 70.3 + - - +
201A ILE* 3.2 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