Contacts of the helix formed by residues 172 - 185 (chain E) in PDB entry 3EXF
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 GLN 172 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E VAL* 3.2 36.1 + - + +
139E GLY* 4.1 1.3 - - - -
169E ALA 3.1 18.0 + - - +
170E ALA 3.6 0.4 - - - -
171E ASN* 1.3 74.6 - - - +
173E GLY* 1.3 65.8 + - - +
174E GLN* 3.1 15.8 + - + +
175E ILE* 2.9 28.7 + - + +
176E PHE* 4.0 4.0 - - - -
1009E TPP 3.5 7.7 - - - +
177G GLU* 4.0 4.5 - - - +
57H ILE* 2.9 36.2 + - - +
58H SER* 5.3 0.2 - - - -
59H GLU* 3.4 12.5 + - - -
88H GLN* 3.4 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 173 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E GLN* 1.3 70.7 - - - +
174E GLN* 1.3 55.8 + - - +
176E PHE* 2.9 35.3 + - - +
177E GLU 3.3 4.5 + - - -
173G GLY* 3.3 32.3 - - - -
177G GLU* 2.7 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 174 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E VAL 3.9 0.4 + - - -
139E GLY* 3.1 12.1 - - - +
140E ALA* 3.0 29.9 - - - +
143E PRO* 3.3 34.4 - - + +
172E GLN* 3.4 25.7 + - + +
173E GLY* 1.3 75.7 - - - +
175E ILE* 1.3 58.5 + - - +
177E GLU* 3.9 15.8 - - - +
178E ALA 3.1 19.8 + - - -
60F MET* 3.6 33.0 - - + +
91F ASP* 5.4 0.2 + - - -
92F GLN* 3.5 14.8 + - - +
173G GLY* 4.4 0.8 - - - -
177G GLU* 4.4 1.6 + - - +
88H GLN* 3.8 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E GLY* 4.0 10.5 - - - +
142E VAL* 3.3 41.1 - - + -
165E TYR* 4.4 12.1 - - + -
169E ALA* 3.0 30.7 - - + +
170E ALA* 4.7 6.3 - - - +
172E GLN* 2.9 30.4 + - + +
174E GLN* 1.3 76.6 - - - +
176E PHE* 1.3 58.8 + - + +
178E ALA* 3.2 3.5 + - - +
179E TYR* 2.9 63.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 176 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170E ALA 3.9 17.7 - - - -
171E ASN* 4.8 6.7 - - - -
172E GLN 4.0 10.1 - - - -
173E GLY* 2.9 21.7 + - - +
175E ILE* 1.3 70.4 - - + +
177E GLU* 1.3 62.0 + - - +
179E TYR* 3.6 29.9 + + - +
180E ASN* 3.3 23.0 + - - +
216E ARG* 3.4 46.0 - - + -
219E PHE* 5.3 0.9 - - - -
171G ASN 5.2 2.2 - - - +
176G PHE* 3.5 64.5 - + + -
218G ASP* 6.6 0.4 - - + -
219G PHE* 6.0 2.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E GLY 3.3 2.3 + - - +
174E GLN* 3.9 9.7 - - - +
175E ILE 3.3 0.4 - - - -
176E PHE* 1.3 73.2 - - - +
178E ALA* 1.3 68.3 + - - +
179E TYR 3.2 0.3 + - - -
180E ASN* 3.3 4.3 + - - +
181E MET* 3.1 30.8 + - - +
58F SER* 3.2 38.3 - - - -
59F GLU 3.9 0.7 + - - -
60F MET* 3.5 15.7 + - - +
61F GLY* 2.9 31.2 + - - -
88F GLN* 4.9 0.3 + - - -
171G ASN 3.2 22.0 - - - +
172G GLN* 3.8 10.4 + - - +
173G GLY* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E VAL* 3.5 28.9 - - + +
143E PRO* 4.0 17.8 - - + +
146E ALA* 4.5 8.4 - - + +
174E GLN 3.1 14.3 + - - +
175E ILE 3.4 8.7 - - - +
177E GLU* 1.3 75.4 - - - +
179E TYR* 1.3 61.3 + - - +
181E MET* 4.0 6.9 - - - +
182E ALA* 3.0 25.8 + - - +
191E PHE* 4.0 7.8 - - + -
65F ILE* 5.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E TYR* 2.7 27.3 + - - -
170E ALA* 5.4 2.9 + - - +
175E ILE* 2.9 44.4 + - + +
176E PHE* 3.7 35.8 - + - +
177E GLU 3.1 0.4 - - - -
178E ALA* 1.3 73.8 - - - +
180E ASN* 1.3 60.1 + - - +
182E ALA 3.3 0.7 + - - -
183E ALA* 2.8 30.5 + - - +
191E PHE* 4.0 19.5 - + - -
216E ARG* 4.0 10.3 - - + +
217E GLY* 4.0 25.1 - - - -
219E PHE* 4.1 8.7 - + + -
220E ILE* 3.6 27.7 - - + +
252E LEU* 3.8 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E PHE 3.3 13.6 + - - +
177E GLU* 3.3 3.9 + - - +
179E TYR* 1.3 79.3 - - - +
181E MET* 1.3 58.9 + - - +
183E ALA 3.8 0.3 - - - -
184E LEU* 2.9 30.0 + - - +
219E PHE* 3.7 21.2 - - + -
56F PRO* 3.7 16.2 - - - +
58F SER* 4.7 2.2 + - - -
171G ASN* 3.5 27.3 + - + +
207G ALA 3.2 18.4 + - - +
208G ALA* 3.5 3.5 - - - -
209G ALA* 2.7 34.8 + - - +
216G ARG* 4.7 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 181 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E GLU* 3.1 30.6 + - + +
178E ALA 4.2 0.4 - - - +
180E ASN* 1.3 74.3 - - - +
182E ALA* 1.3 62.1 + - - +
184E LEU* 3.0 5.2 + - - +
185E TRP* 2.8 73.0 + - + +
55F THR* 4.8 0.2 - - - -
56F PRO* 3.4 36.1 - - + -
58F SER* 4.1 7.2 - - - -
61F GLY* 3.6 28.9 - - - -
62F PHE* 3.8 13.9 - - - +
65F ILE* 3.5 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E ALA* 4.9 3.3 - - + +
178E ALA 3.0 19.0 + - - +
179E TYR 3.7 2.7 - - - +
181E MET* 1.3 75.6 - - - +
183E ALA* 1.3 61.6 + - - +
186E LYS 3.2 3.1 + - - -
187E LEU* 3.1 49.3 + - + +
189E CYS* 4.6 2.9 - - + -
191E PHE* 3.7 26.2 - - + -
250E PRO* 3.3 14.2 - - + +
65F ILE* 5.4 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E TYR 2.8 20.7 + - - +
182E ALA* 1.3 75.6 - - - +
184E LEU* 1.3 61.9 + - - +
186E LYS* 3.7 15.2 + - - +
219E PHE* 3.6 30.3 - - + -
220E ILE* 3.8 12.1 - - + +
250E PRO* 3.7 11.2 - - + +
209G ALA* 3.8 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E ASN 2.9 16.1 + - - +
181E MET* 3.0 5.8 + - - +
183E ALA* 1.3 79.6 - - - +
185E TRP* 1.3 75.9 + - + +
186E LYS* 3.2 5.4 + - - +
56F PRO* 4.5 14.4 - - + -
205G GLU 5.2 4.7 - - - +
206G ARG 3.2 29.8 - - - +
207G ALA* 3.5 20.6 - - - +
208G ALA 3.7 8.7 - - - +
209G ALA* 3.5 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 185 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E LEU* 4.5 14.8 - - + -
153E LYS* 2.3 38.6 + - - +
181E MET* 2.8 61.8 + - + +
184E LEU* 1.3 90.6 - - + +
186E LYS* 1.3 65.2 + - - +
187E LEU* 3.4 28.8 - - + +
26F LEU* 5.0 4.0 - - + -
53F ILE* 3.9 30.9 - - + +
54F ASP 4.1 10.2 + - - -
55F THR* 4.4 9.2 - - + -
56F PRO* 4.3 7.2 - - + -
65F ILE* 3.7 26.7 - - + -
206G ARG 5.7 0.2 + - - -
----------------------------------------------------------
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