Contacts of the helix formed by residues 51 - 65 (chain A) in PDB entry 1AII
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 ASN 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A SER* 1.3 71.7 - - - +
52A ALA* 1.3 61.8 + - - +
54A ARG* 3.1 15.6 + - - +
55A GLN* 3.0 40.5 + - - +
87A ALA 4.9 1.0 + - - -
88A LEU* 3.4 17.2 + - - +
90A THR 3.1 22.4 + - - -
92A PRO* 3.5 28.9 - - + +
278A VAL* 5.9 2.8 - - - +
282A GLU* 2.6 26.0 + - - +
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Residues in contact with ALA 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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15A ASP* 4.8 4.7 - - - +
50A SER* 3.2 9.0 + - - +
51A ASN* 1.3 78.3 - - - +
53A GLN* 1.3 64.0 + - + +
55A GLN* 3.3 16.2 + - - +
56A LEU* 3.4 18.6 + - + +
282A GLU* 4.8 1.4 + - - -
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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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15A ASP* 3.8 12.1 - - - +
16A TYR* 2.9 49.7 + - - +
19A PHE* 3.3 49.7 - - + +
49A ARG* 3.7 13.8 - - + +
50A SER* 3.1 29.7 + - - +
52A ALA* 1.3 77.4 - - + +
54A ARG* 1.3 58.1 + - - +
56A LEU* 2.8 21.1 + - + -
57A ILE* 2.9 11.1 + - - +
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Residues in contact with ARG 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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13A VAL* 3.7 20.8 - - - +
46A LEU* 2.9 34.5 + - + +
47A THR* 4.6 3.2 - - - +
49A ARG* 2.8 30.5 + - + +
50A SER 3.0 13.7 + - - +
51A ASN* 3.1 29.3 + - - +
53A GLN* 1.3 74.8 - - - +
55A GLN* 1.4 62.4 - - - +
57A ILE* 3.0 13.3 + - - +
58A VAL* 2.9 31.5 + - - +
88A LEU* 2.9 61.6 + - - +
89A VAL* 4.3 15.1 - - + +
278A VAL* 5.6 1.6 - - - +
281A SER* 5.3 3.8 + - - -
282A GLU* 4.2 4.0 + - - -
319A ILE* 6.1 0.2 - - - +
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Residues in contact with GLN 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 ASN* 3.0 39.2 + - - +
52A ALA* 3.6 9.2 - - - +
53A GLN 3.1 0.4 - - - -
54A ARG* 1.4 77.3 - - - +
56A LEU* 1.3 60.1 + - + +
58A VAL* 3.4 13.7 + - - +
59A LYS* 3.0 32.7 + - - +
89A VAL* 3.0 35.7 + - - +
91A PRO* 3.7 28.0 - - + +
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Residues in contact with LEU 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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19A PHE* 4.0 24.5 - - + -
21A PRO* 4.0 12.9 - - + +
52A ALA* 3.6 14.8 - - + +
53A GLN* 2.8 12.8 + - + +
55A GLN* 1.3 76.4 - - + +
57A ILE* 1.3 64.6 + - - +
59A LYS* 3.5 24.9 + - + +
60A GLU* 3.0 25.6 + - - +
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Residues in contact with ILE 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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19A PHE* 3.7 16.6 - - + -
21A PRO* 4.7 4.0 - - + -
24A ASP* 3.7 31.0 - - + +
25A ALA* 4.2 13.5 - - + +
28A ILE* 3.6 23.8 - - + -
45A ILE* 4.2 8.5 - - + -
46A LEU* 4.3 9.4 - - + -
49A ARG* 4.0 15.5 - - + -
53A GLN 2.9 12.9 + - - +
54A ARG* 3.0 17.7 + - - +
56A LEU* 1.3 77.5 - - - +
58A VAL* 1.3 56.1 + - - +
60A GLU* 3.3 6.0 + - - +
61A TYR* 2.9 29.7 + - + +
69A LEU* 3.9 12.6 - - + -
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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 ARG 2.9 20.3 + - - +
55A GLN* 3.4 18.4 - - - +
57A ILE* 1.3 77.2 - - - +
59A LYS* 1.3 64.0 + - - +
61A TYR* 3.2 14.7 + - - +
62A GLN* 3.2 15.2 + - + +
67A LYS 5.3 0.2 - - - +
68A GLU* 3.8 24.9 - - - +
69A LEU* 4.3 20.8 + - + +
70A LYS 6.0 0.7 - - - +
89A VAL* 4.3 30.1 - - + +
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Residues in contact with LYS 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 GLN* 3.0 17.9 + - - +
56A LEU* 4.0 26.0 - - + +
57A ILE 3.4 0.2 - - - -
58A VAL* 1.3 77.6 - - - +
60A GLU* 1.3 62.9 + - + +
61A TYR 3.5 0.3 + - - -
62A GLN* 3.6 6.4 + - - +
63A ALA* 3.6 20.6 + - - +
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Residues in contact with GLU 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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21A PRO* 3.7 18.1 - - + +
22A SER* 3.7 39.3 + - - +
25A ALA* 4.3 5.9 - - + +
56A LEU 3.0 19.5 + - - +
57A ILE 3.7 3.8 - - - +
58A VAL 3.3 0.2 - - - -
59A LYS* 1.3 78.3 - - + +
61A TYR* 1.3 57.0 + - - +
63A ALA* 3.9 8.2 - - - +
64A ALA* 3.5 32.4 + - + +
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Residues in contact with TYR 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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25A ALA* 3.5 37.4 - - + +
28A ILE* 3.8 10.7 - - + +
29A GLN* 3.3 38.6 - - + +
32A ILE* 3.8 8.0 - - - +
57A ILE* 2.9 17.4 + - + +
58A VAL 3.2 4.7 + - - +
60A GLU* 1.3 74.4 - - - +
62A GLN* 1.3 59.0 + - - +
63A ALA 3.3 0.2 - - - -
65A TYR* 3.0 43.5 + + + +
67A LYS* 3.7 20.0 - - + +
69A LEU* 3.9 34.3 - - + -
72A ASP* 2.9 35.9 + - - +
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Residues in contact with GLN 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* 3.2 14.9 + - + +
59A LYS* 3.6 6.3 + - - +
60A GLU 3.5 0.2 - - - -
61A TYR* 1.3 76.0 - - - +
63A ALA* 1.3 58.7 + - - +
66A GLY* 3.1 36.3 + - - +
67A LYS 3.2 28.4 + - - +
68A GLU* 2.6 35.0 + - - +
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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 LYS 3.6 14.5 + - - +
60A GLU* 3.9 13.2 - - - +
62A GLN* 1.3 80.2 - - - +
64A ALA* 1.3 62.0 + - + +
65A TYR 3.9 0.2 + - - -
66A GLY* 4.4 2.3 + - - -
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Residues in contact with ALA 64 (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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25A ALA* 6.0 0.4 - - + -
60A GLU* 3.5 23.8 + - + +
63A ALA* 1.3 80.8 - - - +
65A TYR* 1.3 85.3 + - + +
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Residues in contact with TYR 65 (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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25A ALA* 3.8 16.4 - - + -
26A GLU* 3.5 30.0 + - - +
29A GLN* 3.6 52.8 + - + +
30A LYS* 5.2 1.9 + - - -
33A ARG* 5.5 2.2 - - - -
61A TYR* 3.0 32.7 + + + +
64A ALA* 1.3 96.2 - - + +
66A GLY* 1.3 65.2 + - - +
67A LYS* 3.1 28.4 + - + +
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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