Contacts of the helix formed by residues 50 - 63 (chain A) in PDB entry 1Q6H
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A LYS 3.8 1.2 + - - -
49A LEU* 1.3 71.1 - - - +
51A LYS* 1.3 62.1 + - - +
52A ASP* 2.8 26.3 + - - +
53A GLN* 3.2 22.1 + - + +
54A LEU* 3.1 16.5 + - - +
20B ASP* 3.0 26.7 + - + +
21B GLN* 3.9 18.3 + - + +
24B ALA* 3.3 7.9 - - - +
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLU* 4.4 23.8 + - - +
39A LEU* 3.9 29.7 - - + +
40A LYS* 4.7 7.5 - - - +
49A LEU 3.3 6.1 + - - +
50A ASP* 1.3 73.6 + - - +
52A ASP* 1.3 63.5 + - - +
54A LEU* 3.2 5.6 + - - +
55A ILE* 3.1 27.1 + - - +
62B PHE* 3.7 37.2 + - + +
64B ASP* 5.6 1.6 + - - -
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Residues in contact with ASP 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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50A ASP* 2.8 11.6 + - - +
51A LYS* 1.3 76.3 - - - +
53A GLN* 1.3 64.4 + - + +
55A ILE* 3.4 6.2 + - - +
56A ALA* 3.0 27.1 + - - +
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Residues in contact with GLN 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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50A ASP* 3.2 17.1 + - - +
52A ASP* 1.3 76.8 - - + +
54A LEU* 1.3 66.1 + - - +
56A ALA* 3.6 6.6 - - - +
57A GLY 2.9 19.6 + - - -
15B ALA 4.8 4.2 + - - -
16B PHE* 3.4 28.4 - - - -
21B GLN* 3.8 53.9 + - + +
24B ALA* 4.0 1.6 - - + -
25B TYR* 3.5 21.4 - - - +
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Residues in contact with LEU 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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35A MSE 3.8 31.4 - - + -
39A LEU* 3.8 36.1 - - + -
49A LEU* 4.9 0.4 - - + -
50A ASP 3.1 13.8 + - - +
51A LYS* 3.2 12.3 + - - +
53A GLN* 1.3 79.3 - - - +
55A ILE* 1.3 66.6 + - + +
57A GLY 3.3 0.5 + - - -
58A VAL* 3.1 27.4 + - + +
24B ALA* 3.5 27.5 - - + +
27B LEU* 4.3 8.1 - - + -
28B GLY* 3.4 14.6 - - - +
31B LEU* 5.5 0.4 - - + -
58B VAL* 6.4 0.2 - - + -
62B PHE* 4.0 13.7 - - + -
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Residues in contact with ILE 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 LYS 3.1 11.1 + - - +
52A ASP* 4.0 5.4 - - - +
54A LEU* 1.3 80.4 - - + +
56A ALA* 1.3 58.8 + - - +
58A VAL* 3.2 7.0 + - + +
59A GLN* 3.0 50.1 + - + +
58B VAL* 4.5 16.8 - - + -
59B GLN* 4.1 22.0 - - + -
62B PHE* 3.2 46.0 - - + -
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Residues in contact with ALA 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 ASP 3.0 17.6 + - - +
53A GLN* 3.3 12.3 + - - +
55A ILE* 1.3 76.4 - - - +
57A GLY* 1.3 57.5 + - - +
59A GLN* 3.7 14.3 - - - +
60A ASP* 2.8 40.1 + - - +
25B TYR* 3.8 13.5 - - + -
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Residues in contact with GLY 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 GLN 2.9 11.5 + - - -
54A LEU 3.7 1.8 - - - -
56A ALA* 1.3 76.8 - - - +
58A VAL* 1.3 61.3 + - - +
61A ALA 3.0 19.8 + - - -
25B TYR* 3.6 40.2 - - - -
29B ALA* 3.3 16.7 - - - +
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Residues in contact with VAL 58 (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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54A LEU* 3.1 24.4 + - + +
55A ILE* 3.2 16.8 + - + +
57A GLY* 1.3 75.3 - - - +
59A GLN* 1.3 59.3 + - + +
62A PHE* 2.9 32.7 + - - +
28B GLY* 3.3 23.0 - - - +
31B LEU* 4.0 16.4 - - + -
32B GLY* 3.8 5.0 - - - -
35B MSE 3.8 28.9 - - + -
55B ILE* 4.1 17.3 - - + -
58B VAL* 4.5 10.1 - - + -
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Residues in contact with GLN 59 (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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55A ILE* 3.0 33.7 + - + +
56A ALA* 3.7 14.8 - - - +
58A VAL* 1.3 78.4 - - + +
60A ASP* 1.3 67.2 + - - +
62A PHE* 3.2 4.1 + - - +
63A ALA* 3.1 24.5 + - - +
55B ILE* 4.1 18.2 - - + -
59B GLN* 2.8 31.2 + - - +
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Residues in contact with ASP 60 (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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56A ALA* 2.8 25.2 + - - +
57A GLY 4.1 0.2 - - - +
59A GLN* 1.3 76.3 + - - +
61A ALA* 1.3 62.6 + - - +
63A ALA* 3.1 6.5 + - - +
64A ASP 3.1 3.6 + - - -
65A LYS* 2.8 41.0 + - - +
66A SER* 3.8 2.9 - - - -
67A LYS* 3.3 21.7 + - - -
25B TYR* 2.6 38.5 + - + +
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Residues in contact with ALA 61 (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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57A GLY 3.0 19.0 + - - +
58A VAL 4.0 1.3 - - - +
60A ASP* 1.3 76.8 - - - +
62A PHE* 1.3 58.2 + - - +
64A ASP* 2.8 26.8 + - - +
66A SER* 4.1 13.8 - - - +
29B ALA* 3.3 34.1 - - + +
32B GLY* 4.1 3.1 - - - +
33B ARG* 4.0 17.0 + - + +
36B GLU* 4.1 5.0 - - - +
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Residues in contact with PHE 62 (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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58A VAL 2.9 20.2 + - - +
59A GLN* 3.2 7.2 + - - +
61A ALA* 1.3 77.1 - - - +
63A ALA* 1.3 59.2 + - + +
64A ASP* 3.3 6.3 + - - +
32B GLY* 3.8 20.4 - - - -
35B MSE 3.7 30.5 - - + -
36B GLU* 4.1 16.1 - - + +
39B LEU* 3.7 25.6 - - + -
51B LYS* 3.9 27.4 - - + -
54B LEU* 3.6 20.2 - - + -
55B ILE* 3.5 27.6 - - + -
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Residues in contact with ALA 63 (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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59A GLN 3.1 15.4 + - - +
60A ASP* 3.1 5.1 + - - +
61A ALA 3.0 0.6 - - - -
62A PHE* 1.3 78.3 - - - +
64A ASP* 1.3 72.0 + - - +
65A LYS* 3.2 23.5 + - + +
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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