Contacts of the helix formed by residues 21 - 35 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12N SER* 3.9 18.5 + - - +
19N THR 3.7 0.2 + - - -
20N PHE* 1.3 73.6 - - - +
22N GLN* 1.3 65.9 + - - +
23N HIS* 2.9 14.5 + - - +
24N GLN* 2.6 45.5 + - + +
25N LEU* 3.0 23.8 + - - +
27N ARG* 4.9 3.0 + - - -
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Residues in contact with GLN 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N PHE* 3.8 4.0 + - - +
21N ASP* 1.3 73.0 + - - +
23N HIS* 1.3 73.7 + - + +
25N LEU* 3.3 5.6 + - - +
26N GLN* 3.0 31.3 + - - +
55N GLY 3.8 13.6 + - - +
56N PRO* 3.2 22.3 - - - +
57N GLU* 3.5 39.6 + - - +
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Residues in contact with HIS 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N ASP* 2.9 14.5 + - - +
22N GLN* 1.3 80.7 + - + +
24N GLN* 1.3 66.2 + - - +
26N GLN* 2.8 23.8 + - - +
27N ARG* 2.7 41.5 + - + +
198N ASP* 5.9 7.6 - - + -
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Residues in contact with GLN 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N PHE* 4.9 4.4 - - - -
12N SER* 3.8 20.8 + - - -
21N ASP* 2.6 29.5 + - + +
23N HIS* 1.3 70.1 - - - +
25N LEU* 1.3 53.7 + - - +
27N ARG* 2.8 27.3 + - - +
28N GLY* 2.7 32.6 + - - -
209N GLU* 3.6 28.3 + - - +
210N ASP* 2.8 35.3 + - - +
213N ALA* 3.7 24.8 - - + +
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Residues in contact with LEU 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N PHE* 3.4 41.3 - - + -
21N ASP 3.0 14.9 + - - +
22N GLN 3.4 7.4 - - - +
24N GLN* 1.3 78.3 - - + +
26N GLN* 1.3 56.9 + - - +
28N GLY* 3.3 1.7 + - - +
29N LEU* 2.9 28.6 + - - +
55N GLY* 3.5 29.8 - - - +
56N PRO* 3.8 14.7 - - + +
213N ALA* 3.3 39.0 - - + +
214N PHE* 3.6 16.4 - - + +
217N TRP* 3.9 10.5 - - + -
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Residues in contact with GLN 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N GLN* 3.0 29.5 + - - +
23N HIS* 2.8 33.1 + - - +
25N LEU* 1.3 73.8 - - - +
27N ARG* 1.3 65.9 + - + +
29N LEU* 3.0 19.5 + - - +
30N GLN* 3.1 9.7 + - - +
56N PRO* 2.8 30.2 + - + +
57N GLU 4.5 1.0 + - - -
58N LEU* 3.5 29.4 - - + +
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Residues in contact with ARG 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N ASP* 4.9 3.0 + - - -
23N HIS* 2.7 38.1 + - + +
24N GLN* 3.2 25.4 - - - +
26N GLN* 1.3 70.6 - - + +
28N GLY* 1.3 56.1 + - - +
30N GLN* 2.8 34.7 + - - +
31N VAL* 3.1 9.5 + - - +
196N TYR* 3.6 51.2 - - + +
198N ASP* 4.6 13.9 + - - +
200N HIS* 3.6 38.7 + - - -
210N ASP* 3.2 29.1 + - - +
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Residues in contact with GLY 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N GLN 2.7 15.9 + - - -
25N LEU 3.6 4.3 - - - -
27N ARG* 1.3 72.8 - - - +
29N LEU* 1.3 51.4 + - - +
31N VAL* 2.8 8.6 + - - +
32N TYR* 2.7 33.3 + - - +
210N ASP* 4.1 1.2 - - - +
211N VAL* 3.8 21.2 - - - +
214N PHE* 3.8 19.7 - - - -
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Residues in contact with LEU 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N LEU 2.9 16.0 + - - +
26N GLN* 3.0 10.3 + - - +
28N GLY* 1.3 71.4 - - - +
30N GLN* 1.3 54.5 + - - +
32N TYR* 3.4 2.3 + - + +
33N THR* 2.6 39.6 + - - +
50N LEU* 3.6 30.7 - - + -
56N PRO* 5.1 5.4 - - + -
58N LEU* 4.0 25.8 - - + -
66N TYR* 3.2 37.5 - - + +
89N PHE* 4.5 4.5 - - + -
214N PHE* 3.8 31.0 - - + -
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Residues in contact with GLN 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N GLN 3.1 8.5 + - - +
27N ARG* 2.8 16.2 + - - +
29N LEU* 1.3 76.0 - - - +
31N VAL* 1.3 52.5 + - - +
33N THR* 3.7 3.5 - - - -
34N GLU* 2.7 72.5 + - + +
194N VAL* 3.1 18.1 - - - +
195N GLU 2.7 26.7 + - - +
196N TYR* 3.3 21.5 - - + -
197N ALA* 4.7 2.9 + - - +
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Residues in contact with VAL 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27N ARG 3.5 8.3 - - - +
28N GLY* 2.8 14.0 + - - +
30N GLN* 1.3 68.0 - - - +
32N TYR* 1.3 61.3 + - - +
35N VAL* 2.7 47.1 + - + +
36N CYS 3.4 0.3 + - - -
189N LEU* 4.7 5.2 - - + -
194N VAL* 4.6 9.0 - - + -
196N TYR* 3.1 31.2 - - + +
207N MET* 4.4 27.6 - - + +
211N VAL* 3.8 22.2 - - + +
301N HEM 4.5 10.1 - - + -
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Residues in contact with TYR 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N GLY 2.7 12.0 + - - +
29N LEU* 3.6 4.9 - - + +
31N VAL* 1.3 76.3 - - - +
33N THR* 1.3 65.8 + - - +
36N CYS* 3.2 23.6 + - + -
37N ALA* 2.6 58.1 + - + +
40N HIS* 3.6 13.5 + - + -
41N GLY* 3.4 28.4 - - - -
42N MET* 3.0 40.9 + - + +
66N TYR* 4.5 2.2 - - - -
70N PHE* 5.4 1.9 - + - -
89N PHE* 3.8 24.7 - + - +
90N PRO* 5.5 2.4 - - - +
100N LEU* 4.7 8.3 - - + -
211N VAL* 3.9 4.2 - - + +
214N PHE* 3.5 23.8 - + + -
215N LEU* 5.1 3.1 - - + -
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Residues in contact with THR 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N LEU* 2.6 26.3 + - - +
30N GLN* 3.7 4.9 - - - -
32N TYR* 1.3 81.7 - - - +
34N GLU* 1.3 67.1 + - + +
35N VAL* 4.6 0.3 - - - -
37N ALA* 3.6 19.5 - - + +
38N ALA 4.8 1.6 + - - -
66N TYR* 2.8 31.4 + - + +
69N GLN* 3.5 32.3 - - - +
70N PHE* 5.5 1.6 - - + -
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Residues in contact with GLU 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N GLN* 2.7 59.5 + - + +
33N THR* 1.3 79.7 - - + +
35N VAL* 1.3 60.5 + - + +
38N ALA* 5.5 2.5 - - - +
193N LEU 4.4 2.3 - - - +
194N VAL* 3.5 31.4 - - + +
195N GLU 4.3 1.7 + - - -
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Residues in contact with VAL 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31N VAL* 2.7 26.1 + - + +
33N THR 3.3 0.6 - - - -
34N GLU* 1.3 79.0 - - - +
36N CYS* 1.3 66.5 + - - +
37N ALA 3.5 1.1 - - - -
38N ALA* 3.1 22.9 - - - +
188N PRO* 3.9 26.7 - - + +
189N LEU* 4.6 2.0 - - + -
193N LEU* 4.0 20.0 - - + -
194N VAL* 4.0 23.3 - - + -
207N MET* 4.7 2.9 - - + -
301N HEM 3.6 28.2 - - + +
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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