Contacts of the helix formed by residues 65 - 78 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B ASN 4.3 0.2 + - - -
64B ILE* 1.3 72.4 - - - +
66B TYR* 1.3 62.3 + - - +
67B ILE* 3.4 11.4 + - - +
68B GLN* 3.1 37.5 + - + +
69B ILE* 3.2 16.9 + - - +
64D ILE 4.1 6.6 - - - +
65D ASP* 3.5 41.6 + - + +
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE* 4.3 15.7 - - + +
32B ILE* 4.4 12.3 - - + +
54B LEU* 3.9 21.5 - - + +
58B ILE* 4.0 20.1 - - + +
60B THR* 4.8 2.8 - - - +
62B ALA 5.1 0.2 + - - -
64B ILE* 3.4 42.7 + - + +
65B ASP* 1.3 72.0 + - - +
67B ILE* 1.3 63.0 + - - +
69B ILE* 3.4 4.5 + - - +
70B ALA* 3.0 23.0 + - - +
95B VAL* 4.4 13.2 - - + -
97B TYR* 3.6 35.2 - + + -
99B LYS* 3.6 34.1 - - + +
67D ILE* 5.4 7.3 - - + +
71D ARG* 6.2 2.0 - - - -
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Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ASP* 3.3 8.4 + - - +
66B TYR* 1.3 77.7 - - - +
68B GLN* 1.3 64.4 + - - +
70B ALA* 3.2 7.3 + - - +
71B ARG* 3.0 54.2 + - - +
93B VAL* 3.7 30.0 - - + +
95B VAL* 4.0 8.5 - - + -
66D TYR* 5.5 7.6 - - + +
67D ILE* 3.9 18.1 - - + +
95D VAL* 3.5 40.4 - - + -
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ASP* 3.1 31.7 + - + +
67B ILE* 1.3 78.1 - - - +
69B ILE* 1.3 60.4 + - + +
71B ARG* 3.3 15.3 + - - +
72B ASP* 2.7 67.4 + - - +
63D ASN* 5.6 4.0 - - - +
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Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 5.6 0.2 - - - -
27B ALA* 3.8 33.2 - - + +
28B ILE* 3.9 13.5 - - + +
31B ALA* 3.1 31.2 - - + -
64B ILE* 4.1 11.2 - - + -
65B ASP* 3.2 15.9 + - + +
66B TYR* 3.9 4.7 - - - +
67B ILE 3.2 0.2 - - - -
68B GLN* 1.3 77.7 - - + +
70B ALA* 1.3 57.0 + - - +
72B ASP* 3.9 10.2 - - + +
73B THR* 2.7 34.4 + - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 4.0 34.3 - - + +
28B ILE* 5.2 0.2 - - - +
52B VAL* 4.7 10.5 - - + -
54B LEU* 4.6 9.4 - - + -
66B TYR 3.0 15.0 + - - +
67B ILE* 3.6 9.6 - - - +
69B ILE* 1.3 77.2 - - - +
71B ARG* 1.3 64.2 + - + +
73B THR* 3.0 4.7 + - - -
74B ILE* 3.0 32.0 + - + +
93B VAL* 5.6 4.0 - - + -
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Residues in contact with ARG 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ILE* 3.0 36.5 + - + +
68B GLN* 3.7 20.0 - - - +
70B ALA* 1.3 77.2 - - + +
72B ASP* 1.3 57.0 + - - +
74B ILE* 3.5 11.8 + - + +
75B LYS* 2.9 30.4 + - - +
91B CYS* 3.3 38.3 + - - +
93B VAL* 3.8 17.7 - - + +
95D VAL* 5.2 9.5 + - - +
97D TYR 5.9 1.0 + - - -
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B GLN* 2.7 55.5 + - - +
69B ILE* 3.9 11.9 - - + +
70B ALA 3.3 0.2 - - - -
71B ARG* 1.3 71.8 - - - +
73B THR* 1.3 58.5 + - - +
75B LYS* 3.3 11.4 + - - +
76B ARG* 2.9 29.5 + - - +
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLN 3.9 21.3 - - - -
24B ILE* 3.9 11.1 - - + +
27B ALA* 3.1 19.8 - - - +
69B ILE* 2.7 18.7 + - - +
70B ALA* 3.0 9.3 + - - -
72B ASP* 1.3 74.9 - - - +
74B ILE* 1.3 60.4 + - - +
76B ARG* 3.3 13.7 + - - +
77B ILE* 3.0 44.1 + - + +
356B GLU* 3.5 21.9 + - - +
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 4.3 11.2 - - + -
24B ILE* 4.1 22.9 - - + -
47B CYS* 6.1 0.9 - - + -
52B VAL* 4.3 19.5 - - + -
70B ALA* 3.0 23.6 + - + +
71B ARG* 3.8 11.0 - - + +
73B THR* 1.3 72.5 - - - +
75B LYS* 1.3 65.5 + - - +
77B ILE* 3.6 10.5 + - - +
78B GLY 3.3 4.3 + - - -
79B TYR* 3.2 46.1 + - + +
91B CYS* 5.2 9.4 - - + -
239B PRO* 6.2 2.9 - - + -
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Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ARG 2.9 18.8 + - - +
72B ASP* 3.4 11.7 - - - +
73B THR 3.2 0.2 - - - -
74B ILE* 1.3 75.1 - - - +
76B ARG* 1.3 67.9 + - - +
78B GLY* 2.9 17.3 + - - -
79B TYR 4.2 11.1 - - - +
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 3.1 29.0 + - - +
23B GLN* 3.1 24.2 + - - -
72B ASP 2.9 16.9 + - - +
73B THR* 3.3 15.7 + - - +
75B LYS* 1.3 80.7 - - - +
77B ILE* 1.3 68.2 + - - +
78B GLY* 3.3 1.4 + - - -
156B ARG* 5.4 0.5 + - - -
157B ARG* 5.1 10.9 - - - -
356B GLU* 2.5 42.2 + - - +
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 3.5 30.3 - - + +
15B GLY* 3.7 15.9 - - - -
20B VAL* 4.2 23.3 - - + -
23B GLN* 3.8 31.9 - - - +
73B THR* 3.0 39.9 + - + +
74B ILE* 3.8 6.5 - - - +
76B ARG* 1.3 80.5 - - - +
78B GLY* 1.3 56.6 + - - +
79B TYR* 3.9 17.7 - - + -
156B ARG* 3.2 27.9 + - - -
166B PRO* 3.7 3.3 - - + +
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ILE 3.3 0.4 + - - -
75B LYS 2.9 13.5 + - - -
76B ARG 4.2 1.3 - - - -
77B ILE* 1.3 80.0 - - - +
79B TYR* 1.3 64.2 + - - +
156B ARG* 4.4 7.0 - - - -
166B PRO* 3.8 19.2 - - - +
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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