Contacts of the helix formed by residues 21 - 35 (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 ASP 21 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12Q SER* 3.9 17.8 + - - +
19Q THR 3.7 0.4 + - - -
20Q PHE* 1.3 73.7 - - - +
22Q GLN* 1.3 67.7 + - - +
23Q HIS* 2.9 14.3 + - - +
24Q GLN* 2.6 45.9 + - + +
25Q LEU* 3.0 24.1 + - - +
27Q ARG* 4.9 3.1 + - - -
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Residues in contact with GLN 22 (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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20Q PHE 3.9 3.6 + - - -
21Q ASP* 1.3 72.9 + - - +
23Q HIS* 1.3 74.9 + - + +
25Q LEU* 3.3 5.5 + - - +
26Q GLN* 3.0 31.6 + - - +
55Q GLY 3.8 13.8 + - - +
56Q PRO* 3.2 26.4 - - - +
57Q GLU* 3.6 34.4 + - - +
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Residues in contact with HIS 23 (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 ASP* 2.9 14.9 + - - +
22Q GLN* 1.3 80.8 - - + +
24Q GLN* 1.3 67.5 + - - +
26Q GLN* 2.8 23.1 + - - +
27Q ARG* 2.7 41.3 + - + +
198Q ASP* 6.1 4.3 - - - -
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Residues in contact with GLN 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q PHE* 4.9 5.3 - - - -
12Q SER* 3.8 20.3 + - - -
21Q ASP* 2.6 29.5 + - + +
23Q HIS* 1.3 69.3 - - - +
25Q LEU* 1.3 55.7 + - + +
27Q ARG* 2.8 27.6 + - - +
28Q GLY* 2.7 32.4 + - - -
209Q GLU* 3.6 27.9 + - - +
210Q ASP* 2.8 39.5 + - - +
213Q ALA* 3.7 22.3 - - + +
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Residues in contact with LEU 25 (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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20Q PHE* 3.4 39.9 - - + -
21Q ASP 3.0 17.2 + - - +
22Q GLN 3.4 7.4 - - - +
24Q GLN* 1.3 75.3 - - + +
26Q GLN* 1.3 57.0 + - - +
28Q GLY* 3.4 1.4 + - - +
29Q LEU* 2.9 28.2 + - - +
55Q GLY* 3.6 29.8 - - - +
56Q PRO* 3.9 14.7 - - + +
213Q ALA* 3.2 37.9 - - + +
214Q PHE* 3.6 17.1 - - + +
217Q TRP* 3.9 10.3 - - + -
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Residues in contact with GLN 26 (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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22Q GLN* 3.0 30.7 + - - +
23Q HIS* 2.8 30.6 + - - +
25Q LEU* 1.3 74.2 - - - +
27Q ARG* 1.3 65.4 + - + +
29Q LEU* 3.0 19.8 + - - +
30Q GLN* 3.1 10.4 + - - +
56Q PRO* 2.8 30.4 + - + +
57Q GLU 4.4 1.0 + - - -
58Q LEU* 3.5 29.9 - - + +
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Residues in contact with ARG 27 (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 ASP* 4.9 2.6 + - - -
23Q HIS* 2.7 37.9 + - + +
24Q GLN* 2.8 25.3 + - - +
26Q GLN* 1.3 71.2 - - + +
28Q GLY* 1.3 55.7 + - - +
30Q GLN* 2.8 34.4 + - - +
31Q VAL* 3.1 9.7 + - - +
196Q TYR* 3.3 52.3 - - + +
198Q ASP* 5.1 10.1 + - - +
200Q HIS* 3.9 35.5 + - - -
210Q ASP* 3.2 28.6 + - - +
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Residues in contact with GLY 28 (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 2.7 16.1 + - - -
25Q LEU 3.6 4.3 - - - -
27Q ARG* 1.3 72.4 - - - +
29Q LEU* 1.3 54.0 + - - +
31Q VAL* 2.7 27.9 + - - +
32Q TYR* 2.7 13.0 + - - +
210Q ASP* 4.1 1.2 - - - +
211Q VAL* 3.8 20.6 - - - +
214Q PHE* 3.8 19.7 - - - -
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Residues in contact with LEU 29 (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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25Q LEU 2.9 14.3 + - - +
26Q GLN* 3.4 11.0 - - - +
28Q GLY* 1.3 73.9 - - - +
30Q GLN* 1.3 54.2 + - - +
32Q TYR* 3.4 2.1 + - + +
33Q THR* 2.6 40.2 + - - +
50Q LEU* 3.6 31.4 - - + -
56Q PRO* 5.1 4.7 - - + -
58Q LEU* 4.0 25.6 - - + -
66Q TYR* 3.2 36.6 - - + +
89Q PHE* 4.5 4.5 - - + -
214Q PHE* 3.8 31.4 - - + -
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Residues in contact with GLN 30 (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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26Q GLN 3.1 8.3 + - - +
27Q ARG* 2.8 15.4 + - - +
29Q LEU* 1.3 80.2 - - - +
31Q VAL* 1.3 51.4 + - - +
33Q THR* 3.3 4.6 + - - -
34Q GLU* 2.7 72.6 + - + +
194Q VAL* 3.1 25.3 - - + +
195Q GLU* 3.3 19.5 + - - +
196Q TYR* 3.5 19.6 - - - -
197Q ALA* 4.6 3.1 + - - +
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Residues in contact with VAL 31 (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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27Q ARG 3.1 12.8 + - - +
28Q GLY* 2.7 15.1 + - - +
30Q GLN* 1.3 68.9 - - - +
32Q TYR* 1.3 60.3 + - - +
35Q VAL* 2.8 46.4 + - + +
36Q CYS 3.4 0.7 + - - -
189Q LEU* 4.6 4.0 - - + -
194Q VAL* 4.6 5.4 - - + -
196Q TYR* 3.5 24.2 - - + +
207Q MET* 4.4 31.4 - - + +
211Q VAL* 3.8 21.5 - - + -
301Q HEM 4.3 13.0 - - + -
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Residues in contact with TYR 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q GLY 2.7 12.6 + - - +
29Q LEU* 3.6 5.6 - - + +
31Q VAL* 1.3 73.3 - - - +
33Q THR* 1.3 64.7 + - - +
36Q CYS* 3.1 27.2 + - + -
37Q ALA* 2.6 59.6 + - + +
40Q HIS* 3.6 14.0 + - + -
41Q GLY* 3.4 26.0 - - - -
42Q MET* 3.1 43.2 + - + +
66Q TYR* 4.8 1.6 - - - -
70Q PHE* 5.8 1.1 - + - -
89Q PHE* 3.8 22.8 - + - +
90Q PRO* 4.9 3.5 + - - +
100Q LEU* 4.7 8.3 - - + -
211Q VAL* 3.9 4.0 - - + +
214Q PHE* 3.5 27.4 - + + -
215Q LEU* 5.1 2.7 - - + -
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Residues in contact with THR 33 (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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29Q LEU* 2.6 26.9 + - - +
30Q GLN* 3.7 4.8 - - - -
32Q TYR* 1.3 80.6 - - - +
34Q GLU* 1.3 65.7 + - + +
35Q VAL* 3.5 0.7 + - - -
37Q ALA* 3.6 18.8 + - + +
38Q ALA 4.8 1.4 + - - -
66Q TYR* 2.8 35.2 + - + +
69Q GLN* 3.8 24.0 - - - +
70Q PHE* 5.0 5.6 - - + -
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Residues in contact with GLU 34 (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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30Q GLN* 2.7 58.9 + - + +
33Q THR* 1.3 79.5 - - + +
35Q VAL* 1.3 60.0 + - - +
38Q ALA* 5.5 2.7 - - - +
193Q LEU 4.4 2.5 - - - +
194Q VAL* 3.5 30.9 - - + +
195Q GLU 4.4 1.7 + - - -
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Residues in contact with VAL 35 (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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31Q VAL* 2.8 27.3 + - + +
33Q THR 3.3 0.2 - - - -
34Q GLU* 1.3 79.1 - - - +
36Q CYS* 1.3 65.6 + - - +
37Q ALA 3.5 1.1 - - - -
38Q ALA* 3.1 24.0 - - - +
188Q PRO* 4.1 24.5 - - + +
189Q LEU* 4.4 2.2 - - + -
193Q LEU* 4.0 21.3 - - + -
194Q VAL* 4.0 22.2 - - + -
207Q MET* 4.7 2.7 - - + -
301Q HEM 3.6 29.3 - - + +
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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
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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