Contacts of the helix formed by residues 203 - 220 (chain Q) in PDB entry 2QJK
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 SER 203 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Q ASP* 3.7 17.7 - - - -
192Q ASP* 5.2 1.5 + - - -
201Q ASP* 2.6 26.3 + - - +
202Q ALA* 1.3 76.4 - - - +
204Q VAL* 1.3 68.4 + - - +
205Q HIS* 3.8 11.5 + - - +
206Q ALA* 2.6 27.2 + - - +
207Q MET* 3.2 8.4 + - - +
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Residues in contact with VAL 204 (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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135Q LEU 4.9 10.1 - - - +
136Q THR* 5.4 6.7 - - - +
189Q LEU* 3.3 27.4 - - + +
190Q MET* 3.2 20.0 - - - +
191Q ASP* 2.9 47.2 + - - +
202Q ALA 3.5 2.8 + - - -
203Q SER* 1.3 70.7 - - - +
205Q HIS* 1.3 62.5 + - - +
207Q MET* 4.5 4.9 - - - -
208Q ALA* 3.2 24.1 + - + +
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Residues in contact with HIS 205 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q VAL* 6.3 0.2 - - - +
132Q TYR* 3.2 35.4 + - - +
136Q THR* 5.4 4.3 - - - -
201Q ASP* 5.6 0.2 + - - -
203Q SER* 2.7 15.1 + - - +
204Q VAL* 1.3 76.8 - - - +
206Q ALA* 1.3 69.1 + - + +
208Q ALA* 4.9 0.4 - - - -
209Q GLU* 3.2 43.4 + - - +
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Residues in contact with ALA 206 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196Q TYR* 5.2 0.2 - - + -
200Q HIS* 5.3 2.7 - - + -
201Q ASP* 3.6 32.5 - - - +
203Q SER* 2.6 21.4 + - - +
205Q HIS* 1.3 81.6 + - - +
207Q MET* 1.3 68.7 + - - +
209Q GLU* 2.7 20.3 + - - +
210Q ASP* 2.8 23.1 + - - +
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Residues in contact with MET 207 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q VAL* 4.4 18.6 - - + +
35Q VAL* 4.7 3.8 - - + -
189Q LEU* 3.7 22.4 - - + -
190Q MET 4.5 6.3 - - - +
193Q LEU* 4.1 16.4 - - + -
194Q VAL* 3.3 46.4 - - + +
196Q TYR* 3.9 20.2 + - + +
202Q ALA* 3.6 28.9 - - + +
203Q SER 3.2 7.1 + - - +
204Q VAL* 4.0 9.4 - - - +
206Q ALA* 1.3 75.7 - - - +
208Q ALA* 1.3 64.6 + - - +
210Q ASP* 3.0 2.8 + - - +
211Q VAL* 2.8 28.5 + - - +
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Residues in contact with ALA 208 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132Q TYR* 3.8 17.3 - - + +
135Q LEU* 3.8 26.9 - - + -
136Q THR* 4.4 4.7 - - - +
189Q LEU* 3.5 9.5 - - + +
204Q VAL* 3.2 16.5 + - + +
205Q HIS 3.8 3.8 - - - +
206Q ALA 3.1 0.6 - - - -
207Q MET* 1.3 76.6 - - - +
209Q GLU* 1.3 65.7 + - - +
211Q VAL* 3.3 7.9 - - - +
212Q SER* 2.8 30.2 + - - -
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Residues in contact with GLU 209 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q VAL* 4.0 19.2 - - + +
10Q PRO 5.3 3.8 - - - +
11Q PHE* 3.1 42.5 - - + -
24Q GLN* 3.6 17.3 + - - +
132Q TYR* 3.5 13.8 - - + -
205Q HIS* 3.2 34.8 + - - +
206Q ALA* 2.7 15.3 + - - +
208Q ALA* 1.3 75.6 - - - +
210Q ASP* 1.3 64.1 + - - +
212Q SER* 4.5 0.2 - - - -
213Q ALA* 3.3 6.4 + - - +
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Residues in contact with ASP 210 (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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24Q GLN* 2.8 43.9 + - + +
27Q ARG* 3.2 27.2 + - - -
28Q GLY* 4.1 14.8 - - - +
196Q TYR* 3.0 26.6 + - - +
200Q HIS* 5.2 1.0 - - - -
206Q ALA* 2.8 21.7 + - - +
207Q MET 3.5 4.5 - - - +
209Q GLU* 1.3 71.6 - - - +
211Q VAL* 1.3 55.9 + - - +
212Q SER 2.7 5.4 + - - -
213Q ALA* 2.7 27.5 + - - +
214Q PHE* 2.8 9.9 + - - +
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Residues in contact with VAL 211 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q GLY* 3.8 15.1 - - - +
31Q VAL* 3.8 31.9 - - + -
32Q TYR* 3.9 16.8 - - + +
36Q CYS* 3.9 14.8 - - - -
135Q LEU* 3.6 25.1 - - + -
207Q MET 2.8 17.1 + - - +
208Q ALA* 3.3 11.9 - - - +
210Q ASP* 1.3 72.4 - - - +
212Q SER* 1.3 60.9 + - - +
214Q PHE* 3.3 2.0 - - + +
215Q LEU* 2.8 38.6 + - + +
301Q HEM 4.0 10.5 - - + -
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Residues in contact with SER 212 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q PHE* 3.8 16.8 - - - -
104Q ALA* 5.2 0.5 - - - +
128Q PRO* 4.0 13.8 - - - +
131Q ILE* 3.9 12.0 - - - +
132Q TYR* 3.5 25.1 + - - +
135Q LEU* 4.5 0.3 - - - +
208Q ALA 2.8 18.8 + - - -
209Q GLU 3.5 4.9 - - - -
210Q ASP 2.7 4.4 + - - -
211Q VAL* 1.3 74.9 - - - +
213Q ALA* 1.3 53.6 + - - -
215Q LEU* 2.6 29.7 + - - +
216Q MET* 2.6 18.8 + - - +
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Residues in contact with ALA 213 (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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11Q PHE* 4.2 5.5 - - + -
13Q PHE* 3.7 27.4 - - + -
20Q PHE* 3.7 2.5 - - + -
24Q GLN* 3.7 32.8 - - + +
25Q LEU* 3.2 15.0 - - + +
209Q GLU 3.3 4.8 + - - +
210Q ASP 2.7 12.2 + - - +
212Q SER* 1.3 75.5 - - - +
214Q PHE* 1.3 61.3 + - - +
216Q MET* 3.2 3.8 + - - +
217Q TRP 3.1 17.0 + - - -
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Residues in contact with PHE 214 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q LEU* 3.6 27.5 - - - +
28Q GLY* 3.8 20.0 - - - -
29Q LEU* 3.8 30.5 - - + -
32Q TYR* 3.5 26.0 - + + -
42Q MET* 3.2 40.4 - - + -
50Q LEU* 4.7 3.1 - - + -
56Q PRO* 4.9 2.2 - - + -
89Q PHE* 5.0 2.5 - + - -
210Q ASP 2.8 6.2 + - - +
211Q VAL* 3.3 10.5 - - + +
213Q ALA* 1.3 75.6 - - - +
215Q LEU* 1.3 65.1 + - + +
217Q TRP* 2.8 40.9 + + - +
218Q ALA* 2.7 32.9 + - + +
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Residues in contact with LEU 215 (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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32Q TYR* 5.1 3.6 - - + -
36Q CYS* 5.6 0.4 - - - -
42Q MET* 4.2 17.5 - - - -
100Q LEU* 3.7 54.7 - - + +
101Q SER 4.8 0.3 - - - +
103Q MET* 5.5 0.9 - - + -
104Q ALA* 3.7 7.0 + - + +
131Q ILE* 4.4 27.4 - - + -
211Q VAL* 2.8 19.6 + - + +
212Q SER* 2.6 15.0 + - - +
214Q PHE* 1.3 81.5 - - + +
216Q MET* 1.3 59.1 + - - -
218Q ALA* 3.5 4.5 - - + +
219Q ALA* 3.2 22.5 + - - +
301Q HEM 4.0 20.6 - - + -
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Residues in contact with MET 216 (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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13Q PHE* 3.5 37.2 - - + -
20Q PHE* 4.0 9.4 - - + -
104Q ALA* 3.7 26.9 - - + +
105Q LYS* 5.6 3.8 - - + -
128Q PRO* 4.3 17.3 - - + -
212Q SER 2.6 14.0 + - - +
213Q ALA 3.3 9.6 - - - +
214Q PHE 3.0 0.2 - - - -
215Q LEU* 1.3 69.2 - - - +
217Q TRP* 1.3 67.0 + - - +
219Q ALA* 3.2 3.1 + - - +
220Q GLU* 2.9 31.2 + - + +
223Q LEU* 4.4 13.5 - - + -
257Q BGL 3.9 22.9 - - - +
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Residues in contact with TRP 217 (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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85P ARG* 6.3 0.2 - - - -
20Q PHE* 3.2 31.1 - + + -
25Q LEU* 3.9 12.1 - - + -
45Q VAL* 4.7 9.2 - - + -
49Q SER* 3.5 48.0 - - - -
50Q LEU* 4.1 10.5 - - + -
52Q GLU* 5.7 1.1 + - + -
54Q GLY 3.8 7.8 + - - -
55Q GLY* 3.5 22.3 - - - +
56Q PRO* 3.6 22.2 - - + -
213Q ALA 3.1 4.2 + - - +
214Q PHE* 2.8 39.5 + + - +
216Q MET* 1.3 75.6 - - - +
218Q ALA* 1.3 89.0 + - + +
220Q GLU 2.9 1.5 + - - +
221Q PRO* 2.8 64.5 + - + +
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Residues in contact with ALA 218 (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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85P ARG* 2.8 31.4 + - - -
42Q MET* 4.1 25.6 - - - -
45Q VAL* 3.9 7.5 - - + +
101Q SER 3.8 6.3 - - - +
214Q PHE* 2.7 19.0 + - + +
215Q LEU* 3.5 19.7 - - + +
217Q TRP* 1.3 93.0 - - + +
219Q ALA* 1.3 57.1 + - - +
221Q PRO* 3.7 0.3 - - - +
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Residues in contact with ALA 219 (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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81P GLU* 4.5 2.6 - - - +
85P ARG* 3.8 7.8 + - - +
101Q SER 3.1 21.1 - - - +
102Q LEU* 3.7 27.7 - - + +
104Q ALA* 4.6 2.0 - - + +
105Q LYS* 3.8 29.4 + - + +
215Q LEU 3.2 12.3 + - - +
216Q MET* 3.8 3.1 - - - +
217Q TRP 3.0 0.6 - - - -
218Q ALA* 1.3 80.3 - - - +
220Q GLU* 1.3 59.0 + - - +
221Q PRO* 3.2 9.3 - - - +
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Residues in contact with GLU 220 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84P MET* 5.0 3.1 - - - +
91P PHE* 5.5 3.1 - - - +
95P TYR* 2.7 29.3 + - - -
272P ASN* 4.2 2.5 + - - +
20Q PHE* 4.0 4.9 - - - -
105Q LYS* 3.8 28.4 + - + -
216Q MET* 2.9 21.9 + - + +
217Q TRP 2.9 5.8 + - - -
219Q ALA* 1.3 75.6 - - - +
221Q PRO* 1.3 66.1 - - - +
222Q LYS* 3.2 9.2 + - - +
223Q LEU* 2.9 35.5 + - + +
226Q ARG* 2.3 35.7 + - - +
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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