Contacts of the helix formed by residues 157 - 173 (chain A) in PDB entry 1PRX
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 PHE 157 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.7 40.2 - + - -
50A GLU* 3.6 32.5 - - + -
51A LEU* 6.3 0.2 - - + -
53A ARG* 3.8 14.4 - - + +
54A ALA* 3.9 18.2 - - + -
57A LEU* 3.6 30.6 - - + +
61A PHE* 4.3 14.7 - + - -
155A ARG* 4.4 11.9 - - + -
156A ASN* 1.3 71.9 - - - +
158A ASP* 1.3 63.7 + - - +
159A GLU 3.2 1.1 - - - -
160A ILE* 3.6 11.8 - - + +
161A LEU* 3.0 24.3 + - - +
179B VAL* 3.8 25.8 - - + -
180B ASP* 2.7 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ARG* 4.8 11.3 + - - -
57A LEU* 5.8 1.2 - - - +
156A ASN* 2.9 13.5 + - - +
157A PHE* 1.3 75.9 - - - +
159A GLU* 1.3 58.4 + - - +
161A LEU* 3.2 7.5 + - - +
162A ARG* 2.9 29.3 + - - +
180B ASP* 4.4 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 5.6 2.9 - - + -
149A TYR* 5.3 2.0 - - - +
156A ASN* 3.2 30.7 + - + +
157A PHE 3.2 0.2 - - - -
158A ASP* 1.3 81.1 - - - +
160A ILE* 1.3 57.8 + - + +
162A ARG* 3.0 34.1 + - - +
163A VAL* 3.0 29.4 + - + +
149B TYR* 2.7 32.4 + - - +
156B ASN* 2.9 35.3 + - - +
159B GLU* 4.2 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 4.2 16.6 - - + -
37A PHE* 4.2 23.1 - - + -
61A PHE* 3.9 22.0 - - + -
134A VAL* 4.7 11.2 - - + -
136A VAL* 5.6 3.8 - - + -
147A ILE* 4.3 19.7 - - + -
155A ARG* 4.4 22.9 - - + -
156A ASN 3.2 15.0 + - - +
157A PHE* 3.2 18.8 + - + +
159A GLU* 1.3 77.4 - - + +
161A LEU* 1.3 61.4 + - - +
163A VAL* 3.1 21.2 - - + +
164A VAL* 3.2 11.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.6 15.9 - - + -
60A GLU* 4.0 29.6 - - + +
61A PHE* 3.9 26.4 - - + -
64A ARG* 4.0 34.5 - - - +
157A PHE 3.0 14.7 + - - +
158A ASP* 3.7 6.5 - - - +
160A ILE* 1.3 74.3 - - - +
162A ARG* 1.3 65.8 + - - +
164A VAL* 3.3 3.9 + - + +
165A ILE* 3.1 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ASP 2.9 17.5 + - - +
159A GLU* 3.0 40.7 + - - +
161A LEU* 1.3 78.5 - - - +
163A VAL* 1.3 70.5 + - - +
165A ILE* 3.3 12.2 + - - +
166A SER* 2.9 27.4 + - - -
177A THR* 4.5 4.8 + - - -
178A PRO 3.9 4.6 + - - -
180A ASP 4.2 2.0 - - - +
181A TRP* 2.8 62.9 + - + +
182A LYS* 5.4 2.5 - - - -
183A ASP 5.6 1.6 - - - +
149B TYR* 4.2 0.8 - - - -
153B THR* 4.8 0.6 - - - +
154B GLY* 2.8 31.3 + - - -
156B ASN* 3.8 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A VAL* 5.6 2.2 - - + -
145A LEU* 4.2 28.3 - - + -
147A ILE* 5.1 3.4 - - + -
159A GLU* 3.0 28.5 + - - +
160A ILE* 3.1 27.1 - - + +
162A ARG* 1.3 82.2 - - - +
164A VAL* 1.3 62.3 + - + +
166A SER* 3.4 7.3 + - - -
167A LEU* 3.0 35.0 + - + +
149B TYR* 3.6 35.7 - - + +
153B THR* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 6.0 2.5 - - + -
35A ILE* 3.9 27.6 - - + -
61A PHE* 4.1 8.7 - - + -
64A ARG* 4.7 11.7 - - - -
66A VAL* 3.8 25.8 - - + -
136A VAL* 4.7 14.8 - - + -
160A ILE* 3.2 15.8 + - + +
161A LEU* 3.3 11.0 + - + +
163A VAL* 1.3 78.3 - - + +
165A ILE* 1.3 59.1 + - - +
167A LEU* 3.4 7.9 + - + +
168A GLN* 3.0 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 3.7 40.8 - - - +
161A LEU* 3.1 22.2 + - + +
162A ARG* 3.4 11.4 - - - +
163A VAL 3.2 0.2 - - - -
164A VAL* 1.3 78.1 - - - +
166A SER* 1.3 60.2 + - - +
168A GLN* 3.9 6.2 - - - +
169A LEU* 3.0 25.7 + - + +
181A TRP* 3.6 26.2 - - + -
183A ASP* 4.0 26.0 - - + +
223A GLN* 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG* 2.9 19.7 + - - -
163A VAL* 3.7 7.9 - - - -
164A VAL 3.3 0.2 - - - -
165A ILE* 1.3 73.4 - - - +
167A LEU* 1.3 61.9 + - - +
169A LEU* 3.0 8.6 + - - +
170A THR* 2.9 34.3 + - - -
177A THR* 3.4 31.8 + - - +
181A TRP* 3.5 14.0 - - - -
152B THR 5.2 0.4 - - - -
153B THR* 3.4 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 4.0 21.5 - - + -
136A VAL* 3.9 28.3 - - + -
144A LYS* 4.1 12.8 - - + +
145A LEU* 4.0 21.8 - - + -
163A VAL 3.0 23.1 + - - +
164A VAL* 3.5 8.5 - - + +
166A SER* 1.3 76.9 - - - +
168A GLN* 1.3 58.5 + - - +
170A THR* 3.4 5.8 + - - -
171A ALA* 3.0 27.9 + - - +
150B PRO* 3.9 23.3 - - + -
152B THR* 5.7 0.7 - - - +
153B THR* 3.3 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 3.4 40.7 - - + +
64A ARG* 2.9 46.0 + - - +
65A ASN* 5.0 0.4 - - - +
66A VAL* 3.7 10.1 - - - +
164A VAL* 3.0 24.2 + - + +
165A ILE* 4.0 5.8 - - - +
167A LEU* 1.3 72.8 - - - +
169A LEU* 1.3 60.1 + - - +
171A ALA* 3.7 6.8 - - - +
172A GLU* 3.0 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ILE* 3.0 14.1 + - + +
166A SER* 3.0 8.9 + - - +
168A GLN* 1.3 75.4 - - - +
170A THR* 1.3 58.6 + - - +
172A GLU* 5.0 0.2 - - - -
173A LYS* 2.7 66.6 + - + +
174A ARG 3.6 0.7 + - - -
175A VAL* 3.8 15.2 - - + +
177A THR* 4.2 7.9 - - + -
181A TRP* 3.8 33.9 - - + -
187A VAL* 4.1 14.1 - - + -
223A GLN* 4.0 28.5 - - + +
224A PRO* 4.6 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A SER 2.9 16.8 + - - -
167A LEU* 3.7 6.2 - - - -
169A LEU* 1.3 75.6 - - - +
171A ALA* 1.3 64.0 + - - +
174A ARG* 3.2 22.0 + - - +
175A VAL 2.6 27.3 + - - +
176A ALA* 4.1 1.0 - - - -
177A THR* 5.0 0.9 + - - +
190A LEU* 4.6 8.9 - - + +
152B THR* 3.8 43.0 + - + +
153B THR* 5.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 4.2 19.7 - - + -
167A LEU 3.0 16.6 + - - +
168A GLN* 3.7 5.8 - - - +
170A THR* 1.3 79.5 - - - +
172A GLU* 1.3 65.1 + - + +
174A ARG* 5.0 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 5.8 1.4 + - - -
168A GLN* 3.0 33.1 + - - +
169A LEU* 5.0 0.2 - - - -
171A ALA* 1.3 85.0 - - + +
173A LYS* 1.3 88.2 + - + +
174A ARG* 3.6 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A LEU* 2.7 40.8 + - + +
172A GLU* 1.3 101.3 + - + +
174A ARG* 1.3 68.7 + - - +
175A VAL* 3.4 2.8 + - + -
201A LEU* 5.2 2.4 - - - +
202A PHE* 3.6 18.2 - - - -
224A PRO* 3.7 43.5 - - + -
----------------------------------------------------------
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