Contacts of the helix formed by residues 43 - 57 (chain A) in PDB entry 2QVO
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ASN 4.8 1.1 - - - +
42A SER* 1.3 91.0 - - - +
44A HIS* 1.3 67.6 + - - +
45A SER* 4.1 13.9 - - - +
46A TYR* 3.1 22.7 + - + +
47A VAL* 3.2 9.6 + - - +
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Residues in contact with HIS 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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33A ILE* 5.4 2.1 - - - +
34A GLN* 5.1 12.4 - - + +
37A ALA* 3.2 28.6 - - + +
42A SER 5.1 0.4 + - - -
43A PRO* 1.3 71.5 - - - +
45A SER* 1.3 56.9 + - - +
47A VAL* 3.3 8.8 + - - +
48A TRP* 3.0 28.5 + - - +
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Residues in contact with SER 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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43A PRO* 4.1 11.5 - - - +
44A HIS* 1.3 78.2 - - - +
46A TYR* 1.3 60.1 + - - +
48A TRP* 3.5 12.6 - - - +
49A LEU* 3.0 25.8 + - - +
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Residues in contact with TYR 46 (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* 3.7 32.3 - - + +
14A ALA* 5.0 1.4 + - - +
17A ILE* 4.5 3.4 - - + -
42A SER* 3.1 19.3 - - - -
43A PRO* 3.1 24.2 + - + +
45A SER* 1.3 80.6 + - - +
47A VAL* 1.3 64.3 + - - +
49A LEU* 3.1 21.3 + - + +
50A ILE* 3.0 56.0 + - + +
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Residues in contact with VAL 47 (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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17A ILE* 4.2 13.4 - - + +
33A ILE* 3.7 27.1 - - + +
36A ILE* 4.0 22.0 - - + -
37A ALA* 4.2 10.1 - - + -
40A VAL* 4.0 18.2 - - + -
42A SER* 3.9 20.9 - - - +
43A PRO 3.2 12.3 + - - +
44A HIS* 3.6 8.5 - - - +
46A TYR* 1.3 75.5 - - - +
48A TRP* 1.3 64.1 + - - +
50A ILE* 3.3 2.4 + - - +
51A ILE* 2.9 35.2 + - + +
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Residues in contact with TRP 48 (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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33A ILE* 4.0 19.3 - - + +
44A HIS 3.0 14.1 + - - +
45A SER* 3.5 14.6 - - - +
46A TYR 3.2 0.2 - - - -
47A VAL* 1.3 77.3 - - - +
49A LEU* 1.3 78.7 + - + +
51A ILE* 3.4 2.6 + - - +
52A LYS* 2.4 70.7 + - + +
69A LYS* 3.4 21.2 - - + +
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Residues in contact with LEU 49 (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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45A SER 3.0 14.7 + - - +
46A TYR* 3.1 29.1 + - + +
48A TRP* 1.3 93.5 - - + +
50A ILE* 1.3 62.5 + - + +
52A LYS* 3.3 7.3 + - + +
53A LYS* 3.1 50.4 + - + +
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Residues in contact with ILE 50 (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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14A ALA* 4.2 16.6 - - + -
17A ILE* 3.8 20.6 - - + -
46A TYR* 3.0 59.6 + - + +
47A VAL 3.8 3.4 - - - +
49A LEU* 1.3 74.1 - - + +
51A ILE* 1.3 61.8 + - - +
53A LYS* 3.0 26.6 + - + +
54A PHE* 2.8 58.7 + - + -
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Residues in contact with ILE 51 (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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17A ILE* 3.7 15.5 - - + -
21A ILE* 3.7 30.1 - - + -
33A ILE* 3.9 17.3 - - + -
36A ILE* 4.2 2.9 - - + -
47A VAL* 2.9 25.9 + - + +
48A TRP 3.6 4.7 - - - +
50A ILE* 1.3 74.7 - - - +
52A LYS* 1.3 58.2 + - - +
54A PHE* 3.1 9.8 + - + +
55A GLU* 2.8 27.4 + - - +
60A VAL* 3.7 5.7 - - + +
62A CYS* 3.5 31.2 - - - -
69A LYS* 4.5 7.2 - - - +
71A ILE* 4.1 20.2 - - + -
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Residues in contact with LYS 52 (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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48A TRP* 2.4 77.9 + - + +
49A LEU* 3.6 10.8 - - + +
50A ILE 3.2 0.2 - - - -
51A ILE* 1.3 74.4 - - - +
53A LYS* 1.3 58.1 + - + +
55A GLU* 3.4 23.9 + - - +
56A GLU* 2.9 28.1 + - - +
69A LYS* 3.4 16.4 - - - +
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Residues in contact with LYS 53 (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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49A LEU* 3.1 43.0 + - + +
50A ILE* 3.0 26.4 + - + +
52A LYS* 1.3 74.8 - - + +
54A PHE* 1.3 63.6 + - + +
56A GLU* 3.3 18.2 + - - +
57A ALA* 2.9 28.1 + - - +
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Residues in contact with PHE 54 (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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14A ALA* 3.4 33.2 - - + -
17A ILE* 4.0 4.7 - - + -
18A LEU* 4.0 27.6 - - + -
21A ILE* 4.7 1.6 - - + -
50A ILE* 2.8 39.5 + - + -
51A ILE* 3.5 15.5 - - + +
53A LYS* 1.3 77.7 - - + +
55A GLU* 1.3 61.4 + - - +
57A ALA* 3.2 5.9 + - + +
58A LYS 3.2 4.2 + - - -
59A MET* 2.9 54.5 + - + -
60A VAL* 3.6 29.2 - - + -
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Residues in contact with GLU 55 (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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51A ILE 2.8 15.1 + - - +
52A LYS* 3.5 30.9 - - - +
54A PHE* 1.3 76.4 - - - +
56A GLU* 1.3 62.4 + - - +
58A LYS* 3.0 17.7 + - - +
60A VAL* 3.5 24.0 - - + +
61A GLU* 4.8 2.0 - - + -
62A CYS* 3.8 35.0 + - - +
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Residues in contact with GLU 56 (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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52A LYS 2.9 14.0 + - - +
53A LYS* 3.4 20.2 - - - +
55A GLU* 1.3 75.6 - - - +
57A ALA* 1.3 56.8 + - - +
58A LYS* 3.2 12.1 + - - +
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Residues in contact with ALA 57 (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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53A LYS 2.9 16.4 + - - +
54A PHE* 3.2 7.1 + - + +
56A GLU* 1.3 73.3 - - - +
58A LYS* 1.3 63.8 + - - +
59A MET* 3.2 21.6 + - - +
76A LYS* 2.8 33.7 + - - +
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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