Contacts of the helix formed by residues 174 - 186 (chain D) in PDB entry 3ESF
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 174 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D TYR* 2.8 29.3 + - + +
172D LYS 3.1 1.2 - - - -
173D ASN* 1.3 84.6 - - - +
175D ARG* 1.3 61.7 + - - +
176D PRO* 3.3 15.1 - - - +
177D ALA* 3.2 35.9 + - + +
178D TYR 3.3 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C TRP* 5.9 2.6 - - - -
117D ALA 2.8 31.0 + - - -
118D VAL* 3.2 21.1 + - + +
120D HIS* 2.7 35.7 + - - +
122D GLY* 3.6 17.2 + - - +
162D VAL* 3.7 20.2 + - - +
164D GLU* 5.3 4.4 + - - +
167D TYR* 3.1 48.4 + - + +
173D ASN 2.9 9.6 + - - +
174D ASP* 1.3 69.6 - - - +
176D PRO* 1.4 72.7 - - + +
178D TYR* 3.1 14.2 + - + +
179D VAL* 2.9 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D VAL* 3.9 34.7 - - + +
173D ASN 4.6 1.8 - - - +
174D ASP* 3.3 15.3 - - - +
175D ARG* 1.4 92.2 - - + +
177D ALA* 1.3 55.1 + - - +
179D VAL* 3.3 2.8 + - - +
180D GLN* 3.0 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D TYR* 3.8 19.1 - - + -
174D ASP* 3.2 30.3 + - - +
175D ARG 3.2 0.2 - - - -
176D PRO* 1.3 75.6 - - - +
178D TYR* 1.3 64.9 + - - +
180D GLN* 3.4 8.7 + - - +
181D THR* 3.1 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ILE* 4.5 16.6 - - + -
79D TYR* 2.8 36.5 + - - -
83D MET* 5.8 0.4 - - - -
160D CYS* 3.6 19.3 - - - -
161D ASP 2.7 28.3 + - - -
162D VAL* 4.4 4.7 - - + -
166D ALA* 3.9 10.3 - - + +
167D TYR* 3.4 44.6 - + + -
171D TYR* 3.8 27.7 - + + -
174D ASP 3.3 6.4 + - - +
175D ARG* 3.1 14.7 + - + +
177D ALA* 1.3 78.8 - - - +
179D VAL* 1.3 60.4 + - + +
181D THR* 3.1 5.6 + - - -
182D PHE* 2.8 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PHE* 5.3 3.6 - - + -
114D THR* 4.3 18.2 - - + -
117D ALA* 3.8 28.3 - - + -
118D VAL* 3.7 17.7 - - + -
160D CYS* 4.9 2.2 - - - -
162D VAL* 4.8 0.9 - - + -
175D ARG* 2.9 27.8 + - + +
176D PRO 3.8 4.7 - - - +
178D TYR* 1.3 84.3 - - + +
180D GLN* 1.3 65.0 + - - +
182D PHE* 3.2 11.8 + - + +
183D TRP* 3.1 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LYS* 4.8 11.4 + - - +
114D THR* 4.2 19.6 + - - +
176D PRO* 3.0 20.0 + - + +
177D ALA* 3.6 12.1 - - - +
178D TYR 3.2 0.2 - - - -
179D VAL* 1.3 76.2 - - - +
181D THR* 1.3 62.0 + - - +
183D TRP* 3.2 36.9 + - - +
184D ASN* 3.4 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 3.8 13.3 - - - -
18D LYS 3.4 21.0 + - - +
19D GLY 3.6 8.7 - - - +
20D ILE* 3.7 20.4 - - + -
171D TYR* 2.7 30.5 + - + +
177D ALA 3.1 11.7 + - - -
178D TYR* 3.1 9.6 + - + +
180D GLN* 1.3 72.3 - - - +
182D PHE* 1.3 67.7 + - - +
184D ASN* 2.9 22.1 + - - +
185D VAL* 3.3 12.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ILE* 5.8 1.3 - - - -
79D TYR* 4.8 1.1 - + - -
82D SER 4.2 4.7 - - - -
83D MET* 3.8 34.3 - - + -
113D PHE* 3.8 29.4 - + - -
158D LEU* 3.9 13.2 - - + -
159D THR 3.5 26.5 - - - -
160D CYS* 3.7 28.3 - - + -
178D TYR* 2.8 19.6 + + + +
179D VAL* 3.2 12.5 + - + +
181D THR* 1.3 73.3 - - - +
183D TRP* 1.3 68.1 + + - +
185D VAL* 3.0 7.9 + - - +
186D VAL* 2.9 57.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLY* 3.3 17.8 - - - -
89D GLY 3.9 6.3 + - - +
106D PHE* 4.4 6.5 - + - -
109D PHE* 3.7 33.2 - + - -
110D LYS* 3.5 60.3 - - + +
113D PHE* 3.5 32.1 - + + -
114D THR* 2.8 20.0 + - - -
158D LEU* 5.9 0.4 - - + -
179D VAL* 3.1 28.1 + - + +
180D GLN* 3.4 24.7 - - - +
181D THR 3.2 0.4 - - - -
182D PHE* 1.3 84.2 - + - +
184D ASN* 1.3 58.7 + - - +
185D VAL 3.4 0.2 - - - -
186D VAL* 3.8 20.7 - - + +
188D TRP* 4.3 13.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR 5.0 9.1 + - - -
63A LYS* 6.3 1.4 - - - +
18D LYS* 3.0 44.5 + - + +
87D GLY 3.3 5.0 - - - +
88D GLY* 3.5 6.8 - - - -
89D GLY 5.6 0.9 + - - -
180D GLN* 3.4 14.9 + - - +
181D THR* 2.9 15.9 + - - +
183D TRP* 1.3 78.6 - - - +
185D VAL* 1.3 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 4.0 15.5 - - + -
18D LYS* 3.5 34.3 - - + +
20D ILE* 4.5 6.1 - - + -
83D MET* 3.3 33.5 - - + -
84D SER 2.8 45.7 + - - +
87D GLY* 3.6 1.3 - - - -
88D GLY 3.6 2.5 - - - +
181D THR* 3.3 14.3 + - + +
182D PHE* 3.0 16.1 + - - +
184D ASN* 1.3 77.5 - - - +
186D VAL* 1.3 68.9 + - - +
187D ASN 3.2 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D SER 3.5 6.5 - - - +
87D GLY* 3.2 3.3 - - - -
88D GLY* 2.8 26.7 + - - +
89D GLY 4.5 0.7 - - - +
158D LEU* 3.5 35.7 - - + -
182D PHE* 2.9 36.2 + - + +
183D TRP* 3.8 24.7 - - + +
185D VAL* 1.3 74.6 - - - +
187D ASN* 1.3 61.5 + - - +
188D TRP* 3.4 41.2 + - + +
----------------------------------------------------------
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