Contacts of the helix formed by residues 21 - 35 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B SER* 3.9 18.1 + - - +
19B THR 3.7 0.2 + - - -
20B PHE* 1.3 74.3 - - - +
22B GLN* 1.3 65.8 + - - +
23B HIS* 2.9 14.6 + - - +
24B GLN* 2.6 45.2 + - + +
25B LEU* 3.0 24.2 + - - +
27B ARG* 4.9 2.6 + - - -
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.9 3.6 + - - +
21B ASP* 1.3 72.1 + - - +
23B HIS* 1.3 73.1 + - + +
25B LEU* 3.3 4.9 + - - +
26B GLN* 3.0 33.4 + - - +
55B GLY 3.8 13.6 + - - +
56B PRO* 3.1 27.7 - - - +
57B GLU* 3.5 37.1 + - - +
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Residues in contact with HIS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASP* 2.9 12.2 + - - +
22B GLN* 1.3 80.2 + - + +
24B GLN* 1.3 68.2 + - - +
26B GLN* 2.9 23.9 + - - +
27B ARG* 2.8 40.5 + - + +
198B ASP* 6.1 4.9 - - - -
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 4.9 5.3 - - - -
12B SER* 3.8 20.8 + - - -
21B ASP* 2.6 29.5 + - + +
23B HIS* 1.3 69.8 - - - +
25B LEU* 1.3 55.7 + - + +
27B ARG* 2.8 27.4 + - - +
28B GLY* 2.7 32.6 + - - -
209B GLU* 3.6 28.1 + - - +
210B ASP* 2.8 35.3 + - - +
213B ALA* 3.8 25.2 - - + +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.4 39.9 - - + -
21B ASP 3.0 15.4 + - - +
22B GLN 3.5 7.2 - - - +
24B GLN* 1.3 78.2 - - + +
26B GLN* 1.3 57.6 + - - +
28B GLY* 3.3 1.6 + - - +
29B LEU* 2.8 28.6 + - - +
55B GLY* 3.6 30.1 - - - +
56B PRO* 3.9 13.9 - - + +
213B ALA* 3.3 37.5 - - + +
214B PHE* 3.6 17.9 - - + +
217B TRP* 3.9 10.5 - - + -
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLN* 3.0 31.0 + - - +
23B HIS* 2.9 31.4 + - - +
25B LEU* 1.3 73.2 - - - +
27B ARG* 1.3 65.0 + - - +
29B LEU* 3.0 19.3 + - + +
30B GLN* 3.1 10.6 + - - +
56B PRO* 2.7 31.5 + - + +
57B GLU 4.5 0.8 + - - -
58B LEU* 3.5 28.5 - - + +
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Residues in contact with ARG 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASP* 4.9 2.6 + - - -
23B HIS* 2.8 37.9 + - + +
24B GLN* 2.8 24.9 + - - +
26B GLN* 1.3 71.9 - - + +
28B GLY* 1.3 64.5 - - - +
30B GLN* 2.8 23.1 + - - +
31B VAL* 3.0 8.8 + - - +
196B TYR* 3.3 54.0 - - + +
198B ASP* 5.0 9.6 + - - +
200B HIS* 3.4 40.9 + - - +
210B ASP* 3.2 29.9 + - - +
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Residues in contact with GLY 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLN 2.7 16.1 + - - -
25B LEU 3.5 4.5 - - - -
27B ARG* 1.3 72.1 - - - +
29B LEU* 1.3 63.9 + - - +
31B VAL* 2.7 17.7 + - - +
32B TYR* 2.8 12.3 + - - +
210B ASP* 4.2 1.0 - - - +
211B VAL* 3.8 21.2 - - - +
214B PHE* 3.8 19.3 - - - -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU 2.8 16.6 + - - +
26B GLN* 3.0 11.6 + - + +
28B GLY* 1.3 70.3 - - - +
30B GLN* 1.3 54.0 + - - +
32B TYR* 3.6 2.2 - - + +
33B THR* 2.6 39.5 + - - +
50B LEU* 3.6 31.9 - - + -
56B PRO* 5.1 4.5 - - + -
58B LEU* 4.0 25.1 - - + -
66B TYR* 3.2 37.9 - - + +
89B PHE* 4.5 4.0 - - + -
214B PHE* 3.8 31.6 - - + -
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Residues in contact with GLN 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLN 3.1 8.3 + - - +
27B ARG* 2.8 14.6 + - - +
29B LEU* 1.3 75.2 - - - +
31B VAL* 1.3 56.0 + - - +
33B THR* 3.8 3.5 - - - -
34B GLU* 2.7 72.2 + - + +
194B VAL* 3.0 24.6 - - - +
195B GLU* 3.2 20.6 + - - +
196B TYR* 3.2 22.4 - - + -
197B ALA 4.6 3.1 + - - -
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ARG 3.0 7.5 + - - +
28B GLY* 2.7 13.8 + - - +
30B GLN* 1.3 68.9 - - - +
32B TYR* 1.3 59.7 + - - +
35B VAL* 2.8 42.9 + - + +
36B CYS 3.4 0.7 + - - -
189B LEU* 4.8 2.2 - - + -
194B VAL* 4.5 8.9 - - + +
196B TYR* 3.2 30.7 - - + +
207B MET* 4.4 33.7 - - + +
211B VAL* 3.8 22.0 - - + -
301B HEM 4.5 13.0 - - + -
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Residues in contact with TYR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLY 2.8 8.4 + - - +
29B LEU* 3.6 4.9 - - + +
31B VAL* 1.3 79.6 - - - +
33B THR* 1.3 66.1 + - - +
36B CYS* 3.2 24.2 + - + -
37B ALA* 2.6 58.3 + - + +
40B HIS* 3.7 13.0 + - + -
41B GLY* 3.3 19.6 - - - -
42B MET* 3.3 45.8 + - + +
66B TYR* 4.5 1.3 - - - -
70B PHE* 5.8 0.9 - + - -
89B PHE* 3.8 25.5 - + - +
90B PRO* 5.6 1.4 - - - +
100B LEU* 4.7 8.1 - - + -
211B VAL* 4.0 4.0 - - + +
214B PHE* 3.6 27.6 - + + -
215B LEU* 5.1 3.1 - - + -
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 2.6 27.2 + - - +
30B GLN* 3.8 4.9 - - - -
32B TYR* 1.3 81.2 - - - +
34B GLU* 1.3 66.8 + - + +
35B VAL 4.7 0.3 - - - -
37B ALA* 3.7 19.0 + - + +
38B ALA 4.8 1.6 + - - -
66B TYR* 2.8 32.7 + - + +
69B GLN* 3.5 29.4 - - - +
70B PHE* 5.4 2.2 - - + -
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLN* 2.7 56.6 + - + +
33B THR* 1.3 79.2 - - + +
35B VAL* 1.3 60.6 + - + +
38B ALA* 5.5 2.5 - - - +
193B LEU 4.4 2.5 - - - +
194B VAL* 3.4 31.9 - - + +
195B GLU* 4.3 1.9 + - - +
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 2.8 26.6 + - + +
34B GLU* 1.3 80.6 - - - +
36B CYS* 1.3 65.1 + - - +
37B ALA 3.5 1.8 - - - -
38B ALA* 3.1 22.6 - - - +
188B PRO* 4.0 28.9 - - + +
189B LEU* 4.8 2.0 - - + -
193B LEU* 4.0 19.7 - - + -
194B VAL* 4.0 22.2 - - + -
207B MET* 4.7 3.4 - - + -
301B HEM 3.7 27.2 - - + +
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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