Contacts of the helix formed by residues 64 - 78 (chain C) in PDB entry 1L3C
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 ASN 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C SER* 3.4 29.1 + - - -
13C VAL* 3.6 16.4 - - - +
14C PRO* 5.4 1.6 - - - +
62C ASP* 3.2 14.1 + - - +
63C ARG* 1.3 76.9 - - - +
65C PRO* 1.3 72.5 - - - +
66C GLU* 2.8 25.8 + - - +
67C ALA* 3.0 21.2 + - + +
68C ILE* 3.3 9.2 + - - +
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Residues in contact with PRO 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ARG 3.3 5.6 - - - +
64C ASN* 1.3 91.4 - - - +
66C GLU* 1.3 59.5 + - + +
68C ILE* 3.2 6.3 + - + +
69C SER* 2.9 28.9 + - - -
88C GLU* 3.1 39.0 - - + +
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ASN* 3.7 18.1 + - - +
11C PRO* 6.1 0.2 - - - +
12C SER* 3.4 19.9 + - - +
13C VAL* 3.5 17.0 - - + -
64C ASN* 2.8 15.1 + - - +
65C PRO* 1.3 81.9 - - + +
67C ALA* 1.3 54.4 + - - +
69C SER* 3.3 8.8 - - - -
70C THR* 2.7 37.1 + - - -
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Residues in contact with ALA 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C VAL* 3.5 17.8 - - + +
42C CYS* 4.8 0.7 - - - -
43C GLY* 3.1 16.3 - - - +
62C ASP* 3.3 29.4 - - + +
64C ASN* 3.0 18.6 + - + +
66C GLU* 1.3 76.4 - - - +
68C ILE* 1.3 66.8 + - - +
69C SER 3.1 0.2 - - - -
70C THR* 3.2 0.4 + - - -
71C THR* 2.9 29.8 + - - -
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Residues in contact with ILE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C CYS* 4.1 8.7 - - - -
60C ALA 4.0 7.6 - - - +
62C ASP* 4.0 20.4 - - + +
64C ASN 3.3 5.5 + - - +
65C PRO* 3.2 9.8 + - + +
67C ALA* 1.3 76.2 - - - +
69C SER* 1.3 59.4 + - - +
71C THR* 3.3 3.3 + - - -
72C GLU* 2.9 30.2 + - + +
86C LEU* 3.6 27.4 - - + +
87C MSE 3.6 30.3 - - - +
88C GLU* 4.0 27.6 - - + +
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Residues in contact with SER 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C PRO 2.9 13.9 + - - -
66C GLU* 3.3 16.9 + - - -
68C ILE* 1.3 79.5 - - - +
70C THR* 1.3 61.0 + - - -
72C GLU* 3.2 10.2 - - - +
73C MSE 3.0 37.6 + - - +
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Residues in contact with THR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 3.1 37.2 - - + +
9C LYS* 4.7 4.0 - - - -
10C ASN* 3.6 24.2 + - + +
13C VAL* 4.1 3.2 - - + +
43C GLY 4.4 5.2 - - - -
44C THR* 4.0 13.0 - - + +
66C GLU 2.7 25.0 + - - -
67C ALA* 3.8 4.0 - - - -
69C SER* 1.3 70.0 - - - +
71C THR* 1.3 65.8 + - - +
73C MSE 3.2 13.1 + - - +
74C ASN* 3.0 34.1 + - - +
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Residues in contact with THR 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C CYS* 3.4 16.2 - - - -
43C GLY 3.0 20.8 + - - -
44C THR 3.7 8.5 - - - -
45C GLY* 3.4 19.1 + - - -
48C THR* 4.0 25.8 - - + +
49C LEU* 4.5 0.6 - - + +
67C ALA 2.9 12.7 + - - -
68C ILE* 3.7 4.3 - - - -
70C THR* 1.3 74.9 - - - +
72C GLU* 1.3 63.2 + - - +
74C ASN* 3.3 2.8 + - - +
75C LEU* 2.9 32.4 + - + +
86C LEU* 4.1 15.9 - - + -
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ILE* 2.9 14.9 + - + +
69C SER* 3.2 15.0 - - - +
71C THR* 1.3 78.0 - - - +
73C MSE 1.3 62.6 + - + +
75C LEU* 3.3 11.5 + - - +
76C GLN* 3.2 48.0 + - - +
86C LEU* 3.7 24.2 - - + +
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Residues in contact with MSE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 3.9 31.4 - - + -
10C ASN* 5.7 5.2 - - + +
69C SER* 3.0 32.4 + - - +
70C THR* 3.5 22.4 - - - +
71C THR 3.2 0.2 - - - -
72C GLU* 1.3 76.1 - - + +
74C ASN* 1.3 65.3 + - - +
76C GLN* 3.3 9.3 + - - +
77C ARG* 2.9 53.9 + - - +
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Residues in contact with ASN 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C GLU 4.4 2.4 - - - +
7C PHE* 3.5 16.7 - - + -
8C ILE* 2.7 53.3 + - - +
44C THR* 3.0 28.6 + - - +
49C LEU* 3.9 17.3 - - + +
70C THR* 3.0 17.9 + - - +
71C THR 3.9 2.7 - - - +
73C MSE 1.3 79.2 - - - +
75C LEU* 1.3 62.9 + - - +
77C ARG* 3.4 4.0 + - - +
78C HIS* 3.0 32.7 + - + -
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C THR* 4.3 7.4 - - + -
49C LEU* 3.7 26.2 - - + +
52C ALA* 4.5 0.4 - - + -
71C THR* 2.9 33.6 + - + +
72C GLU* 3.4 14.8 - - - +
74C ASN* 1.3 76.9 - - - +
76C GLN* 1.3 63.8 + - + +
78C HIS* 3.2 4.0 + - - -
79C GLY 3.1 4.0 + - - -
80C LEU* 3.0 40.8 + - + +
81C GLY* 4.1 22.9 - - - +
84C VAL* 4.0 34.8 - - + -
86C LEU* 4.1 9.0 - - + -
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Residues in contact with GLN 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLU* 3.2 41.9 + - - +
73C MSE 3.6 11.6 - - - +
75C LEU* 1.3 77.6 - - + +
77C ARG* 1.3 74.0 + - - +
79C GLY* 2.8 20.6 + - - +
80C LEU 4.1 4.7 + - - +
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Residues in contact with ARG 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 3.4 27.5 - - + +
73C MSE 2.9 49.3 + - - +
74C ASN* 3.9 6.3 - - - +
75C LEU 3.4 0.2 - - - -
76C GLN* 1.3 89.2 + - - +
78C HIS* 1.3 71.6 + - + +
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Residues in contact with HIS 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ILE* 3.9 29.3 - - + +
6C GLU* 3.4 34.0 + - + -
7C PHE* 5.4 1.8 - + - -
49C LEU* 3.9 25.1 - - + -
74C ASN* 3.0 31.5 + - + +
75C LEU 3.2 2.0 + - - +
76C GLN 3.0 1.0 - - - -
77C ARG* 1.3 90.3 + - + +
79C GLY* 1.3 64.2 + - - +
80C LEU* 3.3 15.2 + - + +
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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