Contacts of the helix formed by residues 150 - 167 (chain A) in PDB entry 1PJS
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 HIS 150 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PRO* 3.5 2.9 - - + +
149A GLN* 1.3 89.7 - - + +
151A LEU* 1.3 63.6 + - - +
152A GLY 3.1 2.9 - - - -
153A GLN* 2.9 54.9 + - - +
154A VAL* 3.7 6.9 + - - +
189A ALA 5.9 0.9 - - - +
193A ALA* 3.8 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 4.1 8.7 - - + -
122A LEU* 4.5 18.8 - - + -
147A LEU* 4.3 20.6 - - + -
148A PRO* 3.8 31.7 + - + +
149A GLN 3.3 3.2 + - - -
150A HIS* 1.3 78.0 - - - +
152A GLY* 1.3 61.3 + - - +
153A GLN 3.3 0.3 + - - -
154A VAL* 3.3 19.5 + - + +
155A ALA* 3.2 21.0 + - - +
183A PHE* 6.6 0.2 - - + -
506A PGE 3.6 40.6 - - - +
135B LEU* 4.6 13.0 - - + +
139B LEU* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 3.1 31.3 + - - +
120A SER 3.2 13.0 - - - -
121A PRO* 3.3 11.3 - - - +
122A LEU* 4.7 0.2 - - - -
149A GLN 4.4 1.4 + - - -
150A HIS 3.1 1.6 - - - -
151A LEU* 1.3 79.8 - - - +
153A GLN* 1.3 56.1 + - - +
155A ALA* 3.4 3.8 + - - -
156A ARG* 2.8 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A HIS* 2.9 48.7 + - - +
152A GLY* 1.3 73.6 - - - +
154A VAL* 1.3 68.4 + - + +
156A ARG* 3.2 7.5 + - - +
157A TYR* 2.9 25.5 + - - +
189A ALA 4.9 0.2 - - - +
192A LEU* 3.1 20.4 - - + +
193A ALA* 3.0 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A HIS 4.2 10.3 - - - +
151A LEU* 3.3 20.8 + - + +
153A GLN* 1.3 77.1 - - + +
155A ALA* 1.3 58.3 + - - +
157A TYR* 3.4 2.9 + - - +
158A ALA* 2.9 26.9 + - - +
182A PHE* 3.7 23.7 - - + +
183A PHE* 3.9 20.4 - - + -
188A LEU* 6.5 0.2 - - + -
189A ALA* 4.4 21.3 - - + +
192A LEU* 3.7 22.0 - - + -
506A PGE 6.1 0.2 - - - +
135B LEU* 5.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO* 4.1 8.7 - - + -
122A LEU* 4.5 8.7 - - + -
151A LEU 3.2 10.1 + - - +
152A GLY* 3.6 10.3 - - - +
153A GLN 3.2 0.4 - - - -
154A VAL* 1.3 78.8 - - - +
156A ARG* 1.3 63.4 + - - +
158A ALA* 3.3 6.7 + - - +
159A GLY 3.2 9.0 + - - -
183A PHE* 5.2 0.2 - - - -
128B SEP 5.9 0.2 - - - -
131B THR* 3.1 35.1 - - - +
132B SER* 5.3 0.7 - - - -
135B LEU* 3.7 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO* 3.9 18.8 - - + +
152A GLY 2.8 17.9 + - - +
153A GLN* 3.2 7.6 + - - +
155A ALA* 1.3 76.2 - - - +
157A TYR* 1.3 62.0 + - - +
159A GLY* 3.4 3.1 + - - -
160A GLN* 3.1 53.8 + - + +
131B THR* 4.3 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLN 2.9 16.4 + - - +
154A VAL 3.7 4.0 - - - +
156A ARG* 1.3 74.9 - - - +
158A ALA* 1.3 63.6 + - - +
160A GLN* 3.1 32.6 + - + +
161A LEU* 3.1 38.2 + - + +
182A PHE* 3.8 20.9 - + - -
188A LEU* 4.0 10.5 - - + -
192A LEU* 4.1 23.6 - - + -
200A VAL* 3.4 23.3 + - + +
201A ASN* 4.4 6.5 + - - -
204A THR* 2.6 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A VAL 2.9 17.6 + - - +
155A ALA 3.3 7.4 + - - +
157A TYR* 1.3 77.0 - - - +
159A GLY* 1.3 62.4 + - - +
161A LEU* 3.3 2.2 + - - -
162A ARG* 3.3 17.8 + - - +
179A TRP* 3.4 20.6 - - + -
182A PHE* 3.8 22.2 - - + -
183A PHE* 3.9 18.8 - - + -
131B THR 4.5 1.6 - - - -
132B SER* 3.9 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ALA 3.2 7.7 + - - -
156A ARG 3.4 3.3 + - - -
157A TYR 3.2 0.6 - - - -
158A ALA* 1.3 78.2 - - - +
160A GLN* 1.3 62.4 + - - +
162A ARG* 3.2 21.6 + - - +
163A ALA 4.6 0.2 + - - -
131B THR* 3.8 30.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 3.1 50.5 - - - +
157A TYR* 3.1 32.4 + - + +
159A GLY* 1.3 78.9 - - - +
161A LEU* 1.3 62.5 + - + +
162A ARG 3.5 0.3 + - - -
163A ALA* 4.3 9.0 + - - +
164A ARG* 5.0 0.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
157A TYR* 3.1 46.5 + - + +
158A ALA 3.3 4.5 + - - +
159A GLY 3.2 0.2 - - - -
160A GLN* 1.3 78.1 - - + +
162A ARG* 1.3 65.7 + - - +
163A ALA 3.3 1.8 - - - -
164A ARG* 3.1 17.9 + - + +
165A VAL* 2.9 32.9 + - + +
178A PHE* 4.3 5.2 - - + -
179A TRP* 4.5 2.7 - - + -
182A PHE* 3.7 30.1 - - + -
204A THR* 4.3 7.2 - - + +
207A LEU* 5.6 0.4 - - + -
208A PHE* 4.0 31.6 - - + -
----------------------------------------------------------
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 ALA 3.3 12.0 + - - +
159A GLY* 3.2 16.2 + - - +
161A LEU* 1.3 78.5 - - - +
163A ALA* 1.3 64.0 + - - +
165A VAL* 3.3 6.5 + - - +
166A LYS* 3.2 22.0 + - - +
179A TRP* 4.2 15.9 - - + +
106B PRO* 6.1 2.0 - - - +
130B GLY 3.9 11.8 + - - -
131B THR 3.6 16.6 + - - +
133B PRO* 3.5 37.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY 4.6 0.4 + - - -
160A GLN 4.3 8.1 + - - +
161A LEU 3.3 0.8 - - - -
162A ARG* 1.3 79.0 - - - +
164A ARG* 1.3 62.0 + - - +
166A LYS* 3.6 4.4 + - - +
167A LYS* 3.4 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLN 5.0 0.8 + - - +
161A LEU* 3.1 20.5 + - + +
163A ALA* 1.3 75.6 - - - +
165A VAL* 1.3 67.1 + - - +
167A LYS* 3.1 17.0 + - + +
168A GLN* 3.2 19.0 + - + +
204A THR* 3.9 15.0 - - - +
205A GLU* 3.1 38.0 + - - -
208A PHE* 3.4 48.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 2.9 20.9 + - + +
162A ARG 3.6 5.8 - - - +
164A ARG* 1.3 76.6 - - - +
166A LYS* 1.3 61.2 + - - +
169A PHE* 3.1 37.2 + - + +
175A ARG* 3.9 29.8 - - + -
178A PHE* 3.5 41.7 - - + -
179A TRP* 3.9 21.5 - - + +
208A PHE* 3.7 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG 3.2 11.8 + - - +
163A ALA* 4.0 4.9 - - - +
164A ARG 3.2 0.2 - - - -
165A VAL* 1.3 80.1 - - + +
167A LYS* 1.3 62.6 + - + +
168A GLN 3.2 0.9 + - - -
169A PHE 2.9 18.9 + - - +
170A ALA* 5.1 0.3 - - - -
175A ARG* 3.1 44.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA* 3.4 15.5 + - + +
164A ARG* 3.1 9.5 + - + +
166A LYS* 1.3 80.0 - - + +
168A GLN* 1.3 59.0 + - - +
----------------------------------------------------------
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