Contacts of the helix formed by residues 161 - 177 (chain M) in PDB entry 6NR8
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 ASP 161 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156M LEU* 3.1 43.1 - - + +
157M VAL 2.9 14.6 + - - +
158M ASP* 2.9 26.7 - - - +
160M LYS* 1.3 72.9 - - - +
162M THR* 1.3 65.8 + - - +
163M GLU 3.2 0.4 - - - -
164M PRO* 3.5 11.6 - - - +
165M LEU* 3.4 28.7 + - - +
202M ARG* 5.9 0.9 + - - -
412M LEU* 4.6 13.5 - - + +
416M ASN* 3.6 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 162 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158M ASP 3.4 19.7 - - - +
159M ILE* 2.9 17.8 + - + +
161M ASP* 1.3 80.7 + - - +
163M GLU* 1.3 54.2 + - - +
165M LEU* 3.1 11.1 + - + +
166M ILE* 2.5 44.5 + - - +
190M VAL* 4.2 25.8 - - + +
191M ASN* 5.5 3.4 - - - +
194M LEU* 4.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159M ILE 5.5 0.4 - - - +
160M LYS* 3.0 16.0 + - + +
162M THR* 1.3 78.7 + - - +
164M PRO* 1.3 60.9 - - + +
166M ILE* 3.2 34.9 + - - +
167M GLN* 2.7 48.4 + - - +
187M GLU* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 164 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156M LEU* 4.9 13.2 - - + -
160M LYS* 3.3 21.1 - - + +
161M ASP* 3.5 15.0 - - - +
163M GLU* 1.3 90.7 - - + +
165M LEU* 1.3 49.5 + - + +
167M GLN* 3.1 18.8 + - + +
168M THR* 2.5 41.2 + - - -
507M ILE* 4.4 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161M ASP* 3.4 20.1 + - - +
162M THR* 3.1 11.5 + - + +
164M PRO* 1.3 74.4 - - + +
166M ILE* 1.3 61.1 + - - +
167M GLN 3.2 0.2 - - - -
168M THR* 3.8 17.2 - - + +
169M ALA* 2.8 32.9 + - - +
190M VAL* 3.8 14.0 - - + +
405M ALA 5.9 0.2 - - - +
408M VAL* 5.0 9.9 - - + -
409M ILE* 3.7 37.5 - - + -
412M LEU* 3.8 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 166 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162M THR* 2.5 30.7 + - - +
163M GLU* 3.3 43.5 - - - +
165M LEU* 1.3 72.0 - - - +
167M GLN* 1.3 55.5 + - + +
170M LYS* 3.2 14.6 + - - +
183M ARG* 2.8 47.2 + - - +
186M ALA* 3.9 14.8 - - - +
187M GLU* 3.7 33.7 - - + +
190M VAL* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 167 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163M GLU* 2.7 37.5 + - - +
164M PRO* 3.1 20.0 + - - +
166M ILE* 1.3 75.6 - - + +
168M THR* 1.3 61.4 + - - +
170M LYS* 3.3 16.4 - - + +
171M THR* 3.1 24.9 + - - -
505M HIS* 2.8 59.1 + - + +
507M ILE* 5.7 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 168 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164M PRO 2.5 28.7 + - - -
165M LEU* 3.2 20.5 + - + +
167M GLN* 1.3 74.1 - - - +
169M ALA* 1.3 58.1 + - - +
171M THR* 3.1 22.6 + - - -
172M THR* 3.2 18.3 + - + +
408M VAL* 5.4 10.3 - - + -
505M HIS 5.1 3.5 + - - -
507M ILE* 3.7 29.5 + - - +
508M GLU* 5.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M LEU 2.8 16.6 + - - +
168M THR* 1.3 73.2 - - - +
170M LYS* 1.3 60.5 + - - +
171M THR 3.2 0.2 - - - -
172M THR* 2.9 24.9 + - - +
173M LEU* 3.0 24.2 + - + +
186M ALA* 3.7 26.2 - - + +
189M ALA* 5.8 2.7 - - + -
190M VAL* 5.9 1.8 - - + -
405M ALA* 4.3 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166M ILE 3.2 20.6 + - - +
167M GLN* 3.3 16.6 - - + +
168M THR 3.2 0.4 - - - -
169M ALA* 1.3 77.6 - - - +
171M THR* 1.3 54.8 + - - +
174M GLY* 2.7 32.0 + - - -
180M SER 5.3 0.6 + - - -
181M CYS* 3.5 40.2 - - + +
183M ARG* 3.5 19.3 - - - +
186M ALA* 4.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M PRO* 4.7 23.9 - - + +
167M GLN 3.1 13.2 + - - -
168M THR* 3.1 13.2 + - - -
170M LYS* 1.3 81.1 - - - +
172M THR* 1.3 63.8 + - + +
174M GLY 5.7 0.2 - - - -
175M SER* 3.9 20.5 + - - -
176M LYS* 5.0 1.7 - - - +
494M LEU* 5.8 8.3 - - + -
505M HIS 5.1 5.0 + - - -
506M VAL* 5.9 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 172 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104M ASP* 4.0 20.4 - - - +
168M THR* 3.2 17.9 + - + +
169M ALA* 2.9 20.3 + - - +
171M THR* 1.3 82.0 - - + +
173M LEU* 1.3 67.2 + - - +
176M LYS* 3.6 20.2 - - - +
401M SER* 3.5 35.6 + - - +
404M ASP* 6.2 0.2 - - + -
405M ALA* 4.6 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169M ALA* 3.0 18.4 + - + +
170M LYS* 4.3 1.6 - - - +
172M THR* 1.3 81.3 + - - +
174M GLY* 1.3 57.7 + - - +
175M SER 2.9 9.8 + - - -
176M LYS 3.4 8.1 + - - -
177M VAL* 3.6 16.3 + - + -
178M VAL* 2.8 25.4 + - + +
181M CYS* 4.8 10.5 - - - -
182M HIS* 4.1 15.9 - - + +
185M MET* 3.7 38.1 - - + -
186M ALA* 4.2 11.9 - - + +
398M ALA* 4.4 1.3 - - - +
401M SER* 3.8 16.6 - - - -
402M LEU* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 174 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170M LYS 2.7 25.0 + - - -
171M THR 4.6 0.2 - - - -
172M THR 3.6 0.2 - - - -
173M LEU* 1.3 70.1 - - - +
175M SER* 1.3 58.9 + - - +
178M VAL 3.2 11.7 - - - -
179M ASN 3.1 20.3 - - - +
180M SER 4.7 0.2 - - - -
181M CYS* 3.8 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 175 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516J ARG* 4.8 10.6 + - - -
54M PRO* 3.5 34.7 + - - +
171M THR* 3.9 14.9 + - - -
173M LEU 3.1 0.6 - - - -
174M GLY* 1.3 80.1 - - - +
176M LYS* 1.3 70.6 + - - +
178M VAL 4.5 3.1 - - - -
179M ASN* 5.1 3.1 - - - +
494M LEU* 5.5 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 176 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516J ARG* 5.5 10.7 + - - +
53M GLY 4.9 1.3 - - - +
54M PRO* 2.9 41.2 + - + +
56M GLY 3.0 24.0 + - - -
58M ASP* 4.2 5.8 + - - +
72M ASN* 3.1 24.7 - - + +
171M THR 5.0 1.8 - - - +
172M THR* 3.6 20.6 + - - +
173M LEU 3.4 1.2 + - - -
175M SER* 1.3 98.4 - - - +
177M VAL* 1.3 63.5 + - - +
178M VAL 4.5 0.4 - - - +
397M GLU* 3.0 17.1 - - + +
401M SER* 4.5 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173M LEU* 3.6 32.5 + - + +
176M LYS* 1.3 77.9 - - - +
178M VAL* 1.3 75.0 + - + +
179M ASN 4.3 0.2 - - - -
182M HIS* 6.2 0.2 - - + -
394M ILE* 3.3 40.0 - - + +
397M GLU* 3.7 29.2 - - + +
398M ALA* 3.5 20.2 - - + +
401M SER* 4.0 7.9 - - - +
----------------------------------------------------------
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