Contacts of the helix formed by residues 160 - 170 (chain M) in PDB entry 3J7Y
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 SER 160 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M GLN* 5.8 1.5 + - - -
140M LEU 3.2 13.1 + - - -
141M VAL* 4.8 1.1 - - - -
142M GLU* 3.1 40.5 + - - +
159M ALA* 1.3 76.5 - - - +
161M GLU* 1.3 65.3 + - - +
162M LEU 4.3 0.2 - - - -
163M ALA* 3.1 21.7 - - - +
164M ILE* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 161 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159M ALA 5.5 0.7 - - - +
160M SER* 1.3 73.3 - - - +
162M LEU* 1.3 57.7 + - - +
164M ILE* 3.2 12.5 + - + +
165M ALA* 2.9 28.6 + - - +
218M LYS* 4.3 21.4 - - - +
219M ASN* 6.5 0.2 - - + -
236M LEU* 3.6 28.4 - - + +
239M LYS* 5.1 10.1 + - - +
240M TYR* 5.0 11.1 - - - +
145p ARG* 5.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142M GLU* 3.6 19.5 - - + -
145M ALA* 3.8 21.5 - - + -
160M SER* 3.3 0.8 + - - -
161M GLU* 1.3 79.7 - - - +
163M ALA* 1.3 57.1 + - - +
165M ALA* 3.2 6.7 + - + +
166M ALA* 2.9 26.8 + - + +
240M TYR* 4.4 13.7 + - + -
142p TYR* 3.7 33.2 - - + -
144p PHE* 3.8 27.8 - - + -
145p ARG* 3.5 44.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M LEU* 3.9 17.8 - - + +
140M LEU* 4.2 20.4 - - + +
141M VAL 3.9 20.2 - - - +
142M GLU* 4.4 1.2 - - - +
160M SER* 3.1 24.8 + - - +
162M LEU* 1.3 78.5 - - - +
164M ILE* 1.3 63.3 + - - +
166M ALA* 3.2 4.3 + - - +
167M ILE* 3.1 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159M ALA* 3.6 31.9 - - + +
160M SER 3.1 17.5 + - - +
161M GLU* 3.4 12.1 - - + +
163M ALA* 1.3 79.2 - - - +
165M ALA* 1.3 61.9 + - - +
167M ILE* 3.4 4.0 + - - +
168M GLU* 3.0 48.4 + - - +
174M VAL* 3.8 24.4 - - + +
218M LYS 4.6 4.3 - - - +
219M ASN* 4.3 16.6 - - - -
220M ARG* 3.5 26.5 - - - +
236M LEU* 3.6 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161M GLU 2.9 12.0 + - - +
162M LEU* 3.3 11.0 - - - +
164M ILE* 1.3 77.9 - - - +
166M ALA* 1.3 55.3 + - - +
168M GLU* 3.2 3.1 + - - +
169M LYS* 2.9 55.2 + - + +
236M LEU* 4.0 14.8 - - + -
240M TYR* 4.3 24.7 - - + -
144p PHE* 5.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M LEU* 3.7 22.4 - - + -
145M ALA* 4.0 17.7 - - - +
148M PHE* 4.6 6.1 - - + -
162M LEU* 2.9 14.6 + - + +
163M ALA 3.2 9.4 + - - +
165M ALA* 1.3 77.8 - - - +
167M ILE* 1.3 63.3 + - - +
169M LYS* 3.4 2.7 + - - +
170M ASN* 3.2 30.0 + - - +
144p PHE* 4.7 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M LEU* 3.9 13.0 - - + -
140M LEU* 3.7 13.0 - - + -
148M PHE* 3.8 26.2 - - + -
151M LYS 5.9 0.9 - - - +
152M VAL* 3.7 15.5 - - + +
154M ILE* 3.5 25.1 - - + -
163M ALA 3.1 12.1 + - - +
164M ILE 3.8 0.2 - - - +
166M ALA* 1.3 76.9 - - - +
168M GLU* 1.3 62.2 + - - +
170M ASN* 3.2 10.7 + - - +
171M GLY 3.2 0.2 + - - -
172M GLY* 2.9 42.8 + - - -
173M VAL 3.8 0.4 - - - +
174M VAL* 3.3 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 168 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164M ILE* 3.0 28.0 + - + +
165M ALA* 3.2 5.6 + - - +
167M ILE* 1.3 77.1 - - - +
169M LYS* 1.3 61.8 + - + +
171M GLY* 2.9 17.8 + - - -
172M GLY 3.9 14.0 + - - +
173M VAL* 5.6 0.7 - - - -
174M VAL* 5.2 8.1 + - + +
220M ARG* 2.8 41.5 + - - +
233M ARG* 3.3 45.0 + - - +
236M LEU* 3.8 7.7 - - - +
244M LEU* 4.1 10.7 - - + +
245M PRO* 3.4 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M ALA* 2.9 43.1 + - - +
166M ALA 3.8 5.2 - - - +
167M ILE 3.3 0.2 - - - -
168M GLU* 1.3 80.9 + - - +
170M ASN* 1.3 58.8 + - - +
171M GLY 3.1 4.5 + - - -
233M ARG 4.9 0.4 + - - -
236M LEU* 3.5 13.1 + - - +
237M ALA* 3.3 33.1 - - - +
240M TYR* 4.5 6.0 - - - +
241M GLY 3.3 23.3 - - - -
242M TYR* 3.3 35.4 - - + -
243M ILE 4.6 6.2 - - - +
244M LEU* 5.1 5.0 - - + +
245M PRO* 3.3 19.4 - - - +
144p PHE* 4.3 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 170 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148M PHE* 3.0 34.8 + - + +
149M THR* 3.3 29.2 + - - +
150M ALA 3.9 1.7 + - - +
151M LYS* 3.3 35.0 - - - +
166M ALA* 3.2 18.3 + - - +
167M ILE* 3.2 11.7 + - - +
169M LYS* 1.3 80.7 - - - +
171M GLY* 1.3 57.0 + - - +
245M PRO* 4.5 1.8 - - - -
----------------------------------------------------------
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