Contacts of the helix formed by residues 21 - 35 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E SER* 3.9 13.5 + - - +
19E THR 3.7 0.4 + - - -
20E PHE* 1.3 74.2 - - - +
22E GLN* 1.3 67.6 + - - +
23E HIS* 2.9 14.2 + - - +
24E GLN* 2.6 50.4 + - + +
25E LEU* 3.0 23.9 + - - +
27E ARG* 4.9 2.5 + - - -
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Residues in contact with GLN 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E PHE* 3.9 4.0 + - - +
21E ASP* 1.3 71.9 + - - +
23E HIS* 1.3 73.6 + - + +
25E LEU* 3.3 4.9 + - - +
26E GLN* 3.0 33.4 + - - +
55E GLY 3.8 13.7 + - - +
56E PRO* 3.1 28.1 - - - +
57E GLU* 3.3 38.3 + - - +
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Residues in contact with HIS 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ASP* 2.9 12.1 + - - +
22E GLN* 1.3 79.2 + - + +
24E GLN* 1.3 68.0 + - - +
26E GLN* 2.9 23.0 + - - +
27E ARG* 2.7 40.8 + - + +
198E ASP* 6.1 4.3 - - - -
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Residues in contact with GLN 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E PHE* 4.9 4.3 - - - -
12E SER* 3.8 20.6 + - - -
21E ASP* 2.6 29.8 + - + +
23E HIS* 1.3 70.1 - - - +
25E LEU* 1.3 55.7 + - + +
27E ARG* 2.8 25.8 + - - +
28E GLY* 2.7 32.7 + - - -
209E GLU* 3.6 29.3 + - - +
210E ASP* 2.8 34.9 + - - +
213E ALA* 3.7 25.5 - - + +
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Residues in contact with LEU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E PHE* 3.4 40.6 - - + -
21E ASP 3.0 14.5 + - - +
22E GLN 3.5 7.2 - - - +
24E GLN* 1.3 79.1 - - + +
26E GLN* 1.3 57.2 + - - +
28E GLY* 3.2 1.8 + - - +
29E LEU* 2.8 28.4 + - - +
55E GLY* 3.6 29.6 - - - +
56E PRO* 3.9 15.0 - - + +
213E ALA* 3.2 38.4 - - + +
214E PHE* 3.6 16.4 - - - +
217E TRP* 3.9 11.2 - - + -
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Residues in contact with GLN 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E GLN* 3.0 30.0 + - - +
23E HIS* 2.9 28.2 + - - +
25E LEU* 1.3 74.4 - - - +
27E ARG* 1.3 69.3 + - + +
29E LEU* 3.0 19.5 + - - +
30E GLN* 3.1 9.9 + - - +
56E PRO* 2.7 32.1 + - + +
57E GLU 4.5 1.0 + - - -
58E LEU* 3.4 29.9 - - + +
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Residues in contact with ARG 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ASP* 4.9 2.8 + - - -
23E HIS* 2.7 37.7 + - + +
24E GLN* 2.8 23.7 + - - +
26E GLN* 1.3 71.7 - - - +
28E GLY* 1.3 65.0 + - - +
30E GLN* 2.8 24.3 + - - +
31E VAL* 3.0 8.7 + - - +
196E TYR* 3.5 52.7 - - + +
198E ASP* 4.9 11.9 + - - +
200E HIS* 3.5 41.6 + - - -
210E ASP* 3.2 27.8 + - - +
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Residues in contact with GLY 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E GLN 2.7 16.3 + - - -
25E LEU 3.5 3.8 - - - -
27E ARG* 1.3 72.1 - - - +
29E LEU* 1.3 63.1 + - - +
31E VAL* 2.7 18.5 + - - +
32E TYR* 2.7 13.2 + - - +
210E ASP* 4.2 1.2 - - - +
211E VAL* 3.8 21.0 - - - +
214E PHE* 3.8 20.0 - - - -
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Residues in contact with LEU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU 2.8 16.0 + - - +
26E GLN* 3.0 12.1 + - - +
28E GLY* 1.3 70.5 - - - +
30E GLN* 1.3 54.3 + - - +
32E TYR* 3.4 2.5 + - + +
33E THR* 2.5 39.8 + - - +
50E LEU* 3.6 32.1 - - + -
56E PRO* 5.1 4.9 - - + -
58E LEU* 4.0 25.1 - - + -
66E TYR* 3.2 38.4 - - + +
89E PHE* 4.5 4.3 - - + -
214E PHE* 3.8 30.7 - - + -
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Residues in contact with GLN 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E GLN 3.1 8.1 + - - +
27E ARG* 2.8 14.8 + - - +
29E LEU* 1.3 77.4 - - - +
31E VAL* 1.3 54.2 + - - +
33E THR* 4.4 2.9 - - - -
34E GLU* 2.7 71.7 + - + +
194E VAL* 3.0 25.8 - - + +
195E GLU 3.4 16.1 + - - +
196E TYR* 3.3 23.4 - - + -
197E ALA* 4.4 4.3 + - - +
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ARG 3.0 9.3 + - - +
28E GLY* 2.7 14.2 + - - +
30E GLN* 1.3 69.7 - - - +
32E TYR* 1.3 60.6 + - - +
35E VAL* 2.8 43.4 + - + +
36E CYS 3.4 0.5 + - - -
189E LEU* 4.7 1.8 - - + -
194E VAL* 4.5 9.0 - - + -
196E TYR* 3.3 31.2 - - + +
207E MET* 4.4 31.6 - - + +
211E VAL* 3.8 22.4 - - + -
301E HEM 4.4 13.2 - - + -
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Residues in contact with TYR 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLY 2.7 11.5 + - - +
29E LEU* 3.6 5.2 - - + +
31E VAL* 1.3 76.1 - - - +
33E THR* 1.3 65.2 + - - +
36E CYS* 3.2 24.4 + - + -
37E ALA* 2.6 59.2 + - + +
40E HIS* 3.6 13.3 + - + -
41E GLY* 3.3 29.5 - - - -
42E MET* 3.1 41.4 + - + +
66E TYR* 4.6 1.1 - - - -
70E PHE* 5.8 1.1 - + - -
89E PHE* 3.8 24.0 - + - +
90E PRO* 5.0 2.1 + - - +
100E LEU* 4.7 7.9 - - + -
211E VAL* 4.0 4.2 - - + +
214E PHE* 3.5 24.2 - + + -
215E LEU* 5.1 2.9 - - + -
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Residues in contact with THR 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LEU* 2.5 26.8 + - - +
30E GLN* 3.7 5.1 - - - -
32E TYR* 1.3 82.4 - - - +
34E GLU* 1.3 66.4 + - + +
35E VAL 4.7 0.3 - - - -
37E ALA* 3.7 18.7 + - + +
38E ALA 4.8 1.4 + - - -
66E TYR* 2.8 30.4 + - + +
69E GLN* 3.4 30.3 - - - +
70E PHE* 5.3 2.5 - - + -
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Residues in contact with GLU 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E GLN* 2.7 57.7 + - + +
33E THR* 1.3 78.9 - - + +
35E VAL* 1.3 60.7 + - - +
38E ALA* 5.5 2.3 - - - +
193E LEU 4.4 2.6 - - - +
194E VAL* 3.4 30.7 - - + +
195E GLU 4.4 1.7 + - - -
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Residues in contact with VAL 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E VAL* 2.8 26.7 + - + +
33E THR 3.3 0.4 - - - -
34E GLU* 1.3 78.5 - - - +
36E CYS* 1.3 66.0 + - - +
37E ALA 3.5 0.9 - - - -
38E ALA* 3.1 23.3 - - - +
188E PRO* 3.7 27.6 - - + +
189E LEU* 4.5 1.8 - - + -
193E LEU* 4.0 20.6 - - + -
194E VAL* 4.0 22.0 - - + -
207E MET* 4.7 3.1 - - + -
301E HEM 3.7 27.8 - - + +
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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