Contacts of the helix formed by residues 21 - 35 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12H SER* 3.9 18.9 + - - +
19H THR 3.7 0.2 + - - -
20H PHE* 1.3 73.6 - - - +
22H GLN* 1.3 66.4 + - - +
23H HIS* 2.9 14.7 + - - +
24H GLN* 2.6 44.0 + - + +
25H LEU* 3.0 23.4 + - - +
27H ARG* 4.9 3.3 + - - -
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Residues in contact with GLN 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H PHE 3.9 3.8 + - - -
21H ASP* 1.3 72.1 + - - +
23H HIS* 1.3 73.1 + - + +
25H LEU* 3.3 5.0 + - - +
26H GLN* 3.0 31.3 + - - +
55H GLY 3.8 12.6 - - - +
56H PRO* 3.2 27.5 - - - +
57H GLU* 3.3 37.7 + - - +
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Residues in contact with HIS 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ASP* 2.9 14.7 + - - +
22H GLN* 1.3 79.8 + - + +
24H GLN* 1.3 66.4 + - - +
26H GLN* 2.8 23.2 + - - +
27H ARG* 2.7 41.4 + - + +
198H ASP* 6.0 6.1 - - - -
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Residues in contact with GLN 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H PHE* 4.9 4.7 - - - -
12H SER* 3.8 20.8 + - - -
21H ASP* 2.6 30.5 + - + +
23H HIS* 1.3 70.4 - - - +
25H LEU* 1.3 53.7 + - + +
27H ARG* 2.8 27.8 + - - +
28H GLY* 2.7 32.2 + - - -
209H GLU* 3.6 28.5 + - - +
210H ASP* 2.8 34.7 + - - +
213H ALA* 3.8 25.8 - - + +
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Residues in contact with LEU 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H PHE* 3.4 40.2 - - + -
21H ASP 3.0 14.7 + - - +
22H GLN 3.5 7.9 - - - +
24H GLN* 1.3 78.2 - - + +
26H GLN* 1.3 56.7 + - - +
28H GLY* 3.3 1.6 + - - +
29H LEU* 2.9 28.1 + - - +
55H GLY* 3.6 29.8 - - - +
56H PRO* 3.9 14.0 - - + +
213H ALA* 3.3 38.4 - - + +
214H PHE* 3.6 17.5 - - + +
217H TRP* 4.0 10.5 - - + -
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Residues in contact with GLN 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H GLN* 3.0 29.9 + - - +
23H HIS* 2.8 31.4 + - - +
25H LEU* 1.3 74.7 - - - +
27H ARG* 1.3 66.9 + - + +
29H LEU* 3.1 19.0 + - + +
30H GLN* 3.1 9.9 + - - +
56H PRO* 2.7 30.3 + - + +
57H GLU 4.5 1.0 + - - -
58H LEU* 3.5 29.0 - - + +
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Residues in contact with ARG 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ASP* 5.0 2.4 + - - -
23H HIS* 2.7 38.1 + - + +
24H GLN* 2.8 24.3 + - - +
26H GLN* 1.3 71.6 - - + +
28H GLY* 1.3 63.9 + - - +
30H GLN* 2.8 24.1 + - - +
31H VAL* 3.1 8.7 + - - +
196H TYR* 3.5 48.3 - - + +
198H ASP* 4.7 12.7 + - - +
200H HIS* 3.2 44.5 + - - -
210H ASP* 3.2 27.7 + - - +
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Residues in contact with GLY 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H GLN 2.7 16.3 + - - -
25H LEU 3.6 3.8 - - - -
27H ARG* 1.3 71.5 - - - +
29H LEU* 1.3 63.8 + - - +
31H VAL* 2.8 18.3 + - - +
32H TYR* 2.8 12.5 + - - +
210H ASP* 4.2 1.2 - - - +
211H VAL* 3.8 19.9 - - - +
214H PHE* 3.8 20.9 - - - -
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Residues in contact with LEU 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H LEU 2.9 16.0 + - - +
26H GLN* 3.4 10.8 - - - +
28H GLY* 1.3 70.4 - - - +
30H GLN* 1.3 53.0 - - - +
32H TYR* 3.6 2.2 - - + +
33H THR* 2.6 38.9 + - - +
50H LEU* 3.6 31.2 - - + -
56H PRO* 5.1 4.7 - - + -
58H LEU* 4.0 25.4 - - + -
66H TYR* 3.2 39.5 - - + +
89H PHE* 4.5 4.3 - - + -
214H PHE* 3.8 32.5 - - + -
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Residues in contact with GLN 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H GLN 3.1 9.1 + - - +
27H ARG* 2.8 15.7 + - - +
29H LEU* 1.3 79.3 - - - +
31H VAL* 1.3 50.4 - - - +
33H THR* 3.7 4.0 - - - -
34H GLU* 2.7 71.8 + - + +
194H VAL* 3.1 24.8 - - - +
195H GLU 3.2 17.2 + - - -
196H TYR* 3.2 22.8 - - + -
197H ALA* 4.6 3.6 + - - +
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Residues in contact with VAL 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ARG 3.1 6.0 + - - +
28H GLY* 2.8 13.8 + - - +
30H GLN* 1.3 68.9 - - - +
32H TYR* 1.3 61.6 + - - +
35H VAL* 2.7 43.0 + - + +
36H CYS 3.4 0.2 + - - -
189H LEU* 4.5 17.3 - - + -
194H VAL* 4.5 9.4 - - + -
196H TYR* 3.0 32.5 - - + +
207H MET* 4.4 23.6 - - + +
211H VAL* 3.8 22.4 - - + -
301H HEM 4.5 5.6 - - + -
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Residues in contact with TYR 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H GLY 2.8 7.6 + - - +
29H LEU* 3.6 4.9 - - + +
31H VAL* 1.3 80.0 - - - +
33H THR* 1.3 67.3 + - - +
36H CYS* 3.2 23.7 + - + -
37H ALA* 2.7 58.5 + - + +
40H HIS* 3.6 13.5 + - + -
41H GLY* 3.3 29.5 - - - -
42H MET* 3.3 37.0 + - + +
66H TYR* 4.6 1.6 - - - -
70H PHE* 5.8 1.1 - + - -
89H PHE* 3.8 23.3 - + - +
90H PRO* 5.4 3.1 - - - +
100H LEU* 4.7 8.3 - - + -
211H VAL* 3.9 3.9 - - + +
214H PHE* 3.6 26.7 - + + -
215H LEU* 5.1 3.4 - - + -
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Residues in contact with THR 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H LEU* 2.6 26.6 + - - +
30H GLN* 3.7 4.7 - - - -
32H TYR* 1.3 81.4 - - - +
34H GLU* 1.3 66.1 + - + +
35H VAL 4.7 0.2 - - - -
37H ALA* 3.7 18.4 + - + +
38H ALA 4.8 1.4 + - - -
66H TYR* 2.8 27.3 + - + +
69H GLN* 3.5 35.7 - - - +
70H PHE* 5.1 4.5 - - + -
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Residues in contact with GLU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H GLN* 2.7 58.9 + - + +
33H THR* 1.3 78.2 - - + +
35H VAL* 1.3 58.4 + - - +
38H ALA* 5.5 2.3 - - - +
193H LEU 4.4 2.5 - - - +
194H VAL* 3.5 30.6 - - + +
195H GLU 4.4 1.7 + - - -
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Residues in contact with VAL 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H VAL* 2.7 31.2 + - + +
34H GLU* 1.3 79.5 - - + +
36H CYS* 1.3 66.3 + - - +
37H ALA 3.5 1.3 - - - -
38H ALA* 3.2 22.6 - - - +
188H PRO* 4.3 21.8 - - + +
189H LEU* 4.5 4.9 - - + -
193H LEU* 4.0 21.8 - - + -
194H VAL* 4.0 22.0 - - + -
301H HEM 3.7 26.9 - - + +
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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