Contacts of the helix formed by residues 67 - 83 (chain C) in PDB entry 1E3S
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 SER 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C ASN* 3.0 14.9 + - - -
66C THR* 1.3 80.5 + - - +
68C GLU* 1.3 59.5 + - - +
69C LYS* 3.3 8.8 + - - +
70C GLU* 3.0 38.8 + - - +
71C VAL* 3.1 23.9 + - - +
127C ASN* 3.7 2.2 - - - -
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Residues in contact with GLU 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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66C THR 3.8 2.6 + - - -
67C SER* 1.3 71.6 - - - +
69C LYS* 1.3 74.2 + - + +
72C GLN* 3.1 26.0 + - - +
127C ASN* 3.6 14.7 - - - +
130C ARG* 2.8 39.3 + - - +
131C LEU* 4.1 7.3 - - + +
111D LEU* 4.0 13.5 + - + +
112D GLU* 3.6 26.9 - - - +
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Residues in contact with LYS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C SER* 3.3 6.2 + - - +
68C GLU* 1.3 88.7 - - + +
70C GLU* 1.3 60.8 + - + +
72C GLN* 3.7 4.5 - - - +
73C ALA* 3.0 28.8 + - - +
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Residues in contact with GLU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PRO* 5.8 3.5 - - - +
62C PRO 4.6 4.5 - - - +
63C ALA* 3.5 26.0 - - + +
64C ASN* 2.9 36.6 + - - +
67C SER* 3.0 23.5 + - - +
69C LYS* 1.3 75.3 - - + +
71C VAL* 1.3 66.2 + - - +
73C ALA* 3.5 5.9 + - - +
74C ALA* 3.1 17.2 + - - +
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 4.8 12.3 - - + -
63C ALA* 4.6 3.8 - - + -
64C ASN 3.9 3.6 - - - +
65C VAL* 3.8 26.7 - - - +
67C SER 3.1 21.6 + - - +
70C GLU* 1.3 74.8 - - - +
72C GLN* 1.3 65.5 + - - +
74C ALA* 3.1 5.4 + - - +
75C LEU* 3.0 38.4 + - + +
127C ASN* 3.9 8.1 - - - +
128C VAL* 4.4 25.4 - - + -
131C LEU* 3.7 23.6 - - + -
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Residues in contact with GLN 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 GLU 3.1 20.2 + - - +
69C LYS* 3.7 5.6 - - - +
71C VAL* 1.3 78.8 - - - +
73C ALA* 1.3 62.8 + - - +
75C LEU* 3.5 12.8 + - - +
76C THR* 3.1 35.8 + - - +
131C LEU* 3.8 30.3 - - + +
135C VAL* 5.3 5.2 - - - +
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Residues in contact with ALA 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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69C LYS 3.0 18.2 + - - +
70C GLU* 3.9 7.0 - - - +
71C VAL 3.2 0.2 - - - -
72C GLN* 1.3 77.6 - - - +
74C ALA* 1.3 57.7 + - - +
76C THR* 3.4 7.8 + - - -
77C LEU* 3.0 27.8 + - - +
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Residues in contact with ALA 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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14C VAL* 5.8 0.8 - - + +
38C VAL* 4.9 3.0 - - + +
40C LEU* 3.7 26.7 - - + -
61C ALA* 3.9 27.5 - - + +
62C PRO 5.1 1.1 - - - +
63C ALA* 4.4 4.3 - - + -
70C GLU 3.1 13.3 + - - +
71C VAL 3.1 8.8 + - - +
73C ALA* 1.3 74.4 - - - +
75C LEU* 1.3 63.7 + - - +
77C LEU* 3.3 6.5 + - - +
78C ALA* 3.1 22.7 + - - +
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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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14C VAL* 4.3 22.4 - - + -
40C LEU* 5.1 4.5 - - + -
71C VAL* 3.0 31.1 + - + +
72C GLN* 4.0 10.8 - - - +
74C ALA* 1.3 73.4 - - - +
76C THR* 1.3 65.4 + - - +
78C ALA* 3.4 3.9 + - - +
79C LYS* 3.1 23.7 + - - +
85C ILE* 3.9 25.8 - - + +
128C VAL* 4.9 5.8 - - + +
131C LEU* 3.8 20.4 - - + +
132C VAL* 3.7 40.8 - - + +
135C VAL* 4.8 9.9 - - + +
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Residues in contact with THR 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 GLN* 3.1 24.9 + - - +
73C ALA* 3.6 10.7 - - - -
74C ALA 3.3 0.2 - - - -
75C LEU* 1.3 77.4 - - - +
77C LEU* 1.3 61.4 + - - +
79C LYS* 3.4 5.2 + - - +
80C GLU* 3.1 48.8 + - + +
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Residues in contact with LEU 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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38C VAL* 5.9 0.2 - - + -
59C ILE* 4.3 18.8 - - + -
60C PHE 4.5 6.3 - - - +
61C ALA* 4.0 25.8 - - + -
62C PRO* 5.9 1.1 - - + -
73C ALA 3.0 14.2 + - - +
74C ALA* 3.5 8.3 - - - +
75C LEU 3.3 0.2 - - - -
76C THR* 1.3 75.7 - - - +
78C ALA* 1.3 63.3 + - - +
80C GLU* 3.9 8.3 - - + +
81C LYS* 2.9 38.9 + - + +
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Residues in contact with ALA 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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12C VAL* 5.3 2.7 - - + -
14C VAL* 4.1 18.4 - - + -
38C VAL* 3.7 30.7 - - + +
59C ILE* 5.1 0.7 - - - -
74C ALA 3.1 13.3 + - - +
75C LEU* 3.7 8.1 - - - +
76C THR 3.3 0.4 - - - -
77C LEU* 1.3 78.6 - - - +
79C LYS* 1.3 57.5 + - - +
81C LYS* 4.6 2.7 - - - -
82C PHE* 2.9 35.3 + - + +
84C ARG 4.3 3.0 - - - +
85C ILE* 4.3 7.4 - - + -
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Residues in contact with LYS 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU 3.1 13.7 + - - +
76C THR* 3.9 6.1 - - - +
78C ALA* 1.3 78.2 - - - +
80C GLU* 1.3 63.0 + - + +
83C GLY* 2.6 44.0 + - - +
84C ARG* 4.1 25.1 - - - +
85C ILE* 4.7 1.9 - - + +
135C VAL* 4.3 18.6 - - + -
138C GLN* 3.8 26.4 + - - +
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Residues in contact with GLU 80 (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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76C THR* 3.1 40.0 + - + +
77C LEU* 4.0 8.4 - - + +
79C LYS* 1.3 85.8 - - + +
81C LYS* 1.3 61.6 + - - +
83C GLY* 4.2 2.3 + - - -
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Residues in contact with LYS 81 (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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56C GLY 4.7 9.7 + - - -
59C ILE* 4.1 29.8 - - + +
77C LEU* 2.9 28.0 + - + +
78C ALA 3.9 2.7 - - - +
80C GLU* 1.3 77.9 - - - +
82C PHE* 1.3 91.3 + - + +
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Residues in contact with PHE 82 (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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12C VAL* 3.9 33.0 - - + +
36C THR* 4.0 33.0 - - + -
37C ALA 4.6 2.9 - - - -
38C VAL* 3.8 28.3 - - + -
56C GLY 4.6 13.2 - - - -
57C ASN* 4.6 9.4 - - - -
59C ILE* 4.0 25.4 - - + -
78C ALA 2.9 17.5 + - - +
81C LYS* 1.3 100.9 - - + +
83C GLY* 1.3 58.6 + - - +
84C ARG* 3.4 5.5 + - - +
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Residues in contact with GLY 83 (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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79C LYS* 2.6 36.7 + - - +
80C GLU 4.2 2.5 + - - -
81C LYS 3.8 1.2 - - - -
82C PHE* 1.3 70.2 - - - +
84C ARG* 1.3 62.4 + - - +
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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