Contacts of the helix formed by residues 34 - 45 (chain A) in PDB entry 2KQ5
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 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.9 25.1 - - + +
30A HIS* 5.6 5.2 - - + -
32A LEU* 3.7 20.4 - - + -
33A THR* 1.3 86.8 - - - +
35A GLU* 1.3 63.8 + - - +
36A GLN 3.2 0.4 - - - -
37A VAL* 2.8 15.3 + - + +
38A VAL* 2.7 43.3 + - + +
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A THR* 5.8 0.9 - - - +
19A VAL* 3.6 23.3 - - + +
22A LEU* 3.7 29.3 - - + +
26A LEU* 3.8 40.8 - - + +
33A THR* 3.1 6.3 - - + -
34A PRO* 1.3 86.8 - - - +
36A GLN* 1.3 57.8 + - - +
37A VAL 3.1 4.3 + - - -
38A VAL* 4.1 12.1 - - - +
39A ALA* 3.1 35.0 + - + +
40A ILE 3.3 3.1 + - - -
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Residues in contact with GLN 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 3.6 11.1 - - + +
23A LEU* 4.9 10.0 - - + +
32A LEU 4.7 3.1 + - - +
33A THR* 3.1 28.9 + - + +
35A GLU* 1.3 77.9 - - - +
37A VAL* 1.3 67.2 + - + +
40A ILE* 3.4 29.7 - - + +
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 5.2 9.6 - - + +
33A THR 3.8 13.2 - - - +
34A PRO* 2.8 18.2 + - + +
35A GLU 3.0 0.2 - - - -
36A GLN* 1.3 93.9 - - + +
38A VAL* 1.3 59.7 + - - +
40A ILE* 4.5 0.2 - - - +
41A ALA* 3.0 29.3 + - - +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PRO* 2.7 34.4 + - + +
35A GLU* 4.1 12.8 - - - +
37A VAL* 1.3 72.1 - - + +
39A ALA* 1.3 64.0 + - + +
41A ALA* 3.2 5.3 + - - +
42A SER* 2.7 43.5 + - - +
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 4.3 21.2 - - + +
18A THR* 4.5 14.6 - - + -
19A VAL* 4.8 2.7 - - + -
35A GLU* 3.1 27.2 + - + +
38A VAL* 1.3 81.9 - - + +
40A ILE* 1.3 61.5 + - - +
42A SER* 3.2 18.3 + - - -
43A HIS* 3.3 12.3 + - - +
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Residues in contact with ILE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA 4.7 4.9 - - - +
16A LEU* 5.3 9.0 - - + -
19A VAL* 3.9 26.9 - - + -
35A GLU 3.3 2.6 + - - +
36A GLN* 3.4 39.9 - - + +
37A VAL 4.5 0.7 - - - +
38A VAL 3.3 0.4 - - - -
39A ALA* 1.3 75.3 - - - +
41A ALA* 1.3 53.9 + - - +
43A HIS* 3.1 6.2 + - + +
44A ASP* 2.8 41.6 + - + +
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL 3.0 20.2 + - - +
38A VAL* 3.2 6.3 + - - +
40A ILE* 1.3 81.0 - - - +
42A SER* 1.3 58.2 + - - +
44A ASP* 4.6 2.0 - - - -
45A GLY* 2.8 38.2 + - - +
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Residues in contact with SER 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 6.0 1.3 - - - -
38A VAL* 2.7 28.8 + - - +
39A ALA* 3.2 13.0 + - - -
41A ALA* 1.3 77.1 - - - +
43A HIS* 1.3 50.7 + - - +
45A GLY 5.2 0.2 - - - -
46A GLY* 3.4 4.6 - - - -
47A LYS* 2.7 33.4 + - - +
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 6.1 5.8 - - + -
15A ALA* 3.7 25.4 - - + +
16A LEU* 5.6 11.5 - - + +
39A ALA 3.3 1.7 + - - +
40A ILE* 3.1 7.9 + - + +
42A SER* 1.3 80.8 - - - +
44A ASP* 1.3 65.8 + - + +
47A LYS* 2.9 42.1 + - + +
48A GLN* 2.9 35.8 + - - +
51A GLU* 2.8 45.5 + - + +
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Residues in contact with ASP 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 2.8 30.7 + - + +
41A ALA* 4.6 1.8 - - - -
43A HIS* 1.3 80.3 - - + +
45A GLY* 1.3 59.4 + - - +
46A GLY 3.2 3.3 + - - -
48A GLN* 3.2 36.1 + - - +
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Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 2.8 24.4 + - - +
42A SER* 5.2 0.3 - - - -
44A ASP* 1.3 77.1 + - - +
46A GLY* 1.3 54.2 + - - -
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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