Contacts of the helix formed by residues 177 - 193 (chain B) in PDB entry 1QN6
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 MET 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLU* 5.4 0.2 - - - -
114B LYS* 5.9 3.8 - - - +
115B ILE* 5.9 1.6 - - + +
118B ILE* 3.5 5.8 - - - -
175B ALA* 3.4 13.7 - - - +
176B LYS* 1.3 98.0 - - + +
178B ARG* 1.3 64.6 + - - +
179B ASP* 4.2 10.8 - - + +
180B GLU* 3.1 29.2 + - + +
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Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.5 26.2 - - + +
86B SER* 4.3 10.9 - - - -
87B GLU* 2.9 38.9 + - - +
118B ILE* 3.3 13.3 - - + +
177B MET* 1.3 71.6 - - - +
179B ASP* 1.3 69.3 + - - +
181B THR* 3.1 21.0 + - - +
182B TYR* 3.1 49.1 + - + -
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Residues in contact with ASP 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 3.0 35.2 + - - +
177B MET* 3.1 8.2 - - + +
178B ARG* 1.3 84.1 - - - +
180B GLU* 1.3 58.4 + - + +
182B TYR* 3.5 13.9 + - - +
183B LYS* 2.9 29.2 + - - +
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Residues in contact with GLU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PRO* 3.6 22.0 - - + +
159B LYS 6.1 0.4 - - - -
160B ILE* 3.8 10.7 - - + +
175B ALA* 3.5 8.7 - - + -
176B LYS* 2.9 31.9 + - - +
177B MET* 3.1 26.3 + - + +
179B ASP* 1.3 76.5 - - + +
181B THR* 1.3 60.1 + - - +
183B LYS* 4.3 5.6 - - - -
184B ALA* 2.8 32.6 + - - +
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Residues in contact with THR 181 (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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23B PRO* 4.2 20.6 - - + +
25B LEU* 4.2 16.6 - - + -
118B ILE* 3.9 16.6 + - - +
120B GLY* 4.5 8.1 - - - +
160B ILE* 5.0 0.2 - - - -
172B ILE* 4.1 31.1 + - + +
175B ALA* 3.6 19.2 - - - +
178B ARG* 3.2 12.9 + - - -
180B GLU* 1.3 79.5 - - - +
182B TYR* 1.3 60.0 + - + +
184B ALA* 3.7 2.1 - - - +
185B PHE* 3.1 28.8 + - - +
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Residues in contact with TYR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 4.1 15.0 - - + +
17B HIS* 3.2 39.5 - + + +
22B VAL* 4.0 9.1 - - + +
23B PRO* 3.8 35.0 + - + -
25B LEU* 4.8 12.2 - - + +
178B ARG* 3.1 62.2 + - + +
179B ASP* 3.6 20.4 - - - +
180B GLU 3.2 0.2 - - - -
181B THR* 1.3 76.5 - - - +
183B LYS* 1.3 59.4 + - - +
185B PHE* 3.3 4.6 + - - +
186B GLU* 2.9 35.9 + - - +
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PRO* 3.8 21.3 - - + -
179B ASP 2.9 19.0 + - - +
180B GLU* 3.9 5.2 - - - +
182B TYR* 1.3 72.4 - - - +
184B ALA* 1.3 55.6 + - - +
186B GLU* 3.1 9.0 + - + +
187B ASN* 2.7 60.3 + - - +
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Residues in contact with ALA 184 (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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155B MET* 3.4 24.1 - - - +
158B PRO* 4.0 1.7 - - + +
160B ILE* 3.6 34.3 - - + -
162B LEU* 4.4 5.8 - - + -
172B ILE* 4.0 5.8 - - + -
180B GLU 2.8 19.1 + - - +
181B THR 3.7 4.9 - - - +
183B LYS* 1.3 76.0 - - - +
185B PHE* 1.3 56.6 + - - +
187B ASN* 3.1 4.3 + - - +
188B ILE* 2.9 25.3 + - - +
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Residues in contact with PHE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 3.3 24.7 - - - -
21B ILE* 3.8 31.2 - - + -
23B PRO* 3.9 15.0 - - + -
122B CYS* 3.5 24.5 - - - -
124B VAL* 3.8 19.7 - - + -
162B LEU* 4.6 0.8 - - - +
170B ILE* 4.6 5.2 - - + -
172B ILE* 3.8 15.7 - - + -
181B THR 3.1 15.2 + - - +
182B TYR 3.8 2.5 - - - +
184B ALA* 1.3 79.6 - - - +
186B GLU* 1.3 69.4 + - + +
188B ILE* 3.1 15.9 + - + +
189B TYR* 2.9 54.1 + + + +
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Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A SER* 5.5 0.5 - - - -
16B LYS 4.3 8.1 - - - +
17B HIS* 3.4 16.3 + - - +
18B PRO* 3.5 27.5 - - + +
19B SER* 2.6 45.6 + - - -
21B ILE 3.5 9.2 - - - +
182B TYR 2.9 26.4 + - - +
183B LYS* 3.8 10.3 - - + +
185B PHE* 1.3 77.7 - - + +
187B ASN* 1.3 59.3 + - - +
189B TYR* 4.6 2.4 - - - -
190B PRO* 3.2 23.2 - - - +
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Residues in contact with ASN 187 (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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198A ILE* 4.3 3.6 - - - +
155B MET* 3.6 17.9 - - + -
157B VAL 3.0 28.1 + - - -
158B PRO* 3.7 8.3 - - - +
183B LYS* 2.7 41.7 + - - +
184B ALA 3.3 5.6 - - - +
185B PHE 3.1 0.2 - - - -
186B GLU* 1.3 80.5 - - - +
188B ILE* 1.3 61.5 + - - +
190B PRO* 3.7 11.9 - - - +
191B VAL* 4.0 10.6 - - - +
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 5.4 0.4 - - + -
153B TYR* 3.8 45.1 - - + +
155B MET* 4.1 5.6 - - + -
162B LEU* 3.7 25.1 - - + -
164B ILE* 4.0 11.4 - - + -
170B ILE* 5.2 2.2 - - + -
184B ALA 2.9 10.7 + - - +
185B PHE* 3.1 18.4 + - + +
187B ASN* 1.3 78.3 - - - +
189B TYR* 1.3 68.8 + - - +
190B PRO 3.5 0.2 - - - -
191B VAL* 3.0 20.3 + - + +
192B LEU* 2.9 52.2 + - + +
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Residues in contact with TYR 189 (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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190A PRO 4.5 1.3 + - - -
193A SER 4.5 1.1 - - - -
194A GLU* 3.3 58.1 + - + +
19B SER* 3.3 32.3 + - - -
21B ILE* 3.9 24.7 - - + +
124B VAL* 3.9 14.4 + - + -
125B LYS* 5.5 0.9 + - - -
126B PHE* 4.1 22.2 - + - -
185B PHE* 2.9 38.9 + + + +
186B GLU* 4.3 3.8 - - - +
188B ILE* 1.3 78.6 - - - +
190B PRO* 1.3 69.5 - - + +
191B VAL 3.1 0.3 + - - -
192B LEU* 3.1 7.3 + - - +
193B SER* 3.1 21.8 + - - -
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Residues in contact with PRO 190 (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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129A ARG* 4.1 1.9 + - - -
193A SER 3.7 12.6 - - - +
194A GLU 3.3 20.1 - - - +
196A ARG* 3.7 32.6 - - + +
198A ILE* 3.6 23.5 - - + +
186B GLU 3.2 18.8 - - - +
187B ASN* 3.7 5.8 - - - +
188B ILE 3.8 0.4 - - - -
189B TYR* 1.3 95.6 - - + +
191B VAL* 1.3 57.4 + - - +
193B SER* 3.1 12.5 + - - -
194B GLU* 3.5 14.2 - - - +
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Residues in contact with VAL 191 (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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198A ILE* 3.5 24.5 - - + -
133B LEU* 3.5 30.7 - - + -
137B HIS* 3.6 28.3 - - + +
153B TYR* 5.4 2.0 - - - +
187B ASN 4.0 10.3 - - - +
188B ILE* 3.0 21.4 + - + +
190B PRO* 1.3 75.8 - - - +
192B LEU* 1.3 60.7 + - - +
194B GLU* 2.8 37.3 + - - +
195B PHE* 3.3 11.2 - - + -
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Residues in contact with LEU 192 (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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124B VAL* 3.7 26.7 - - + -
126B PHE* 3.6 16.9 - - + -
128B ILE* 4.0 15.2 - - + +
133B LEU* 4.0 26.2 - - + -
164B ILE* 4.1 13.0 - - + -
170B ILE* 3.7 20.0 - - + -
188B ILE* 2.9 48.4 + - + +
189B TYR* 3.5 7.2 - - - +
191B VAL* 1.3 78.5 - - - +
193B SER* 1.3 60.6 - - - +
195B PHE* 3.0 18.9 + - - +
196B ARG 3.5 7.8 + - - -
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 3.2 13.1 + - - -
194A GLU* 2.7 49.4 + - - -
195A PHE* 4.1 13.3 - - - -
126B PHE* 3.9 12.7 - - - -
189B TYR 3.1 7.8 + - - -
190B PRO 3.1 13.9 + - - -
192B LEU* 1.3 75.6 - - - +
194B GLU* 1.3 59.1 + - - +
195B PHE 3.4 0.2 + - - -
196B ARG* 3.7 15.1 + - - +
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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
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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