Contacts of the helix formed by residues 24 - 35 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214M TRP* 4.0 16.9 - - + +
218M SER* 3.9 18.2 - - - +
20P HIS* 3.8 34.7 - - + +
22P ARG 4.1 1.3 - - - -
23P LEU* 1.3 82.7 - - + +
25P ILE* 1.3 63.4 + - - +
26P VAL* 3.1 3.6 - - + +
27P ALA* 3.0 26.5 + - + +
28P LEU* 3.1 12.5 + - - +
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Residues in contact with ILE 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211M ILE* 4.6 19.1 - - + -
214M TRP* 3.3 34.8 - - + -
19P LEU* 4.8 8.5 - - + -
23P LEU* 2.6 37.3 + - + +
24P PRO* 1.3 72.5 - - - +
26P VAL* 1.3 72.1 + - + +
28P LEU* 3.6 4.5 + - + +
29P ALA* 3.2 20.8 + - + +
505P ANJ 5.3 8.2 - - + +
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Residues in contact with VAL 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P TYR* 3.3 37.2 - - + +
16P GLU* 5.5 4.7 - - + -
19P LEU* 3.7 31.6 - - + -
24P PRO* 3.1 1.4 - - - +
25P ILE* 1.3 79.0 - - + +
27P ALA* 1.3 66.4 + - - +
29P ALA* 3.3 8.7 + - + +
30P TYR* 3.0 20.7 + - + +
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Residues in contact with ALA 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P TYR* 3.3 32.4 - - + -
20P HIS* 4.2 9.0 - - + +
24P PRO* 3.0 24.3 + - + +
26P VAL* 1.3 76.7 - - - +
28P LEU* 1.3 65.1 + - - +
30P TYR* 2.8 21.0 + - - +
31P ASP* 2.9 16.9 + - - +
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Residues in contact with LEU 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214M TRP* 3.7 33.2 - - + -
24P PRO 3.1 7.1 + - - +
25P ILE* 3.6 11.0 - - + +
27P ALA* 1.3 79.4 - - - +
29P ALA* 1.3 63.8 + - - +
30P TYR 3.0 0.5 + - - -
31P ASP* 3.1 10.8 + - + +
32P THR* 2.9 32.0 + - - +
505P ANJ 6.0 6.5 - - + -
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Residues in contact with ALA 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P ILE* 3.2 10.6 + - + +
26P VAL* 3.5 12.6 - - + +
28P LEU* 1.3 79.0 - - - +
30P TYR* 1.3 62.8 + - - +
32P THR* 3.3 7.3 + - - +
33P ILE* 2.9 27.0 + - - +
505P ANJ 3.3 34.9 - - + +
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Residues in contact with TYR 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P ASP* 3.4 27.4 + - - -
8P HIS 3.3 8.8 + - - -
9P TYR* 3.1 52.0 - + + -
26P VAL* 3.0 12.4 + - + +
27P ALA 2.8 9.7 + - - +
29P ALA* 1.3 72.6 - - - +
31P ASP* 1.3 71.0 + - - +
32P THR 2.9 4.0 - - - -
33P ILE* 2.8 13.8 + - + +
34P MET* 2.7 78.2 + - + +
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Residues in contact with ASP 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P HIS* 5.0 9.2 + - + -
8P HIS* 3.8 12.8 - - - +
9P TYR* 3.7 9.3 + - - +
27P ALA* 2.9 23.5 + - - +
28P LEU* 3.7 10.9 + - + +
30P TYR* 1.3 96.6 - - - +
32P THR* 1.3 60.3 + - - +
33P ILE 3.4 0.2 - - - -
34P MET* 4.1 2.5 - - - +
35P ILE* 3.7 20.6 + - - +
217P HIS* 4.3 3.1 + - - -
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Residues in contact with THR 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P LEU* 2.9 19.5 + - - +
29P ALA* 3.5 11.4 - - - +
30P TYR 2.9 0.8 - - - -
31P ASP* 1.3 80.7 - - - +
33P ILE* 1.3 64.7 - - + +
34P MET 3.7 0.2 + - - -
35P ILE* 4.0 4.7 - - - +
213P ILE* 5.7 2.5 - - + -
217P HIS* 3.2 33.2 + - + +
244P PHE* 4.6 4.0 - - - -
505P ANJ 3.9 43.5 - - + +
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Residues in contact with ILE 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P ALA 2.9 14.7 + - - +
30P TYR* 2.8 16.8 + - + +
32P THR* 1.3 83.7 - - + +
34P MET* 1.3 69.5 + - + +
35P ILE 3.6 0.2 - - - -
244P PHE* 3.4 17.6 - - + +
245P TRP* 3.2 36.2 + - + +
249P ILE* 3.3 33.4 - - + -
505P ANJ 5.1 14.1 - - + +
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Residues in contact with MET 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7P ASP* 5.7 1.6 - - - +
30P TYR* 2.7 67.0 + - + +
31P ASP* 4.9 1.6 - - - -
33P ILE* 1.3 80.3 - - + +
35P ILE* 1.3 72.7 + - - +
36P PRO* 3.3 2.6 - - - +
243P PRO* 3.6 31.3 - - + +
244P PHE* 3.3 9.9 + - - -
245P TRP* 3.9 35.0 - - + +
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Residues in contact with ILE 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P ILE* 5.3 4.0 - - + -
6P HIS* 6.4 0.2 - - + -
31P ASP 3.7 12.1 + - - +
32P THR 4.0 3.6 - - - +
34P MET* 1.3 81.6 - - - +
36P PRO* 1.3 84.7 - - + +
37P THR* 3.2 12.1 + - - +
217P HIS* 3.7 56.8 - - + +
220P GLY* 4.8 9.9 - - - -
221P ASN* 4.3 18.8 - - - +
244P PHE* 3.0 28.1 + - + -
505P ANJ 5.8 2.2 - - + +
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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