Contacts of the helix formed by residues 67 - 79 (chain A) in PDB entry 7ICL
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 THR 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LYS* 3.6 27.7 - - - +
66A GLY* 1.3 73.1 - - - -
68A LYS* 1.3 79.9 + - - +
70A ALA* 3.6 3.1 + - - +
71A GLU* 3.1 23.2 + - - +
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Residues in contact with LYS 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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35A LYS* 5.8 6.1 - - - +
66A GLY* 3.3 0.8 - - - -
67A THR* 1.3 90.0 - - - +
69A ILE* 1.3 66.8 + - + +
71A GLU* 2.8 34.0 - - + +
72A LYS* 3.1 28.2 + - - +
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Residues in contact with ILE 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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19A LEU* 4.3 26.0 - - + -
38A ALA* 4.7 5.4 - - + +
39A TYR* 3.8 28.7 - - + +
41A LYS* 4.2 22.2 - - - +
42A ALA* 4.2 13.2 - - + -
64A GLY 4.2 9.2 - - - +
65A VAL* 4.9 8.7 - - + -
66A GLY* 3.7 11.6 + - - +
67A THR 3.3 0.2 - - - -
68A LYS* 1.3 81.4 - - + +
70A ALA* 1.3 49.9 + - - +
71A GLU 2.9 0.2 - - - -
72A LYS* 2.9 8.7 + - + +
73A ILE* 2.8 46.0 + - + +
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Residues in contact with ALA 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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56A GLY* 3.8 24.9 - - - +
57A ALA* 4.8 0.4 - - - +
60A LYS* 4.1 15.5 - - + +
65A VAL* 4.8 1.0 - - - +
66A GLY 3.4 17.9 + - - +
67A THR* 3.7 6.7 - - - +
69A ILE* 1.3 77.7 - - - +
71A GLU* 1.3 53.4 + - - +
73A ILE* 3.7 12.1 - - - +
74A ASP* 2.9 38.8 + - - +
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Residues in contact with GLU 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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67A THR* 3.1 16.9 + - - +
68A LYS* 2.8 26.7 + - + +
70A ALA* 1.3 78.6 - - - +
72A LYS* 1.3 70.3 + - + +
74A ASP* 4.1 3.0 - - - +
75A GLU* 3.2 24.6 + - - +
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Residues in contact with LYS 72 (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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18A MET* 3.5 20.5 - - - +
19A LEU* 5.6 0.9 - - + -
22A LEU* 4.6 9.0 - - + -
39A TYR* 3.6 27.3 + - + +
68A LYS* 3.1 36.3 + - - +
69A ILE* 2.9 13.4 + - + +
71A GLU* 1.3 90.6 - - + +
73A ILE* 1.4 59.9 + - - +
75A GLU* 3.5 4.6 + - - +
76A PHE* 3.1 18.9 + - - +
82A LEU* 3.8 28.8 - - + +
84A LYS* 4.8 21.7 - - + +
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Residues in contact with ILE 73 (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 ILE* 3.4 30.7 - - + -
18A MET* 4.4 8.7 - - + +
19A LEU* 5.7 0.9 - - + -
46A ILE* 5.9 2.5 - - + -
53A ILE* 4.7 2.9 - - + -
55A SER 4.7 1.8 - - - +
56A GLY* 4.1 14.4 - - - +
59A ALA* 3.0 37.5 - - + -
65A VAL* 4.8 0.4 - - + -
69A ILE* 2.8 33.8 + - + +
70A ALA* 3.4 8.9 + - - +
72A LYS* 1.4 67.1 - - - +
74A ASP* 1.3 58.5 + - - +
77A LEU* 2.5 75.0 + - + +
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Residues in contact with ASP 74 (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 LYS 4.6 1.0 - - - +
55A SER* 3.4 12.8 - - - -
56A GLY* 2.8 36.8 + - - -
57A ALA* 3.8 5.0 + - - +
70A ALA* 2.9 16.1 + - - +
71A GLU* 4.2 3.1 - - - +
73A ILE* 1.3 78.1 - - - +
75A GLU* 1.3 52.7 + - - +
77A LEU* 3.6 4.7 - - - +
78A ALA* 2.7 36.7 + - - +
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Residues in contact with GLU 75 (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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71A GLU* 3.2 19.2 + - - +
72A LYS* 4.0 3.9 - - - +
73A ILE 3.2 0.2 - - - -
74A ASP* 1.3 72.5 - - - +
76A PHE* 1.3 62.8 + - - +
78A ALA* 3.1 5.3 + - - -
79A THR* 2.7 40.2 + - + +
81A LYS 3.6 10.1 - - - +
82A LEU* 3.6 13.6 - - - +
83A ARG* 2.9 35.1 + - - +
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Residues in contact with PHE 76 (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 GLY* 4.0 35.9 - - - -
15A ILE* 4.4 9.0 - - + -
18A MET* 3.0 42.4 - - + -
72A LYS 3.1 5.7 + - - +
73A ILE 4.1 0.2 - - - +
75A GLU* 1.3 76.9 - - - +
77A LEU* 1.3 81.9 + - + +
79A THR 2.6 23.7 - - - +
80A GLY* 4.0 13.6 + - - -
81A LYS* 3.3 22.9 - - - +
82A LEU* 4.7 4.7 - - + -
85A LEU* 5.6 2.0 - - + -
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Residues in contact with LEU 77 (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 ILE* 3.4 20.6 - - + -
53A ILE 3.5 12.1 - - - +
54A LYS* 3.0 39.9 - - - +
55A SER* 3.8 6.7 - - - +
73A ILE* 2.5 50.9 + - + +
74A ASP* 3.7 5.8 - - - +
76A PHE* 1.3 86.8 - - + +
78A ALA* 1.3 61.0 + - - +
79A THR* 4.5 1.0 - - - -
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Residues in contact with ALA 78 (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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74A ASP 2.7 18.5 + - - +
75A GLU* 3.4 8.7 - - - +
77A LEU* 1.3 78.2 - - - +
79A THR* 1.3 62.6 + - + +
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Residues in contact with THR 79 (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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75A GLU* 2.7 27.0 + - + +
76A PHE 2.6 21.0 - - - +
77A LEU 4.6 0.9 - - - -
78A ALA* 1.3 82.3 - - + +
80A GLY* 1.3 49.8 + - - +
81A LYS* 2.3 48.6 + - - +
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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