Contacts of the helix formed by residues 24 - 35 (chain M) 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 PRO 24 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M TYR* 6.0 0.2 - - + -
20M HIS* 3.9 33.3 - - + +
22M ARG 4.1 1.1 - - - -
23M LEU* 1.3 82.2 - - + +
25M ILE* 1.3 64.6 + - - +
26M VAL* 3.1 3.1 - - + +
27M ALA* 3.0 27.0 + - + +
28M LEU* 3.1 12.0 + - - +
214P TRP* 3.9 19.8 - - + +
218P SER* 3.9 18.4 - - - +
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Residues in contact with ILE 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M LEU* 4.8 8.5 - - + -
23M LEU* 2.6 36.2 + - + +
24M PRO* 1.3 73.7 - - - +
26M VAL* 1.3 71.7 + - + +
28M LEU* 3.5 4.8 + - + +
29M ALA* 3.2 21.9 + - + +
505M ANJ 6.2 5.4 - - + -
211P ILE* 4.6 19.3 - - + -
214P TRP* 3.3 32.8 - - + -
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Residues in contact with VAL 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M TYR* 3.0 35.0 - - + +
16M GLU* 5.5 5.8 - - + -
19M LEU* 3.7 31.9 - - + -
23M LEU 4.4 0.2 + - - -
24M PRO* 3.1 1.2 - - + -
25M ILE* 1.3 77.7 - - + +
27M ALA* 1.3 66.3 + - - +
29M ALA* 3.3 8.5 + - + +
30M TYR* 3.0 21.0 + - + +
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Residues in contact with ALA 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M TYR* 3.2 35.3 - - + -
20M HIS* 4.2 7.4 - - + +
24M PRO* 3.0 24.5 + - + +
26M VAL* 1.3 77.5 - - - +
28M LEU* 1.3 64.6 + - - +
30M TYR* 2.8 20.4 + - - +
31M ASP* 2.9 17.2 + - - +
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Residues in contact with LEU 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M PRO 3.1 7.1 + - - +
25M ILE* 3.6 10.8 - - + +
27M ALA* 1.3 79.4 - - - +
29M ALA* 1.3 64.8 + - - +
30M TYR 3.0 0.3 + - - -
31M ASP* 3.1 11.2 + - + +
32M THR* 2.9 30.9 + - - +
214P TRP* 3.7 31.4 - - + -
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Residues in contact with ALA 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M ILE* 3.2 12.1 + - + +
26M VAL* 3.5 12.3 - - + +
27M ALA 3.3 0.2 - - - -
28M LEU* 1.3 78.8 - - - +
30M TYR* 1.3 57.7 + - - +
32M THR* 3.3 8.7 + - - +
33M ILE* 2.9 32.3 + - - +
505M ANJ 4.3 30.5 - - + +
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Residues in contact with TYR 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M HIS* 5.7 1.6 - + - -
7M ASP* 3.5 20.8 + - - -
8M HIS* 3.5 10.7 + - - -
9M TYR* 3.4 43.1 - + + -
26M VAL* 3.0 12.0 + - + +
27M ALA 2.8 11.6 + - - +
29M ALA* 1.3 71.9 - - - +
31M ASP* 1.3 79.0 + - - +
32M THR 2.9 3.4 - - - -
33M ILE* 2.7 31.7 + - + +
34M MET* 2.8 57.1 + - + +
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Residues in contact with ASP 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M HIS* 4.4 16.1 + - - +
8M HIS* 4.3 9.3 - - - +
9M TYR* 4.3 7.0 + - - +
27M ALA* 2.9 23.9 + - - +
28M LEU* 3.7 12.1 + - + +
30M TYR* 1.3 96.7 - - - +
32M THR* 1.3 59.3 + - - +
34M MET* 4.1 2.0 - - - +
35M ILE* 3.7 20.1 + - - +
217M HIS* 4.6 2.9 + - - -
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Residues in contact with THR 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M LEU* 2.9 20.3 + - - +
29M ALA* 3.5 12.3 - - - +
30M TYR 2.9 0.8 - - - -
31M ASP* 1.3 79.7 - - - +
33M ILE* 1.3 66.1 + - + +
34M MET 3.8 0.3 + - - -
35M ILE* 4.0 5.0 - - - +
213M ILE* 5.6 2.5 - - + -
217M HIS* 3.2 33.0 + - + +
244M PHE* 4.6 3.8 - - - -
505M ANJ 3.6 39.5 - - + +
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Residues in contact with ILE 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M ALA 2.9 13.8 + - - +
30M TYR* 2.7 22.9 + - + +
32M THR* 1.3 80.4 - - + +
34M MET* 1.3 69.6 + - + +
35M ILE 3.6 0.2 - - - -
244M PHE* 3.4 16.9 - - + +
245M TRP* 3.2 31.7 + - + +
249M ILE* 3.3 36.3 - - + -
505M ANJ 4.8 13.5 - - + +
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Residues in contact with MET 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M TYR* 2.8 62.7 + - + +
31M ASP* 5.1 0.9 - - - -
33M ILE* 1.3 79.9 - - + +
35M ILE* 1.3 71.1 + - - +
36M PRO* 3.3 3.0 - - - +
243M PRO* 3.7 24.4 - - + +
244M PHE* 3.5 8.8 + - - -
245M TRP* 3.5 52.0 - - + +
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Residues in contact with ILE 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M ILE* 5.4 4.9 - - + -
6M HIS* 5.6 3.6 - - + -
31M ASP* 3.7 17.7 + - - +
32M THR 4.0 3.1 - - - +
34M MET* 1.3 81.1 - - - +
36M PRO* 1.3 85.4 - - + +
37M THR* 3.2 12.4 + - - +
217M HIS* 3.8 53.2 - - + +
220M GLY* 4.8 11.2 - - - -
221M ASN* 4.6 15.7 - - - +
244M PHE* 3.0 28.7 + - + -
505M ANJ 5.8 1.8 - - + +
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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