Contacts of the helix formed by residues 178 - 195 (chain Q) in PDB entry 3H1J
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 THR 178 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166Q ASN* 3.0 10.3 - - - +
176Q PRO* 2.5 24.2 + - + +
177Q ALA* 1.3 75.2 - - - +
179Q MET* 1.3 66.5 + - - +
181Q GLN* 3.0 24.1 + - - +
182Q ILE* 2.9 20.1 + - - +
13U LEU* 3.7 15.7 - - + -
14U VAL 3.7 9.9 - - - +
15U ASP* 3.2 41.0 + - - -
16U PRO* 3.9 10.1 - - + +
77U LEU* 4.3 1.2 - - - +
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Residues in contact with MET 179 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131Q LEU 4.4 10.5 - - - +
132Q THR* 4.2 30.5 - - + +
134Q TYR* 5.9 2.7 - - + -
162Q PRO* 5.2 8.3 - - + -
164Q ILE* 2.9 43.0 - - + +
165Q TYR* 4.4 7.6 - - + -
166Q ASN* 3.0 28.0 + - - +
177Q ALA 3.7 1.4 + - - -
178Q THR* 1.3 70.2 - - - +
180Q SER* 1.3 58.5 + - - +
182Q ILE* 3.1 11.2 + - - +
183Q ALA* 3.0 22.7 + - - +
15U ASP* 3.5 8.4 + - - +
17U LEU* 4.7 9.2 - - - -
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Residues in contact with SER 180 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128Q PHE* 3.5 17.8 - - - -
132Q THR* 4.3 4.7 - - - -
179Q MET* 1.3 75.9 - - - +
181Q GLN* 1.3 68.5 + - - +
183Q ALA* 3.2 7.1 + - - -
184Q LYS* 2.8 25.3 + - - +
15U ASP* 2.9 24.8 + - - -
17U LEU* 3.8 25.2 - - - +
73U LEU* 4.0 4.8 - - - +
77U LEU* 3.3 20.5 - - - +
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Residues in contact with GLN 181 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q ARG* 3.6 1.6 - - - +
171Q TYR* 3.9 5.8 - - + -
175Q THR* 3.5 26.5 - - + +
176Q PRO 3.5 16.4 - - - +
178Q THR* 3.0 26.3 + - - +
180Q SER* 1.3 80.9 + - - +
182Q ILE* 1.3 65.2 + - - +
184Q LYS* 3.3 5.6 + - - +
185Q ASP* 2.8 58.8 + - - +
77U LEU* 3.5 16.4 - - + +
78U LYS* 2.9 37.0 + - - +
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Residues in contact with ILE 182 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Q VAL* 3.6 28.9 - - + -
164Q ILE* 3.5 23.1 - - + -
165Q TYR 4.2 6.3 - - - +
168Q ILE* 3.5 19.3 - - + -
169Q LEU* 3.3 28.9 - - + -
171Q TYR* 3.1 21.7 + - + +
177Q ALA 4.0 15.9 - - - +
178Q THR 2.9 14.7 + - - +
179Q MET* 3.3 7.6 - - - +
180Q SER 3.1 0.2 - - - -
181Q GLN* 1.3 76.0 - - - +
183Q ALA* 1.3 65.2 + - - +
185Q ASP* 2.8 14.7 + - - +
186Q VAL* 2.9 12.0 + - - +
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Residues in contact with ALA 183 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128Q PHE* 3.4 24.5 - - + -
131Q LEU* 4.2 10.8 - - + -
132Q THR* 3.8 16.2 - - + -
164Q ILE* 3.9 12.1 - - + -
179Q MET 3.0 12.9 + - - +
180Q SER 3.6 3.1 - - - +
182Q ILE* 1.3 75.9 - - - +
184Q LYS* 1.3 57.3 + - - +
186Q VAL* 3.2 11.7 - - - +
187Q CYS* 2.9 34.5 + - - +
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Residues in contact with LYS 184 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q TRP* 3.7 7.2 - - + -
13Q SER* 5.6 5.6 + - - +
22Q ASP* 4.0 7.7 + - - +
25Q SER* 3.3 23.4 + - - +
128Q PHE* 3.3 15.1 - - + -
180Q SER 2.8 16.8 + - - +
181Q GLN* 3.5 7.9 - - - +
183Q ALA* 1.3 77.0 - - - +
185Q ASP* 1.3 67.0 + - - +
188Q THR* 2.9 36.7 + - - -
74U PHE* 3.8 33.2 - - + -
77U LEU* 4.2 15.0 - - + -
78U LYS* 2.8 36.7 + - - +
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Residues in contact with ASP 185 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q SER* 2.6 31.5 + - - +
28Q ARG* 2.8 29.6 + - + -
29Q GLY* 3.2 24.6 - - - +
32Q VAL* 4.9 0.2 - - + -
171Q TYR* 2.9 23.4 + - - +
181Q GLN* 2.8 31.7 + - - +
182Q ILE 2.8 7.7 + - - +
184Q LYS* 1.3 78.2 + - - +
186Q VAL* 1.3 59.5 + - - +
188Q THR* 3.2 1.7 + - - -
189Q PHE 2.9 22.3 + - - -
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Residues in contact with VAL 186 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q GLY* 3.6 15.9 - - - +
32Q VAL* 3.7 31.8 - - + +
33Q TYR* 4.5 4.0 - - + +
37Q CYS* 4.1 6.1 - - - -
131Q LEU* 3.8 20.2 - - + -
182Q ILE* 2.9 6.9 + - + +
183Q ALA* 3.2 23.6 - - - +
185Q ASP* 1.3 73.5 - - - +
187Q CYS* 1.3 66.2 + - - +
189Q PHE* 3.1 2.5 + - + +
190Q LEU* 2.7 42.2 + - + +
501Q HEC 3.9 22.7 - - + -
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Residues in contact with CYS 187 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q TRP* 3.6 20.2 - - + -
117Q VAL* 4.6 0.4 - - - +
124Q GLU* 3.7 15.0 - - + +
127Q VAL* 3.4 22.4 - - - -
128Q PHE* 3.3 39.9 - - - -
131Q LEU* 4.7 1.3 - - - -
183Q ALA 2.9 22.8 + - - +
186Q VAL* 1.3 75.3 - - - +
188Q THR* 1.3 67.0 + - - +
190Q LEU* 3.0 20.2 + - - +
191Q ARG* 3.1 13.0 + - - +
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Residues in contact with THR 188 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q TRP* 3.9 14.6 - - - -
13Q SER* 6.0 0.4 - - - +
14Q HIS* 4.1 15.7 - - - +
21Q LEU* 4.1 12.2 - - + +
22Q ASP* 4.2 6.1 - - + +
25Q SER* 3.7 21.0 + - - +
26Q VAL* 3.5 30.4 - - + +
184Q LYS* 2.9 25.4 + - - +
185Q ASP 3.2 5.6 + - - -
187Q CYS* 1.3 79.6 - - - +
189Q PHE* 1.3 62.7 + - - +
191Q ARG* 3.4 4.5 + - - +
192Q TRP* 3.4 13.2 + - - +
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Residues in contact with PHE 189 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Q VAL* 3.4 31.6 - - + +
29Q GLY* 3.6 11.9 - - - -
30Q PHE* 3.5 35.4 - + + -
33Q TYR* 3.7 25.4 - + + -
43Q MET* 3.1 39.7 - - + -
51Q LEU* 4.7 4.0 - - + -
91Q PHE* 4.4 1.1 - + - -
185Q ASP 2.9 13.0 + - - +
186Q VAL* 3.2 9.2 - - + +
188Q THR* 1.3 73.9 - - - +
190Q LEU* 1.3 68.8 + - + +
191Q ARG 3.0 3.8 - - - -
192Q TRP* 2.9 30.2 + + - +
193Q ALA* 2.8 26.5 + - + +
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Residues in contact with LEU 190 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q TYR* 5.3 2.5 - - + -
43Q MET* 4.9 2.0 - - - -
113Q LEU* 4.1 33.8 - - + +
114Q SER 4.6 1.4 - - - +
116Q ILE* 3.6 19.9 - - + +
117Q VAL* 3.6 19.1 + - + +
127Q VAL* 4.1 19.1 - - + -
186Q VAL* 2.7 27.3 + - + +
187Q CYS* 3.0 9.6 + - - +
189Q PHE* 1.3 87.3 - - + +
191Q ARG* 1.3 60.5 + - - +
193Q ALA* 3.9 8.2 - - + +
194Q ALA* 3.3 22.0 + - - +
501Q HEC 3.9 24.2 - - + -
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Residues in contact with ARG 191 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249P ASN* 5.5 0.8 - - - +
14Q HIS* 3.8 8.1 - - + +
21Q LEU* 3.6 21.8 - - + -
117Q VAL* 3.2 30.3 + - - +
118Q ASN* 3.4 15.0 + - - -
123Q GLY* 4.7 2.4 - - - -
124Q GLU* 2.8 42.4 + - - +
187Q CYS 3.1 8.9 + - - +
188Q THR 3.5 9.9 - - - +
189Q PHE 3.0 0.4 - - - -
190Q LEU* 1.3 75.9 - - - +
192Q TRP* 1.3 66.7 + - - +
194Q ALA* 3.1 3.3 + - - +
195Q GLU* 2.8 58.2 + - - +
198Q HIS* 4.1 13.2 - - + -
201Q ARG* 5.4 0.8 - - - +
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Residues in contact with TRP 192 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Q LEU* 3.5 30.3 - - + +
23Q HIS* 5.9 2.2 - + - -
26Q VAL* 3.9 17.5 - - + -
46Q VAL* 3.8 30.5 - - + -
50Q ASN* 3.5 35.0 - - + -
51Q LEU* 4.4 10.8 - - + -
54Q VAL* 3.3 32.7 - - + +
55Q THR* 5.7 0.7 - - + -
188Q THR 3.4 3.4 + - - +
189Q PHE* 2.9 36.4 + + - +
191Q ARG* 1.3 79.5 - - - +
193Q ALA* 1.3 87.7 + - + +
195Q GLU 3.1 3.3 + - - +
196Q PRO* 3.0 59.1 + - + +
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Residues in contact with ALA 193 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P ARG* 2.6 36.6 + - - -
43Q MET* 3.8 30.7 - - + -
46Q VAL* 4.3 5.3 - - + +
113Q LEU 4.9 0.2 - - - +
114Q SER 3.5 7.8 - - - +
189Q PHE* 2.8 16.8 + - + +
190Q LEU* 3.9 12.3 - - + +
192Q TRP* 1.3 94.6 - - + +
194Q ALA* 1.3 53.0 + - - +
196Q PRO* 3.9 0.8 - - - +
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Residues in contact with ALA 194 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P ARG* 3.8 4.3 + - - +
114Q SER 3.2 14.8 + - - +
115Q TYR* 3.8 31.4 - - - -
117Q VAL* 3.6 20.9 - - + -
118Q ASN* 3.9 16.0 + - - +
190Q LEU 3.3 15.5 + - - +
191Q ARG 3.1 4.0 + - - +
193Q ALA* 1.3 78.8 - - - +
195Q GLU* 1.3 63.3 + - + +
196Q PRO* 4.0 0.4 - - - +
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Residues in contact with GLU 195 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248P PRO* 5.8 2.1 - - - +
249P ASN* 4.4 8.0 + - - -
118Q ASN* 3.9 11.4 + - - +
191Q ARG* 2.8 47.2 + - - +
192Q TRP* 3.1 7.4 + - - -
194Q ALA* 1.3 84.6 - - + +
196Q PRO* 1.3 59.3 - - - +
197Q GLU* 3.1 22.4 - - - +
198Q HIS* 2.7 41.7 + - + +
201Q ARG* 2.7 38.1 + - - -
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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
------------------------------------------------------------
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