Contacts of the helix formed by residues 171 - 184 (chain A) in PDB entry 1P9W
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 LEU 171 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 5.7 14.8 - - + -
123A ILE* 3.6 29.2 - - + -
126A LEU* 5.4 7.6 - - + -
151A LEU* 4.2 7.4 - - + -
167A PRO* 4.0 11.0 - - + -
168A SER* 3.0 44.9 + - - +
170A LYS* 1.3 78.8 - - + +
172A SER* 1.3 64.6 + - - +
173A SER 3.4 0.7 - - - -
174A LEU* 3.0 24.4 + - + +
175A LEU* 3.1 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ILE* 5.8 0.8 - - - +
146A THR* 3.5 34.6 + - - +
151A LEU* 4.0 17.9 - - - +
169A ARG* 3.1 23.5 + - - -
170A LYS 3.2 0.2 - - - -
171A LEU* 1.3 76.8 - - - +
173A SER* 1.3 66.3 + - - +
175A LEU* 3.4 4.8 + - - +
176A VAL* 3.1 32.2 + - - +
218A HIS 5.2 0.7 + - - -
219A GLY* 5.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LYS 4.3 6.5 + - - -
171A LEU 3.3 1.0 + - - -
172A SER* 1.3 81.8 + - - +
174A LEU* 1.3 66.0 + - - +
176A VAL* 4.1 4.9 - - - +
177A SER* 3.2 28.1 + - - -
190A LYS* 5.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 3.9 35.0 - - + +
170A LYS 5.0 8.3 - - - +
171A LEU* 3.0 15.0 + - + +
173A SER* 1.3 84.9 + - - +
175A LEU* 1.3 59.5 + - - +
176A VAL 3.2 0.2 - - - -
177A SER* 3.5 6.7 + - - +
178A ARG* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 4.2 14.6 - - + -
126A LEU* 3.9 27.1 - - + -
127A ILE* 3.7 26.4 - - + +
130A MSE 6.0 0.2 - - - -
144A ILE* 4.2 26.7 - - + -
151A LEU* 3.6 30.1 - - + -
153A ILE* 4.9 11.9 - - + -
167A PRO* 5.0 2.7 - - + -
171A LEU* 3.1 20.6 + - + +
172A SER* 3.4 3.1 + - - +
174A LEU* 1.3 75.4 - - - +
176A VAL* 1.3 62.7 + - - +
178A ARG* 3.8 5.4 - - - +
179A VAL* 3.2 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ILE* 5.5 8.1 - - + +
146A THR* 5.6 1.8 - - - +
172A SER* 3.1 22.7 + - - +
173A SER* 4.1 5.8 - - - +
175A LEU* 1.3 75.1 - - + +
177A SER* 1.3 68.5 + - - +
179A VAL* 3.1 5.0 + - - +
180A LYS* 3.0 39.8 + - + +
220A GLU* 3.7 51.4 - - + +
222A VAL* 4.1 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A SER 3.2 17.7 + - - -
174A LEU* 3.8 8.1 - - - +
176A VAL* 1.3 78.8 - - - +
178A ARG* 1.3 66.1 + - - +
180A LYS* 2.9 22.5 + - - +
181A VAL* 2.9 24.7 + - - +
187A ILE* 4.0 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 3.7 16.6 - - + +
124A ILE* 3.6 51.6 - - - +
127A ILE* 3.6 26.4 - - + +
128A ASN* 5.0 1.4 + - - +
174A LEU 2.9 18.5 + - - +
175A LEU 3.8 4.5 - - - +
176A VAL 3.2 0.2 - - - -
177A SER* 1.3 76.8 + - - +
179A VAL* 1.3 61.7 + - - +
181A VAL* 3.5 23.4 + - - +
182A MSE 3.3 57.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 4.2 20.0 - - + -
144A ILE* 4.5 2.9 - - + -
175A LEU 3.2 17.4 + - - +
176A VAL* 3.1 5.4 + - - +
178A ARG* 1.3 72.8 - - - +
180A LYS* 1.3 66.5 + - + +
182A MSE 3.3 9.3 + - - +
183A ALA* 3.1 21.0 + - - +
198A ILE* 4.5 2.4 - - + +
211A VAL* 3.6 33.9 - - + -
213A THR* 5.5 0.9 - - + -
222A VAL* 3.9 17.9 - - + -
224A MSE 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL* 3.0 27.5 + - + +
177A SER* 2.9 11.3 + - - +
179A VAL* 1.3 76.6 - - - +
181A VAL* 1.3 63.4 + - - +
183A ALA 2.8 14.2 + - - -
184A LYS 2.8 10.7 + - - -
185A LEU* 3.2 30.5 + - + +
186A ASP 3.4 18.4 + - - +
187A ILE* 4.1 19.9 + - + -
189A GLU 2.8 29.1 + - - -
194A GLN* 3.5 9.8 - - - +
211A VAL* 5.6 0.2 - - - -
213A THR* 4.1 17.0 - - + -
220A GLU* 2.8 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SER* 2.9 22.9 + - - +
178A ARG* 3.5 37.0 - - - +
180A LYS* 1.3 75.4 - - - +
182A MSE 1.3 63.2 + - + +
184A LYS* 3.5 12.6 + - - +
185A LEU 4.8 5.2 - - - +
187A ILE* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 3.8 23.1 - - - -
128A ASN* 3.7 18.8 - - - +
131A LEU* 4.5 9.0 - - + -
178A ARG* 3.3 49.6 + - - +
179A VAL* 3.3 9.3 + - - +
180A LYS 3.0 0.4 - - - -
181A VAL* 1.3 80.8 - - + +
183A ALA* 1.3 58.0 + - - +
184A LYS* 3.3 10.0 + - - +
197A ARG 4.1 1.6 - - - +
198A ILE* 3.4 36.1 - - + +
200A LEU* 4.0 32.5 - - + -
----------------------------------------------------------
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 VAL 3.1 13.8 + - - +
180A LYS 2.8 2.2 + - - -
182A MSE 1.3 76.1 - - - +
184A LYS* 1.3 71.0 + - - +
185A LEU* 3.8 12.3 - - + +
196A GLY* 3.7 21.8 - - - -
197A ARG 3.5 16.3 + - - +
198A ILE* 3.7 0.7 - - - -
211A VAL* 3.7 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LYS 2.8 5.8 + - - -
181A VAL* 3.5 9.3 + - - +
182A MSE 3.3 9.6 + - - +
183A ALA* 1.3 83.9 - - - +
185A LEU* 1.3 62.3 + - - +
197A ARG 5.5 2.0 + - - +
----------------------------------------------------------
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