Contacts of the helix formed by residues 152 - 172 (chain A) in PDB entry 1QM4
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 PRO 152 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 3.8 27.6 - - + -
144A THR* 3.5 6.4 - - + -
146A GLU* 3.5 13.5 - - - +
151A MET* 1.3 98.4 - - + +
153A LEU* 1.3 64.8 + - - +
154A THR* 3.2 1.2 + - + -
155A ILE* 3.4 18.6 - - + +
156A VAL* 3.1 19.1 + - - +
272A TYR* 4.1 2.9 - - + +
275A TRP* 3.3 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU* 2.8 21.9 + - + +
147A THR* 3.8 25.1 - - + -
151A MET 3.4 1.8 + - - -
152A PRO* 1.3 71.2 - - - +
154A THR* 1.3 55.0 + - - +
156A VAL* 3.3 4.7 + - + -
157A LEU* 2.8 72.3 + - + +
187A VAL* 4.3 11.7 - - + -
189A TYR* 3.5 4.5 + - + +
198A PRO* 3.4 30.1 - - + -
233A PRO* 5.5 1.8 - - + -
236A TYR* 3.9 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.4 17.2 + - + -
23A SER* 2.8 33.9 + - - +
152A PRO* 4.1 3.1 - - + -
153A LEU* 1.3 78.4 - - - +
155A ILE* 1.3 62.5 + - + +
158A ALA* 3.2 25.8 + - - +
185A VAL* 3.0 39.9 + - - +
187A VAL* 4.2 7.5 + - - +
189A TYR* 3.7 4.2 + - - -
275A TRP* 3.2 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER* 3.8 12.3 - - - +
24A GLU 3.1 29.4 - - - +
151A MET* 4.4 9.4 - - + -
152A PRO* 3.4 28.3 - - + +
154A THR* 1.3 77.8 - - + +
156A VAL* 1.3 69.1 + - - +
157A LEU 3.3 0.2 - - - -
158A ALA* 3.6 1.6 - - + +
159A HIS* 3.0 55.0 + - + +
269A VAL* 4.4 5.2 - - - +
271A THR 4.6 3.6 - - - +
272A TYR 3.6 18.8 - - - +
273A GLY* 3.8 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 4.0 10.5 - - + +
149A GLU* 3.6 31.9 - - + +
151A MET* 3.4 33.0 - - + +
152A PRO 3.1 18.8 + - - +
153A LEU* 3.6 7.9 - - + +
155A ILE* 1.3 78.0 - - + +
157A LEU* 1.3 64.5 + - + +
159A HIS* 3.7 5.3 - - - +
160A LYS* 3.0 39.4 + - + +
382A GLY* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 2.8 52.0 + - + +
156A VAL* 1.3 75.2 - - + +
158A ALA* 1.3 61.2 + - - +
160A LYS* 3.7 6.6 - - + +
161A LEU* 2.8 34.5 + - - +
185A VAL* 4.0 22.0 - - + -
187A VAL* 4.7 0.2 - - + -
201A VAL* 3.9 26.7 - - + -
231A VAL* 4.1 17.9 - - + +
232A VAL* 3.9 32.5 - - + -
233A PRO* 4.3 6.3 - - + -
236A TYR* 5.2 0.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
23A SER 4.3 1.6 - - - +
24A GLU* 4.0 16.8 - - - -
25A SER* 3.7 15.9 - - - -
154A THR 3.2 18.3 + - - +
155A ILE* 3.3 8.9 + - - +
157A LEU* 1.3 79.0 - - - +
159A HIS* 1.3 61.3 + - - +
162A ASN* 3.3 16.5 + - - +
183A THR* 3.3 34.0 - - + +
185A VAL* 3.7 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 2.9 34.1 + - - -
151A MET* 5.8 1.0 - - + +
155A ILE* 3.0 39.3 + - + +
156A VAL* 3.7 5.8 - - - +
158A ALA* 1.3 74.7 - - - +
160A LYS* 1.3 60.0 + - + +
161A LEU 3.2 0.2 - - - -
162A ASN* 3.0 6.8 + - - +
163A THR* 2.9 29.3 + - - -
269A VAL* 2.9 30.6 + - + +
271A THR 5.0 5.2 - - - -
378A TYR* 3.3 30.5 + - + +
379A GLY* 3.5 19.6 + - - -
381A PHE 5.0 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU* 5.3 5.5 + - - -
149A GLU* 3.3 27.2 + - - -
156A VAL* 3.0 25.5 + - + +
157A LEU* 3.9 9.2 - - + +
159A HIS* 1.3 72.5 - - + +
161A LEU* 1.3 66.4 + - - +
163A THR* 3.6 12.7 - - + +
164A ARG* 2.9 26.3 + - - +
231A VAL* 4.2 25.7 + - + +
----------------------------------------------------------
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 LEU* 2.8 13.9 + - + +
158A ALA 3.7 5.6 - - - +
159A HIS 3.2 0.2 - - - -
160A LYS* 1.3 79.1 - - - +
162A ASN* 1.3 62.0 + - - +
164A ARG* 3.3 7.4 + - - +
165A MET* 3.2 21.4 + - - +
183A THR* 3.5 28.5 - - + +
185A VAL* 3.6 21.3 - - + -
204A ILE* 4.1 20.6 - - + -
206A ILE* 4.9 5.8 - - + -
227A VAL* 4.0 12.0 - - + +
228A ILE* 3.9 27.1 - - + -
231A VAL* 3.4 27.1 - - + -
232A VAL* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 3.0 34.3 + - - +
26A VAL 4.4 1.3 - - - +
27A GLY* 3.8 8.8 - - - +
158A ALA 3.3 8.4 + - - +
159A HIS 3.0 8.4 + - - +
161A LEU* 1.3 75.2 - - - +
163A THR* 1.3 66.0 + - - +
165A MET* 3.3 17.0 + - - +
166A ALA* 3.3 12.6 + - - +
181A SER* 2.6 41.1 + - - +
183A THR* 3.3 17.2 + - - -
378A TYR* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A HIS* 2.9 13.9 + - - +
160A LYS* 3.6 14.6 - - + +
162A ASN* 1.3 76.5 - - - +
164A ARG* 1.3 63.3 + - + +
166A ALA* 3.2 5.9 + - - +
167A ASP* 3.2 34.7 + - - +
378A TYR* 3.5 36.6 - - - +
383A ARG* 6.1 0.5 - - - -
----------------------------------------------------------
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 LYS 2.9 18.7 + - - +
161A LEU 3.7 3.8 - - - +
162A ASN 3.2 0.2 - - - -
163A THR* 1.3 78.8 - - + +
165A MET* 1.3 62.9 + - - +
167A ASP* 3.2 18.1 + - - +
168A LEU* 3.1 46.7 + - + +
226A GLN* 2.5 35.8 + - - +
227A VAL* 3.6 21.8 - - + +
230A ALA* 3.2 19.0 + - - +
231A VAL* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU 3.2 17.5 - - - +
162A ASN* 3.3 21.6 + - - +
164A ARG* 1.3 76.5 - - - +
166A ALA* 1.3 56.1 + - - +
168A LEU* 4.5 3.6 - - - -
169A ARG* 2.9 24.0 + - - +
177A LEU* 3.0 31.1 - - + +
181A SER* 4.5 2.0 - - - +
206A ILE* 3.2 36.8 - - + -
208A VAL* 3.4 37.5 - - + -
223A LEU* 3.4 16.2 - - + -
227A VAL* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 4.7 0.2 - - - +
162A ASN 3.3 5.5 + - - +
163A THR* 3.4 10.8 - - - +
164A ARG 3.1 0.2 - - - -
165A MET* 1.3 76.5 - - - +
167A ASP* 1.3 57.4 - - - +
169A ARG* 3.2 18.3 + - - +
170A ARG* 2.8 58.9 + - - +
378A TYR* 3.5 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A THR* 3.2 26.2 + - - +
164A ARG* 3.2 20.7 + - - +
166A ALA* 1.3 80.1 - - - +
168A LEU* 1.3 55.3 + - + +
170A ARG* 3.0 6.5 + - - +
171A SER* 2.7 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ARG* 3.1 43.3 + - + +
165A MET* 4.0 4.0 - - - +
167A ASP* 1.3 77.1 - - + +
169A ARG* 1.3 65.0 + - - +
171A SER* 3.5 5.6 - - - +
172A GLY 3.3 0.9 + - - -
173A VAL* 3.3 35.3 + - + -
174A LEU* 3.0 60.2 + - + +
177A LEU* 4.2 0.2 - - + -
226A GLN* 3.7 27.4 - - + +
227A VAL* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 3.9 12.7 + - - +
90A HIS 4.1 0.4 + - - -
91A ILE 2.7 30.9 + - - -
92A GLY* 4.1 5.3 - - - -
165A MET 2.9 19.6 + - - +
166A ALA* 3.3 22.3 - - - +
168A LEU* 1.3 77.4 - - - +
170A ARG* 1.3 100.1 + - - +
171A SER 3.5 0.3 + - - -
172A GLY* 3.6 8.1 + - - -
174A LEU 3.8 11.3 - - - +
175A PRO* 5.2 4.0 - - + +
177A LEU* 3.2 32.5 - - + +
178A ARG* 3.7 19.0 + - - +
179A PRO* 3.9 20.4 + - - +
378A TYR* 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 2.5 42.6 + - - -
90A HIS* 2.7 43.6 + - - -
166A ALA* 2.8 36.2 + - - +
167A ASP* 3.7 4.5 - - - +
169A ARG* 1.3 100.1 - - - +
171A SER* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ASP 2.7 21.1 + - - -
168A LEU* 3.4 7.6 + - - +
170A ARG* 1.3 75.0 - - - +
172A GLY* 1.3 61.3 + - - +
173A VAL* 3.2 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU 3.3 4.5 + - - -
169A ARG 3.6 6.7 + - - -
170A ARG 3.4 1.6 - - - -
171A SER* 1.3 79.6 + - - +
173A VAL* 1.3 65.6 + - - +
174A LEU 3.3 2.9 - - - -
175A PRO* 3.3 24.7 - - - +
----------------------------------------------------------
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