Contacts of the helix formed by residues 152 - 172 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B TYR* 3.8 15.3 - - + -
144B THR* 3.5 5.8 - - + -
146B GLU* 3.5 12.6 - - - +
151B MET* 1.3 100.2 - - + +
153B LEU* 1.3 66.9 + - - +
154B THR* 4.0 0.9 - - + -
155B ILE* 3.4 19.6 - - + +
156B VAL* 3.1 18.5 + - - +
272B TYR* 4.0 2.5 - - + +
275B TRP* 3.3 55.2 - - + -
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLU* 2.9 20.5 + - + +
147B THR* 3.8 24.2 - - + -
151B MET 3.4 1.8 + - - -
152B PRO* 1.3 71.3 - - - +
154B THR* 1.3 53.8 + - - +
156B VAL* 3.3 4.7 + - + -
157B LEU* 2.8 69.2 + - + +
187B VAL* 4.2 12.8 - - + -
189B TYR* 3.7 4.3 - - - +
198B PRO* 3.4 31.0 - - + -
233B PRO* 5.4 2.0 - - + -
236B TYR* 3.9 33.0 - - + +
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Residues in contact with THR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 3.4 17.4 + - + -
22B THR 3.9 0.2 - - - -
23B SER* 2.8 34.0 + - - +
152B PRO* 4.0 2.7 - - + -
153B LEU* 1.3 77.7 - - - +
155B ILE* 1.3 63.4 + - + +
158B ALA* 3.2 24.6 + - - +
185B VAL* 3.0 40.2 + - - +
187B VAL* 4.2 8.2 + - - +
189B TYR* 3.7 5.3 + - - -
275B TRP* 3.2 35.9 - - + -
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Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER* 3.8 11.9 - - - +
24B GLU 3.2 29.2 - - - +
151B MET* 4.4 9.0 - - + -
152B PRO* 3.4 34.1 - - + +
154B THR* 1.3 78.1 - - + +
156B VAL* 1.3 68.8 + - + +
157B LEU 3.3 0.4 - - - -
158B ALA* 3.3 1.4 + - - +
159B HIS* 2.9 56.9 + - + +
269B VAL* 4.4 5.2 - - - +
271B THR 4.6 2.5 - - - +
272B TYR 3.6 13.5 - - - +
273B GLY* 3.9 22.9 - - - +
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B THR* 4.1 12.1 - - + +
149B GLU* 3.6 30.5 - - + +
151B MET* 3.4 33.0 - - + +
152B PRO 3.1 18.4 + - - +
153B LEU* 3.6 7.2 - - + +
155B ILE* 1.3 78.3 - - + +
157B LEU* 1.3 65.0 + - + +
159B HIS* 3.3 6.5 + - - +
160B LYS* 2.9 40.3 + - + +
382B GLY* 6.0 0.4 - - - -
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 2.8 48.7 + - + +
156B VAL* 1.3 78.7 - - + +
158B ALA* 1.3 66.3 + - - +
160B LYS* 3.3 7.8 + - + +
161B LEU* 2.9 27.9 + - + +
185B VAL* 4.0 21.3 - - + -
201B VAL* 3.9 25.6 - - + -
231B VAL* 4.1 23.3 - - + +
232B VAL* 3.9 24.2 - - + -
233B PRO* 4.3 9.0 - - + -
236B TYR* 5.2 0.7 - - + -
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER 4.3 1.3 - - - +
24B GLU* 3.9 17.5 - - - -
25B SER* 3.7 15.9 - - - -
154B THR 3.2 18.5 + - - +
155B ILE* 3.5 9.0 - - - +
157B LEU* 1.3 80.1 - - - +
159B HIS* 1.3 60.7 + - - +
162B ASN* 3.2 23.9 + - - +
183B THR* 3.3 26.4 - - + +
185B VAL* 3.7 5.6 - - + +
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Residues in contact with HIS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 2.9 34.9 + - - -
151B MET* 5.9 1.2 - - + +
155B ILE* 2.9 40.8 + - + +
156B VAL* 3.6 6.3 - - - +
158B ALA* 1.3 73.9 - - - +
160B LYS* 1.3 67.5 + - + +
162B ASN* 2.9 14.4 + - - +
163B THR* 2.9 16.3 + - - -
269B VAL* 2.9 30.4 + - + +
271B THR 5.0 4.0 - - - -
378B TYR* 3.3 30.4 + - + +
379B GLY* 3.5 20.3 + - - -
381B PHE 5.0 6.9 + - - -
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLU* 5.4 4.9 + - - +
149B GLU* 3.3 26.1 + - - -
156B VAL* 2.9 27.9 + - + +
157B LEU* 3.9 9.2 - - + +
159B HIS* 1.3 75.6 - - + +
161B LEU* 1.3 58.7 + - - +
163B THR* 3.5 12.9 - - + +
164B ARG* 2.8 32.2 + - - +
231B VAL* 4.3 27.4 + - + +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 2.9 14.0 + - + +
158B ALA 3.6 5.6 - - - +
159B HIS 3.1 0.2 - - - -
160B LYS* 1.3 78.0 - - - +
162B ASN* 1.3 61.2 + - - +
164B ARG* 3.8 4.5 - - - +
165B MET* 3.1 26.3 + - - +
183B THR* 3.5 28.0 - - + +
185B VAL* 3.6 22.0 - - + -
204B ILE* 4.1 20.0 - - + -
206B ILE* 4.9 5.8 - - + -
227B VAL* 4.0 12.7 - - + +
228B ILE* 3.8 27.1 - - + -
231B VAL* 3.4 27.8 - - + -
232B VAL* 4.5 4.7 - - + -
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Residues in contact with ASN 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 3.0 26.7 + - - +
26B VAL 4.4 1.8 - - - +
27B GLY* 3.8 9.0 - - - +
158B ALA 3.2 9.1 + - - +
159B HIS 2.9 7.6 + - - +
161B LEU* 1.3 77.8 - - - +
163B THR* 1.3 64.4 - - - +
165B MET* 3.2 18.1 + - - +
166B ALA* 3.3 13.2 + - - +
181B SER* 2.6 39.4 + - - +
183B THR* 3.2 25.4 + - - -
378B TYR* 3.7 20.0 + - + -
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Residues in contact with THR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B HIS* 2.9 11.0 + - - +
160B LYS* 3.5 16.6 - - + +
162B ASN* 1.3 76.5 - - - +
164B ARG* 1.3 63.7 + - + +
166B ALA* 3.2 5.5 + - - +
167B ASP* 3.1 34.3 + - - +
378B TYR* 3.4 35.7 - - - +
383B ARG* 6.2 0.2 - - - -
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LYS 2.8 17.7 + - - +
161B LEU 3.8 3.4 - - - +
162B ASN 3.2 0.2 - - - -
163B THR* 1.3 79.5 - - + +
165B MET* 1.3 61.8 + - - +
167B ASP* 3.1 19.7 + - - +
168B LEU* 3.0 47.4 + - + +
226B GLN* 2.5 37.3 + - - +
227B VAL* 3.6 21.5 - - + +
230B ALA* 3.2 17.9 + - - +
231B VAL* 3.6 26.7 - - + -
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Residues in contact with MET 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU 3.1 18.6 - - - +
162B ASN* 3.2 12.2 + - - +
164B ARG* 1.3 75.9 - - - +
166B ALA* 1.3 56.9 + - - +
167B ASP 3.3 0.2 - - - -
168B LEU* 3.9 4.5 - - - -
169B ARG* 3.0 15.9 + - - +
177B LEU* 3.0 40.4 - - + +
181B SER* 4.5 11.4 - - - +
183B THR* 5.1 0.2 - - - -
206B ILE* 3.1 37.0 - - + -
208B VAL* 3.3 36.8 - - + -
223B LEU* 3.4 15.7 - - + -
227B VAL* 4.2 13.7 - - + -
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLU* 4.7 0.2 - - - +
162B ASN 3.3 6.2 + - - +
163B THR* 3.2 10.1 + - - +
164B ARG 3.1 0.4 - - - -
165B MET* 1.3 76.6 - - - +
167B ASP* 1.3 58.7 + - - +
169B ARG* 3.4 16.4 - - - +
170B ARG* 2.8 58.8 + - - +
378B TYR* 3.5 25.4 - - + +
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Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B THR* 3.1 24.6 + - - +
164B ARG* 3.1 22.4 + - - +
166B ALA* 1.3 77.6 - - - +
168B LEU* 1.3 55.6 + - + +
170B ARG* 3.0 5.9 + - - +
171B SER* 2.7 38.9 + - - -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ARG* 3.0 44.6 + - + +
165B MET* 4.1 4.5 - - - +
167B ASP* 1.3 80.3 - - + +
169B ARG* 1.3 61.6 + - - +
171B SER* 3.5 5.4 - - - +
172B GLY 3.3 1.9 + - - -
173B VAL* 3.3 36.7 + - + -
174B LEU* 3.0 59.5 + - + +
177B LEU* 4.2 0.7 - - + -
226B GLN* 3.7 26.5 - - + +
227B VAL* 4.0 11.4 - - + -
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU* 3.8 12.9 + - - +
90B HIS 4.1 0.2 + - - -
91B ILE 2.7 31.9 + - - -
92B GLY* 4.1 5.3 - - - -
165B MET 3.0 20.4 + - - +
166B ALA* 3.4 22.7 - - - +
167B ASP 3.1 0.2 - - - -
168B LEU* 1.3 78.6 - - - +
170B ARG* 1.3 97.5 + - - +
171B SER 3.5 0.2 + - - -
172B GLY* 3.7 7.8 + - - -
174B LEU 3.8 10.0 - - - +
175B PRO* 5.2 3.6 - - + +
177B LEU* 3.1 31.4 - - + +
178B ARG* 3.7 18.8 - - - +
179B PRO* 3.9 20.3 + - - +
378B TYR* 5.2 0.4 + - - -
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Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU* 2.6 42.0 + - - -
90B HIS* 2.7 46.5 + - - -
166B ALA* 2.8 35.3 + - - +
167B ASP* 3.8 4.3 - - - +
169B ARG* 1.3 100.2 - - - +
171B SER* 1.3 63.4 + - - +
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP 2.7 22.1 + - - -
168B LEU* 3.3 7.1 + - - +
170B ARG* 1.3 75.4 - - - +
172B GLY* 1.3 65.4 + - - +
173B VAL* 3.1 28.2 + - - +
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Residues in contact with GLY 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU 3.3 4.9 + - - -
169B ARG 3.7 6.2 + - - -
170B ARG 3.4 2.0 - - - -
171B SER* 1.3 79.6 + - - +
173B VAL* 1.3 66.0 + - - +
174B LEU 3.3 2.5 - - - -
175B PRO* 3.2 27.0 - - - +
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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) + - + + + + + -
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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