Contacts of the helix formed by residues 65 - 78 (chain A) in PDB entry 3IML
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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ASN 4.4 0.2 + - - -
64A ILE* 1.3 72.3 - - - +
66A TYR* 1.3 61.2 + - - +
67A ILE* 3.5 9.4 + - - +
68A GLN* 3.1 38.7 + - + +
69A ILE* 3.2 16.2 + - + +
64C ILE 3.7 7.5 - - - +
65C ASP* 3.4 46.8 + - + +
66C TYR 5.5 0.5 + - - -
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Residues in contact with TYR 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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28A ILE* 4.1 23.8 - - + +
32A ILE* 4.3 6.7 - - + +
54A LEU* 4.1 19.0 - - + +
58A ILE* 3.8 15.4 - - + +
60A THR* 4.9 3.1 - - - +
62A ALA 5.2 1.2 + - - -
64A ILE* 3.1 41.1 + - + +
65A ASP* 1.3 72.3 + - - +
67A ILE* 1.3 62.5 + - - +
69A ILE* 3.7 4.5 + - - +
70A ALA* 3.2 22.3 + - - +
95A VAL* 4.2 16.6 - - + -
97A TYR* 3.7 35.7 - + + -
99A LYS* 3.5 36.8 + - + +
67C ILE* 5.6 6.3 - - + -
71C ARG* 5.6 7.0 - - - -
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Residues in contact with ILE 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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65A ASP* 3.2 7.9 + - - +
66A TYR* 1.3 76.1 - - - +
68A GLN* 1.3 60.6 + - - +
70A ALA* 3.3 6.7 + - - +
71A ARG* 3.0 52.4 + - - +
93A VAL* 3.8 32.7 - - + +
95A VAL* 4.0 9.9 - - + -
66C TYR* 5.8 4.7 - - + -
67C ILE* 3.9 18.6 - - + +
95C VAL* 3.4 42.8 - - + -
99C LYS* 4.4 10.3 - - - +
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Residues in contact with GLN 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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65A ASP* 3.1 32.9 + - + +
67A ILE* 1.3 76.9 - - - +
69A ILE* 1.3 58.2 + - + +
71A ARG* 3.3 16.9 + - - +
72A ASP* 2.8 66.7 + - - +
63C ASN* 3.8 20.6 + - - +
99C LYS* 5.8 1.2 + - - -
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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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24A ILE 5.0 0.2 - - - +
27A ALA* 3.7 28.3 - - + +
28A ILE* 3.8 20.6 - - + +
31A ALA* 3.1 31.9 - - + -
64A ILE* 3.3 29.4 - - + -
65A ASP* 3.2 9.8 + - + +
66A TYR 3.9 4.3 - - - +
67A ILE 3.3 0.2 - - - -
68A GLN* 1.3 78.3 - - + +
70A ALA* 1.3 60.6 + - - +
72A ASP* 3.7 9.1 - - - +
73A THR* 2.8 29.8 + - - -
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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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24A ILE* 4.0 32.4 - - + +
28A ILE* 5.1 0.4 - - + -
52A VAL* 4.8 8.7 - - + -
54A LEU* 4.7 9.4 - - + -
66A TYR 3.2 12.9 + - - +
67A ILE* 3.7 9.2 - - - +
69A ILE* 1.3 77.7 - - - +
71A ARG* 1.3 59.1 + - + +
73A THR* 3.3 4.5 + - - -
74A ILE* 3.0 36.5 + - + +
93A VAL* 5.3 6.1 - - + -
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Residues in contact with ARG 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 ILE* 3.0 32.4 + - + +
68A GLN* 3.6 19.3 - - - +
70A ALA* 1.3 75.8 - - + +
72A ASP* 1.3 65.3 + - - +
74A ILE* 3.3 11.0 + - + +
75A LYS* 3.0 24.2 + - - +
91A CYS* 2.9 44.3 + - - +
93A VAL* 4.4 9.6 - - + +
95C VAL* 5.1 5.9 + - - +
96C ALA* 6.3 0.2 - - - +
97C TYR 5.0 6.9 + - - +
99C LYS* 3.5 33.9 - - - +
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Residues in contact with ASP 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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68A GLN* 2.8 55.8 + - - +
69A ILE* 3.7 9.5 - - - +
71A ARG* 1.3 72.6 - - - +
73A THR* 1.3 57.5 + - - +
75A LYS* 3.3 12.3 + - - +
76A ARG* 2.9 30.8 + - - +
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Residues in contact with THR 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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23A GLN* 4.0 3.8 - - + -
24A ILE* 3.9 33.0 - - + +
27A ALA* 3.2 21.1 - - - +
69A ILE 2.8 22.2 + - - -
70A ALA* 3.5 5.5 - - - -
71A ARG 3.2 0.2 - - - -
72A ASP* 1.3 74.1 - - - +
74A ILE* 1.3 65.5 + - - +
76A ARG* 3.3 6.9 + - - +
77A ILE* 3.0 41.5 + - + +
356A GLU* 3.6 20.5 + - - +
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Residues in contact with ILE 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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20A VAL* 4.3 11.4 - - + -
24A ILE* 4.1 16.6 - - + -
47A CYS* 6.1 0.4 - - + -
52A VAL* 4.1 26.0 - - + -
70A ALA* 3.0 25.3 + - + +
71A ARG* 3.7 10.1 - - + +
73A THR* 1.3 75.0 - - - +
75A LYS* 1.3 62.3 + - - +
77A ILE* 3.4 10.5 + - - +
78A GLY 3.4 4.7 + - - -
79A TYR* 3.2 48.6 + - + +
91A CYS* 4.6 14.8 - - - -
239A PRO* 6.4 1.1 - - + -
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Residues in contact with LYS 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 ARG 3.0 16.6 + - - +
72A ASP* 3.6 12.3 + - - +
73A THR 3.2 0.2 - - - -
74A ILE* 1.3 74.7 - - - +
76A ARG* 1.3 65.8 + - - +
78A GLY* 3.1 15.8 + - - -
79A TYR 4.0 11.3 + - - +
80A ASP* 4.7 17.1 - - + +
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Residues in contact with ARG 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 GLU* 2.8 28.5 + - - -
23A GLN* 3.3 25.4 + - - +
72A ASP 2.9 17.8 + - - +
73A THR* 3.3 11.0 + - - +
75A LYS* 1.3 79.5 - - - +
77A ILE* 1.3 67.4 + - - +
78A GLY* 3.3 1.2 + - - -
157A ARG* 3.4 23.7 + - - +
356A GLU* 2.6 41.3 + - - +
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Residues in contact with ILE 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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14A GLU* 3.3 39.3 - - + +
15A GLY* 3.6 17.3 - - - +
20A VAL* 4.2 21.3 - - + -
23A GLN* 3.8 25.4 - - - +
73A THR* 3.0 35.7 + - + +
74A ILE* 3.7 7.0 - - - +
75A LYS 3.2 0.4 - - - -
76A ARG* 1.3 85.2 - - - +
78A GLY* 1.3 56.5 + - - +
79A TYR* 4.0 13.0 - - + -
156A ARG* 3.1 25.2 + - - -
157A ARG* 4.1 0.2 + - - -
166A PRO* 3.7 3.1 - - + +
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Residues in contact with GLY 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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75A LYS 3.1 11.5 + - - -
76A ARG 3.2 1.5 - - - -
77A ILE* 1.3 80.3 - - - +
79A TYR* 1.3 60.2 + - - +
80A ASP* 3.2 11.0 + - - +
156A ARG* 4.1 9.2 - - - -
166A PRO* 3.8 19.7 - - - +
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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