Contacts of the helix formed by residues 161 - 184 (chain A) in PDB entry 3PM0
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 ARG 161 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PRO* 1.3 80.2 - - - +
162A SER* 1.3 61.9 + - - +
163A ARG* 3.5 7.8 - - - +
164A GLN* 3.0 65.5 + - + +
165A VAL* 3.5 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PHE 4.8 2.9 - - - -
156A PHE* 5.5 0.7 - - - -
157A THR* 4.2 16.6 - - - -
158A ARG* 3.8 18.7 + - - +
159A GLN* 2.8 39.6 + - - +
160A PRO 3.0 3.2 - - - -
161A ARG* 1.3 73.9 - - - +
163A ARG* 1.3 69.5 + - - +
164A GLN 3.0 1.8 - - - -
165A VAL* 2.7 32.8 + - - +
166A LEU* 3.1 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A THR* 4.3 24.4 + - - +
159A GLN 5.4 1.8 - - - -
160A PRO* 5.9 2.8 - - - +
161A ARG 4.7 6.7 - - - +
162A SER* 1.3 79.4 - - - +
164A GLN* 1.3 83.4 + - + +
166A LEU* 3.1 12.4 + - - +
167A GLU* 2.9 31.2 + - - +
372A MET* 6.5 1.1 - - + -
478A MET* 6.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ARG* 3.0 63.7 + - + +
163A ARG* 1.3 94.4 - - - +
165A VAL* 1.3 57.7 + - - +
167A GLU* 3.3 7.8 + - - +
168A GLY* 2.8 26.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
158A ARG* 5.2 9.6 - - - +
161A ARG 3.5 4.9 + - - +
162A SER* 2.7 39.4 + - - +
164A GLN* 1.3 75.9 - - - +
166A LEU* 1.3 65.6 + - + +
168A GLY* 3.4 2.5 + - - -
169A HIS* 3.2 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PHE* 3.8 25.4 - - + -
162A SER 3.1 5.6 + - - +
163A ARG* 3.1 14.1 + - - +
165A VAL* 1.3 81.2 - - + +
167A GLU* 1.3 66.3 + - - +
169A HIS* 2.8 22.6 + - + +
170A VAL* 3.3 14.0 + - + +
204A VAL* 4.5 14.4 - - + -
208A VAL* 4.4 18.2 - - + -
475A LEU* 3.9 23.1 - - + -
478A MET* 3.6 34.3 - - + +
479A GLN* 4.6 4.0 - - + +
482A LEU* 6.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ARG* 2.9 17.7 + - - +
164A GLN* 3.8 8.3 - - - +
166A LEU* 1.3 78.2 - - - +
168A GLY* 1.3 57.3 + - - +
170A VAL* 3.3 2.3 + - - +
171A LEU* 2.8 38.5 + - + +
370A PRO 4.2 1.9 - - - +
371A CYS* 3.1 26.5 - - - +
372A MET* 3.4 32.8 + - + +
482A LEU* 3.4 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLN 2.8 17.5 + - - -
165A VAL* 3.4 3.8 + - - -
166A LEU 3.0 0.4 - - - -
167A GLU* 1.3 77.4 - - - +
169A HIS* 1.3 52.2 + - - +
171A LEU* 3.5 9.7 - - - +
172A SER* 2.6 39.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A VAL* 3.2 38.0 + - + +
166A LEU* 2.8 9.5 + - + +
168A GLY* 1.3 76.1 - - - +
170A VAL* 1.3 62.4 + - - +
172A SER* 3.2 7.0 + - - -
173A GLU* 2.9 29.8 + - + +
204A VAL* 4.2 22.0 - - + +
207A ALA* 3.9 32.2 + - + +
208A VAL* 4.0 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 3.3 14.6 + - + +
167A GLU* 3.7 6.5 - - - +
169A HIS* 1.3 76.6 - - - +
171A LEU* 1.3 55.3 + - - +
173A GLU* 2.9 3.1 + - - +
174A ALA* 2.7 38.0 + - + +
204A VAL* 4.1 16.2 - - + -
479A GLN* 3.6 31.4 - - + -
482A LEU* 3.6 39.0 - - + -
483A PHE* 4.0 26.4 - - + +
486A ILE* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 2.8 29.2 + - + +
168A GLY* 3.5 8.1 - - - +
170A VAL* 1.3 73.0 - - - +
172A SER* 1.3 62.3 - - - +
174A ALA* 3.4 5.9 + - - +
175A ARG* 3.1 23.4 + - + +
369A LEU* 3.5 38.4 - - + -
370A PRO 5.3 1.3 - - - +
482A LEU* 6.1 2.7 - - + +
486A ILE* 4.4 19.1 - - + -
528A LEU* 4.7 10.8 - - + +
530A ASP* 5.4 9.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
168A GLY 2.6 23.7 + - - -
169A HIS* 3.4 8.3 - - - -
170A VAL 3.0 0.2 - - - -
171A LEU* 1.3 75.2 - - - +
173A GLU* 1.3 68.4 + - - +
175A ARG* 3.6 8.4 + - - +
176A GLU* 3.6 18.5 + - - +
213A ARG* 4.7 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A HIS* 2.9 19.2 + - + +
170A VAL 3.8 2.2 - - - +
172A SER* 1.3 76.1 + - - +
174A ALA* 1.3 61.6 + - - +
175A ARG 3.1 1.6 - - - -
176A GLU* 4.0 5.6 - - - +
177A LEU* 2.9 32.5 + - - +
200A ALA* 3.2 34.1 - - + +
203A ASN* 3.2 32.6 + - + +
204A VAL* 3.8 10.3 - - + +
213A ARG* 2.7 43.5 + - - +
483A PHE* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 2.7 16.9 + - + +
171A LEU* 3.6 8.3 - - - +
173A GLU* 1.3 79.0 - - - +
175A ARG* 1.3 52.4 + - - +
177A LEU* 3.6 4.3 - - - +
178A VAL* 2.8 40.3 + - - +
483A PHE* 3.9 19.2 - - + -
486A ILE* 3.9 32.1 - - + -
487A LEU* 4.4 5.4 - - + -
528A LEU* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU 3.1 15.9 + - - +
172A SER* 3.7 8.7 - - - +
173A GLU 3.1 0.2 - - - -
174A ALA* 1.3 78.2 - - - +
176A GLU* 1.3 95.0 + - + +
178A VAL* 3.5 2.6 + - - +
179A ALA* 3.1 35.5 + - - +
183A ARG* 5.4 4.9 - - - +
526A MET* 4.7 6.8 - - - -
528A LEU* 4.3 36.8 - - + +
529A LEU* 3.1 34.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A SER 3.6 9.7 + - - +
173A GLU* 3.5 8.6 + - - +
175A ARG* 1.3 103.3 + - + +
177A LEU* 1.3 60.6 + - - +
179A ALA* 3.6 1.9 + - - +
180A LEU* 3.0 47.4 + - + +
213A ARG* 2.8 38.5 + - - +
215A SER* 5.2 0.5 - - - -
216A HIS* 3.4 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU 2.9 18.1 + - - +
174A ALA 3.6 3.8 - - - +
176A GLU* 1.3 75.0 - - - +
178A VAL* 1.3 65.5 + - - +
180A LEU* 3.4 6.4 + - + +
181A LEU* 3.1 45.6 + - + +
196A LEU* 3.9 39.0 - - + +
197A THR* 4.5 9.0 - - + +
200A ALA* 4.0 18.2 - - + -
339A LEU* 4.7 10.3 - - + -
343A LEU* 5.9 1.8 - - + -
483A PHE* 4.5 12.3 - - + -
487A LEU* 4.2 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ALA* 2.8 17.9 + - + +
175A ARG 3.5 6.5 - - - +
177A LEU* 1.3 73.8 - - - +
179A ALA* 1.3 61.5 + - - +
181A LEU* 4.4 8.7 - - - -
182A VAL* 2.8 36.2 + - - +
486A ILE* 5.3 0.9 - - + -
487A LEU* 3.4 27.6 - - + -
490A GLN* 5.2 1.6 - - + -
491A CYS* 3.8 24.9 - - - -
522A LEU* 4.8 2.7 - - + -
526A MET* 3.3 31.4 - - + -
528A LEU* 3.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG* 3.1 38.7 + - - +
176A GLU* 3.7 4.0 - - - +
178A VAL* 1.3 85.4 - - + +
180A LEU* 1.3 63.2 + - + +
182A VAL* 4.0 3.2 - - - +
183A ARG* 2.9 51.9 + - - +
526A MET* 5.1 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLU* 3.0 30.1 + - + +
177A LEU* 4.0 5.4 - - + +
179A ALA* 1.3 76.9 - - + +
181A LEU* 1.3 58.4 + - - +
183A ARG* 3.7 6.6 - - + +
184A GLY* 2.7 32.9 + - - -
191A LEU* 5.1 0.7 - - - +
196A LEU* 3.6 35.4 - - + +
216A HIS* 3.5 52.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 3.1 42.7 + - + +
178A VAL* 3.8 6.7 - - - +
180A LEU* 1.3 79.2 - - - +
182A VAL* 1.3 59.3 + - - +
184A GLY 3.6 1.7 - - - -
185A SER* 2.8 29.3 + - - -
191A LEU* 3.6 34.9 - - + +
193A PRO* 4.1 17.9 - - + -
196A LEU* 3.7 12.8 - - + -
343A LEU* 4.9 10.8 - - + -
487A LEU* 5.6 3.4 - - + -
491A CYS* 6.1 0.2 - - - -
493A PHE* 4.2 24.5 - - + -
518A VAL* 4.8 0.7 - - + -
520A VAL* 4.0 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL 2.8 26.5 + - - +
179A ALA* 4.1 3.8 - - - +
181A LEU* 1.3 71.2 - - - +
183A ARG* 1.3 75.3 + - - +
185A SER* 3.2 10.4 + - - -
186A ALA* 3.5 10.7 + - - +
491A CYS* 4.2 4.7 - - - -
520A VAL* 3.5 33.0 - - + +
521A THR* 4.2 1.3 - - - -
522A LEU* 3.9 46.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG* 5.4 4.9 - - - +
179A ALA* 2.9 38.0 + - - +
180A LEU* 3.7 7.6 - - + +
182A VAL* 1.3 90.1 - - - +
184A GLY* 1.3 57.4 + - - +
185A SER 3.0 5.7 + - - -
186A ALA* 3.5 16.5 + - - +
522A LEU* 5.4 3.0 - - - +
526A MET* 4.9 15.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU 2.7 20.7 + - - -
181A LEU 3.6 2.7 - - - -
183A ARG* 1.3 71.2 - - - +
185A SER* 1.3 57.8 + - - +
186A ALA 3.7 0.7 - - - -
189A ALA* 4.4 5.0 - - - +
190A PHE 4.3 4.9 - - - +
191A LEU* 3.3 29.0 - - - +
----------------------------------------------------------
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