Contacts of the helix formed by residues 55 - 77 (chain G) in PDB entry 1I3R
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 GLU 55 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G PHE* 1.3 86.5 - - - +
56G ALA* 1.3 61.1 + - - +
57G GLN* 3.1 12.6 - - + +
58G GLY* 3.0 20.0 + - - +
4H VAL* 4.4 19.2 - - + +
5H ILE 4.9 1.4 + - - -
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Residues in contact with ALA 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G VAL* 4.0 8.0 - - + +
39G SER* 3.5 34.3 - - - +
40G GLU 4.0 1.3 - - - +
41G THR* 3.6 23.1 - - - +
54G PHE* 3.2 12.7 + - - -
55G GLU* 1.3 70.9 - - - +
57G GLN* 1.3 62.7 + - + +
58G GLY 3.0 0.4 - - - -
59G ALA* 3.1 14.1 + - - +
60G LEU* 3.1 16.4 + - - +
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Residues in contact with GLN 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G SER* 3.1 21.9 + - - +
55G GLU* 3.1 11.3 + - + +
56G ALA* 1.3 77.9 - - + +
58G GLY* 1.3 57.7 + - - +
60G LEU* 3.8 15.6 - - - +
61G ALA* 2.9 29.5 + - - +
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Residues in contact with GLY 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G PHE* 5.3 0.4 - - - -
54G PHE* 4.5 6.5 - - - -
55G GLU* 3.0 13.9 + - - +
57G GLN* 1.3 77.4 - - - +
59G ALA* 1.3 65.1 + - - +
61G ALA* 3.3 5.8 + - - +
62G ASN* 3.0 32.1 + - - +
7H ALA* 5.5 4.5 - - - -
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Residues in contact with ALA 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G PHE* 3.5 31.7 - - + -
34G VAL* 3.3 42.6 - - + -
54G PHE* 3.9 8.3 - - + -
56G ALA 3.1 4.9 + - - +
58G GLY* 1.3 76.8 - - - +
60G LEU* 1.3 58.2 + - - +
62G ASN* 3.1 4.0 + - - +
63G ILE* 2.9 33.2 + - - +
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Residues in contact with LEU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G VAL* 4.2 8.1 - - + -
35G ASP 4.1 4.0 - - - +
36G ILE* 3.5 44.6 - - + +
39G SER* 3.3 36.8 - - - +
56G ALA 3.1 11.3 + - - +
57G GLN* 3.8 21.3 - - - +
58G GLY 3.3 0.2 - - - -
59G ALA* 1.3 74.3 - - - +
61G ALA* 1.3 64.3 + - - +
63G ILE* 3.5 5.4 + - + +
64G ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G GLN 2.9 18.6 + - - +
58G GLY* 3.5 7.6 - - - +
60G LEU* 1.3 75.8 - - - +
62G ASN* 1.3 65.7 + - - +
64G ALA* 3.3 8.9 + - - +
65G VAL* 3.2 24.4 + - - +
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Residues in contact with ASN 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G GLN* 3.6 2.8 - - - +
11G GLN* 3.4 33.8 + - - +
22G PHE* 4.2 9.0 - - + -
58G GLY* 3.0 20.9 + - - +
59G ALA 3.4 8.5 - - - +
61G ALA* 1.3 77.6 - - - +
63G ILE* 1.3 66.5 + - - +
65G VAL* 2.9 19.6 + - - +
66G ASN* 3.0 14.7 + - - +
7H ALA* 4.9 4.4 - - - +
8H PHE 2.9 28.1 + - - +
9H ASN* 4.8 5.4 - - - +
10H GLU* 4.0 16.3 + - - +
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Residues in contact with ILE 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G GLN* 4.3 6.3 - - + -
12G PHE 3.6 13.2 - - - +
13G TYR* 3.9 26.9 - - + -
20G GLY* 4.5 0.9 - - - -
21G GLU 3.1 33.2 - - - +
22G PHE* 4.3 4.9 - - + -
34G VAL* 6.6 0.2 - - + -
36G ILE* 3.7 28.9 - - + -
59G ALA 2.9 23.3 + - - +
60G LEU* 3.8 7.2 - - + +
61G ALA 3.4 0.2 - - - -
62G ASN* 1.3 74.5 - - - +
64G ALA* 1.3 58.0 + - - +
66G ASN* 2.7 32.9 + - - +
67G LYS* 2.8 12.4 + - + +
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Residues in contact with ALA 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G LEU 3.1 11.7 + - - +
61G ALA* 3.3 13.0 - - - +
62G ASN 3.2 0.2 - - - -
63G ILE* 1.3 80.0 - - - +
65G VAL* 1.3 62.4 + - + +
67G LYS* 3.1 13.7 + - + +
68G ALA* 3.0 22.9 + - - +
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Residues in contact with VAL 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G ALA 3.2 14.2 + - - +
62G ASN* 2.9 13.4 + - - +
64G ALA* 1.3 75.9 - - + +
66G ASN* 1.3 57.9 + - - +
68G ALA* 3.3 2.8 + - - +
69G ASN* 2.9 44.9 + - - +
9H ASN* 6.0 1.1 - - - +
10H GLU* 3.9 23.8 - - + +
11H GLY 3.6 12.6 - - - +
12H LEU* 3.8 33.4 - - + -
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Residues in contact with ASN 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G GLN* 2.6 50.5 + - - +
12G PHE* 4.9 0.9 - - - -
13G TYR* 4.0 17.9 - - + +
62G ASN 3.0 5.4 + - - +
63G ILE* 2.7 17.4 + - - +
65G VAL* 1.3 72.9 - - - +
67G LYS* 1.3 57.5 + - - +
69G ASN* 4.3 3.9 - - - +
70G LEU* 2.8 30.3 + - - +
10H GLU* 4.1 19.0 + - - +
35H GLU* 3.6 28.5 + - + +
37H CYS* 4.7 5.7 - - - +
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Residues in contact with LYS 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G TYR* 3.3 55.5 - - + +
18G LYS* 6.2 2.5 - - - +
63G ILE* 2.8 12.8 + - + +
64G ALA* 3.3 15.7 - - + +
66G ASN* 1.3 74.7 - - - +
68G ALA* 1.3 66.6 + - - +
70G LEU* 3.3 9.9 + - - +
71G ASP* 3.5 20.8 + - - +
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Residues in contact with ALA 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G ALA 3.0 12.7 + - - +
65G VAL* 3.7 7.0 - - - +
67G LYS* 1.3 76.2 - - - +
69G ASN* 1.3 64.6 + - - +
71G ASP* 3.1 20.0 + - - +
72G VAL* 3.4 15.7 + - + +
12H LEU* 4.2 18.6 - - + -
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Residues in contact with ASN 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G VAL* 2.9 28.9 + - - +
66G ASN* 3.8 5.7 - - - +
68G ALA* 1.3 75.9 - - - +
70G LEU* 1.3 63.5 + - - +
72G VAL* 3.1 9.2 + - - +
73G MET* 2.9 27.9 + - - +
10H GLU* 4.6 6.9 - - - +
11H GLY 3.0 21.8 + - - -
12H LEU* 3.5 7.4 - - - +
13H LYS* 2.8 43.3 + - + +
35H GLU* 3.7 23.7 + - + +
56H TYR* 5.9 0.8 - - - -
87H TRP* 5.1 0.4 - - - -
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Residues in contact with LEU 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G TYR* 3.7 20.9 - - + +
15G LEU* 3.6 36.6 - - + +
66G ASN 2.8 18.8 + - - +
67G LYS* 3.5 8.1 - - - +
68G ALA 3.2 0.2 - - - -
69G ASN* 1.3 76.4 - - - +
71G ASP* 1.3 58.1 + - - +
73G MET* 3.1 3.4 + - - +
74G LYS* 2.8 33.3 + - + +
33H PHE* 3.7 30.3 - - + +
35H GLU* 3.9 28.4 - - + +
58H TYR* 4.0 16.8 - - + -
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Residues in contact with ASP 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU* 4.3 17.8 - - - +
67G LYS* 3.5 18.4 + - - +
68G ALA* 3.1 11.2 + - - +
70G LEU* 1.3 78.3 - - - +
72G VAL* 1.3 64.0 + - + +
74G LYS* 3.4 9.8 + - - +
75G GLU* 3.2 27.0 + - - +
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Residues in contact with VAL 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G ALA 3.6 14.4 - - - +
69G ASN* 3.1 11.3 + - - +
71G ASP* 1.3 78.0 - - + +
73G MET* 1.3 59.1 + - + +
75G GLU* 3.2 7.7 + - + +
76G ARG* 2.8 43.8 + - + +
13H LYS* 3.9 23.1 - - + +
14H GLY 3.0 28.9 - - - +
15H GLY* 4.9 2.9 - - - -
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Residues in contact with MET 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ASN 2.9 18.1 + - - +
70G LEU 3.5 7.2 - - - +
72G VAL* 1.3 74.7 - - - +
74G LYS* 1.3 62.7 + - - +
76G ARG* 3.3 38.7 + - - +
77G SER* 2.9 29.5 + - - -
13H LYS* 3.4 22.7 - - + +
35H GLU* 3.3 18.6 - - - +
58H TYR* 3.8 31.5 - - + -
63H ASN* 3.7 27.8 - - - +
79H LEU* 4.1 15.0 - - + +
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Residues in contact with LYS 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU* 4.2 22.6 - - + +
70G LEU* 2.8 22.5 + - + +
71G ASP* 3.8 11.4 - - - +
73G MET* 1.3 75.8 - - - +
75G GLU* 1.3 61.6 + - + +
77G SER* 3.7 0.3 + - - -
78G ASN 3.4 2.1 + - - -
79G ASN* 2.8 53.4 + - - +
33H PHE* 3.6 60.9 - - + -
58H TYR* 3.9 8.7 - - - +
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Residues in contact with GLU 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G ASP 3.2 14.9 + - - +
72G VAL* 3.2 11.3 + - + +
74G LYS* 1.3 75.3 - - + +
76G ARG* 1.3 61.3 + - - +
77G SER 3.1 6.4 + - - -
78G ASN* 3.1 12.7 + - - +
79G ASN* 4.9 10.8 + - - +
18H SER* 4.4 9.1 + - - -
19H LEU 5.3 0.2 - - - +
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Residues in contact with ARG 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G VAL* 2.8 26.4 + - + +
73G MET* 3.3 25.9 + - - +
75G GLU* 1.3 75.8 - - - +
77G SER* 1.3 58.7 + - - +
13H LYS* 4.0 3.4 - - - +
14H GLY 3.7 19.8 + - - +
15H GLY 5.8 0.2 - - - -
16H GLY 3.7 12.1 + - - +
17H GLY 3.6 21.3 - - - +
18H SER* 4.2 9.0 - - - +
19H LEU* 2.8 30.0 + - - +
79H LEU* 2.7 49.7 + - + +
82H PRO* 3.8 20.9 - - - +
83H ASP* 2.8 43.6 + - - -
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Residues in contact with SER 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G MET 2.9 16.3 + - - -
74G LYS 3.9 2.1 + - - -
75G GLU 3.1 1.0 - - - -
76G ARG* 1.3 77.1 - - - +
78G ASN* 1.3 59.2 + - - +
79G ASN 4.2 1.0 + - - -
80G THR* 2.5 37.8 + - - -
19H LEU* 3.8 10.1 - - - +
21H GLY* 4.2 6.0 - - - -
58H TYR* 3.3 27.6 + - - -
79H LEU* 4.0 18.8 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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