Contacts of the helix formed by residues 55 - 71 (chain A) in PDB entry 1QA6
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 SER 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A MET* 5.4 0.7 - - - -
53A ALA* 4.0 1.2 - - - +
54A ALA* 1.3 83.8 - - - +
56A ILE* 1.3 64.8 + - - +
57A GLU* 2.9 36.4 - - - +
58A ALA* 2.8 22.4 + - - +
59A ALA* 3.0 10.8 + - - +
61A ARG* 5.0 1.9 + - - -
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Residues in contact with ILE 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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41A ARG* 3.6 46.0 - - + +
44A ALA* 4.8 4.0 - - + -
45A GLU* 4.2 34.5 - - + +
48A MET* 5.0 11.2 - - + -
54A ALA 4.0 0.2 + - - -
55A SER* 1.3 71.5 - - - +
57A GLU* 1.3 62.6 + - - +
59A ALA* 2.8 14.3 + - + +
60A MET* 2.8 32.7 + - + +
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Residues in contact with GLU 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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41A ARG* 3.5 21.7 + - - -
55A SER* 2.9 29.4 - - - +
56A ILE* 1.3 80.8 + - - +
58A ALA* 1.3 53.7 + - - +
60A MET* 3.6 18.0 - - + +
61A ARG* 2.7 46.1 + - - +
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Residues in contact with ALA 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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53A ALA* 4.1 4.3 - - + -
55A SER* 2.8 19.2 + - - +
57A GLU* 1.3 72.8 - - - +
59A ALA* 1.3 70.8 + - - +
60A MET 2.9 2.4 + - - -
61A ARG* 3.0 27.0 + - - +
62A MET* 3.2 10.0 + - - +
131C U 3.7 20.9 - - - +
132C U 3.2 28.7 - - - +
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Residues in contact with ALA 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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44A ALA* 3.9 13.9 - - + +
48A MET* 3.7 23.8 - - - -
51A LEU* 3.5 26.8 - - + +
53A ALA* 3.6 7.0 - - + +
55A SER 3.0 5.4 + - - +
56A ILE* 2.8 17.9 + - + +
58A ALA* 1.3 76.5 - - - +
60A MET* 1.3 62.2 + - - +
62A MET* 3.4 7.2 + - - +
63A ILE* 3.3 19.1 + - - +
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Residues in contact with MET 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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36A LYS* 5.8 2.5 - - + -
37A ARG* 5.4 8.7 - - + -
40A VAL* 4.2 9.2 - - + -
41A ARG* 2.8 55.9 - - - +
44A ALA* 3.7 19.3 - - + -
56A ILE* 2.8 16.8 + - + +
57A GLU* 3.6 20.2 - - + +
58A ALA 2.9 0.8 + - - -
59A ALA* 1.3 71.4 - - - +
61A ARG* 1.3 68.9 + - - +
62A MET 3.0 2.2 - - - -
63A ILE* 2.6 16.8 + - - +
64A GLU* 2.8 32.6 + - - +
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Residues in contact with ARG 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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55A SER* 5.0 1.2 + - - -
57A GLU* 2.7 39.4 + - - +
58A ALA* 3.0 19.8 + - - +
60A MET* 1.3 78.4 - - - +
62A MET* 1.3 55.6 + - - +
64A GLU* 3.7 14.0 + - - +
65A GLY* 2.9 24.6 + - - -
129C C 5.0 0.2 + - - -
130C A 3.1 39.3 + - - +
131C U 2.6 29.4 + - - -
132C U 5.7 0.4 + - - -
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Residues in contact with MET 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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51A LEU* 4.5 21.8 - - + -
52A ASN* 3.6 10.5 - - - +
53A ALA* 4.9 2.9 - - - -
58A ALA 3.2 5.5 + - - +
59A ALA 3.5 7.6 - - - +
60A MET 2.7 4.2 + - - -
61A ARG* 1.3 70.4 - - - +
63A ILE* 1.3 63.6 + - + +
65A GLY* 2.8 16.8 + - - -
66A THR* 3.0 16.5 + - - -
108C U 3.1 30.1 - - - +
109C G 3.4 35.3 + - + +
130C A 3.0 41.1 + - + +
131C U 3.4 30.1 - - - +
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Residues in contact with ILE 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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10A ALA* 3.9 21.5 - - + -
14A LEU* 3.6 22.1 - - + +
40A VAL* 3.9 17.7 - - + -
43A ILE* 4.1 25.6 - - + -
44A ALA* 4.1 20.2 - - - +
47A LYS* 4.3 21.5 - - + -
51A LEU* 4.6 6.5 - - + -
59A ALA 3.5 13.7 - - - +
60A MET 2.6 11.0 + - - +
62A MET* 1.3 71.9 - - + +
64A GLU* 1.3 64.4 + - - +
66A THR* 2.8 18.5 + - - +
67A ALA 3.0 8.5 + - - -
109C G 4.5 4.9 - - - +
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Residues in contact with GLU 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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36A LYS* 4.7 20.9 - - - +
40A VAL* 3.2 33.8 - - + +
60A MET* 2.8 41.8 + - - +
61A ARG* 3.8 12.8 + - - +
63A ILE* 1.3 72.7 - - - +
65A GLY* 1.3 61.7 + - - +
67A ALA* 3.1 19.3 + - - +
68A ARG* 3.1 12.5 + - - +
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Residues in contact with GLY 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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61A ARG 2.9 13.7 + - - -
62A MET 2.8 11.3 + - - -
64A GLU* 1.3 78.6 - - - +
66A THR* 1.3 58.4 + - - -
68A ARG* 3.6 10.7 + - - +
69A SER* 3.6 6.2 + - - -
109C G 3.9 0.4 - - - -
129C C 3.7 34.9 - - - +
138C A 3.3 14.2 + - - -
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Residues in contact with THR 66 (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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10A ALA* 3.7 24.5 - - + +
11A ALA* 4.2 13.9 - - + +
14A LEU* 3.9 2.9 - - + -
62A MET 3.0 12.0 + - - -
63A ILE* 2.8 11.1 + - - -
65A GLY* 1.3 70.0 - - - +
67A ALA* 1.3 63.7 + - - +
68A ARG 3.2 0.7 - - - -
69A SER* 2.5 22.2 + - - -
70A MET* 3.2 9.8 - - - +
109C G 3.5 4.0 + - - -
110C U 2.9 42.0 + - + +
112C G 3.7 15.5 - - - +
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Residues in contact with ALA 67 (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 LEU* 3.4 31.5 - - + +
40A VAL* 5.8 2.2 - - + -
63A ILE 3.0 6.4 + - - +
64A GLU* 3.1 15.0 + - - +
66A THR* 1.3 79.5 - - - +
68A ARG* 1.3 57.6 + - - +
70A MET* 3.3 7.6 + - - +
71A GLY 2.7 22.5 + - - -
72A ILE* 3.1 30.5 + - + +
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Residues in contact with ARG 68 (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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26A GLU* 3.4 9.2 - - - +
64A GLU 3.1 11.9 + - - +
65A GLY* 3.9 10.8 - - - +
66A THR 3.2 0.4 - - - -
67A ALA* 1.3 72.7 - - - +
69A SER* 1.3 57.3 + - - +
70A MET 2.9 4.7 - - - -
71A GLY* 2.6 25.1 + - - +
72A ILE* 4.6 4.2 + - - -
127C A 4.7 7.2 + - - +
128C U 2.9 35.5 + - - -
129C C 3.6 49.1 + - - +
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Residues in contact with SER 69 (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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26A GLU* 2.9 9.3 - - - +
65A GLY 3.6 3.0 + - - -
66A THR* 2.5 25.5 + - - -
68A ARG* 1.3 77.4 - - - +
70A MET* 1.3 56.5 + - - +
112C G 2.8 69.9 + - - +
113C G 3.4 5.7 - - - -
127C A 5.2 6.1 - - - -
138C A 4.0 21.7 + - - -
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Residues in contact with MET 70 (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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11A ALA* 4.2 20.4 - - + +
14A LEU* 4.1 20.6 - - - -
15A LYS* 3.8 32.3 - - + +
20A ILE* 4.8 1.8 - - + -
23A GLY* 3.6 18.2 - - - -
24A SER* 3.1 21.0 - - - -
26A GLU* 3.6 5.6 - - - -
66A THR* 3.2 19.1 - - - +
67A ALA* 3.3 9.4 - - - +
69A SER* 1.3 78.1 + - - +
71A GLY* 1.3 66.5 + - - +
72A ILE* 3.7 22.9 - - + +
113C G 3.7 27.4 - - - +
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Residues in contact with GLY 71 (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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26A GLU* 3.5 16.8 - - - +
30A ASN* 4.1 14.1 - - - -
31A LYS* 2.9 25.9 + - - +
67A ALA 2.7 3.0 + - - -
68A ARG* 2.6 16.9 + - - -
70A MET* 1.3 80.4 - - - +
72A ILE* 1.3 67.9 + - - +
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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