Contacts of the helix formed by residues 9 - 21 (chain C) in PDB entry 5E0T
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 GLY 9 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C LEU* 4.2 9.2 - - - -
7C VAL 3.1 8.3 + - - -
8C GLN* 1.3 68.8 - - - +
10C SER* 1.3 65.2 + - - +
11C ILE 3.0 2.7 - - - -
12C LEU* 3.0 12.9 + - - +
13C LYS* 3.3 11.1 + - - +
83C GLY 5.4 0.9 - - - -
84C ASN 4.7 1.8 + - - -
85C GLU 5.5 0.2 - - - -
86C ASP 3.3 17.5 + - - -
88C ILE* 3.5 32.2 - - - +
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Residues in contact with SER 10 (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 GLN* 4.0 19.6 + - - +
9C GLY* 1.3 75.3 - - - +
11C ILE* 1.3 61.1 + - - +
13C LYS* 3.2 13.2 + - - +
14C LYS* 2.8 54.1 + - - +
84C ASN* 3.3 37.4 + - - -
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Residues in contact with ILE 11 (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 LEU* 4.2 12.8 - - + -
8C GLN* 3.5 41.7 - - + +
10C SER* 1.3 81.2 + - - +
12C LEU* 1.3 61.8 + - + +
14C LYS* 3.1 6.1 + - + +
15C VAL* 2.8 35.8 + - + +
52C LEU* 4.5 10.3 - - + -
221C LEU* 4.1 9.5 - - + +
241C ILE* 3.8 24.7 - - + -
242C ALA* 4.2 15.0 - - + -
244C MET* 4.0 22.0 - - - -
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Residues in contact with LEU 12 (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 LEU* 4.1 22.4 - - + +
9C GLY 3.0 9.0 + - - +
11C ILE* 1.3 81.0 - - + +
13C LYS* 1.3 62.8 + - - +
15C VAL* 4.3 4.9 - - + +
16C LEU* 3.0 34.3 + - + +
28C TRP* 4.6 20.9 - - + -
52C LEU* 4.4 22.0 - - + -
57C PHE* 5.8 2.5 - - + -
75C MET* 4.7 6.3 - - + -
79C LEU* 3.8 15.8 - - + +
88C ILE* 3.9 27.8 - - + -
90C LEU* 4.1 26.5 - - + -
101C LEU* 5.5 0.2 - - + -
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Residues in contact with LYS 13 (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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146A ARG* 4.7 1.4 - - - +
9C GLY 3.3 7.0 + - - +
10C SER* 3.2 16.8 + - - +
11C ILE 3.2 0.4 - - - -
12C LEU* 1.3 80.3 - - - +
14C LYS* 1.3 63.8 + - + +
16C LEU* 3.9 2.3 - - - +
17C GLU* 3.0 28.2 + - + +
79C LEU* 2.9 49.2 + - + +
80C LYS* 3.9 12.3 + - - +
82C ALA* 2.9 28.9 + - + +
83C GLY 3.8 12.6 - - - +
84C ASN* 3.2 28.7 - - - +
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Residues in contact with LYS 14 (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 SER* 2.8 37.3 + - - +
11C ILE* 3.6 4.7 - - - +
13C LYS* 1.3 77.1 - - + +
15C VAL* 1.3 65.0 + - - +
17C GLU* 3.2 9.2 + - - +
18C ALA* 2.9 24.6 + - - +
84C ASN* 5.9 1.8 - - - -
217C LYS 5.1 1.0 - - - +
218C ALA* 5.6 0.2 - - - -
220C PRO* 3.1 47.7 + - + +
221C LEU* 3.8 23.2 - - + +
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Residues in contact with VAL 15 (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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11C ILE* 2.8 26.4 + - + +
12C LEU* 3.9 9.0 - - + +
13C LYS 3.3 0.2 - - - -
14C LYS* 1.3 75.9 - - - +
16C LEU* 1.3 72.4 + - + +
18C ALA* 3.1 6.3 + - - +
19C LEU* 2.9 35.4 + - + +
28C TRP* 4.8 2.2 - - + -
50C LEU* 3.8 31.6 - - + -
52C LEU* 5.0 3.4 - - + -
221C LEU* 4.0 16.2 - - + -
241C ILE* 3.8 28.9 - - + -
247C LEU* 4.9 3.4 - - + -
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Residues in contact with LEU 16 (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 LEU* 3.0 23.9 + - + +
13C LYS 3.9 2.5 - - - +
15C VAL* 1.3 83.1 - - + +
17C GLU* 1.3 64.3 + - - +
19C LEU* 3.0 2.5 + - + +
20C LYS* 2.9 29.5 + - + +
28C TRP* 3.9 27.6 - - + -
72C LEU* 3.7 44.2 - - + +
75C MET* 3.9 16.2 - - + -
76C SER* 3.9 16.4 - - - +
79C LEU* 3.6 28.5 - - + -
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Residues in contact with GLU 17 (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 LYS* 3.0 19.1 + - + +
14C LYS* 3.2 11.4 + - - +
16C LEU* 1.3 76.3 - - - +
18C ALA* 1.3 61.4 + - - +
19C LEU 3.4 0.3 + - - -
20C LYS* 3.3 40.7 + - - +
21C ASP* 4.5 6.9 + - - +
76C SER* 3.6 10.4 + - - +
80C LYS* 3.3 30.2 + - - +
217C LYS* 4.6 11.2 - - - +
220C PRO* 6.5 1.3 - - + -
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Residues in contact with ALA 18 (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 LYS 2.9 13.1 + - - +
15C VAL 3.5 8.1 - - - +
17C GLU* 1.3 77.7 - - - +
19C LEU* 1.3 62.2 + - - +
21C ASP* 5.0 2.6 + - - +
22C LEU* 4.6 6.9 + - - +
214C PHE 4.8 1.7 - - - +
217C LYS* 3.8 16.8 + - - +
218C ALA* 3.7 23.3 - - - +
221C LEU* 4.9 0.4 - - + -
247C LEU* 3.9 10.1 - - + -
249C TYR* 3.4 29.5 + - - +
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Residues in contact with LEU 19 (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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15C VAL* 2.9 36.6 + - + +
16C LEU* 3.0 4.9 + - + +
18C ALA* 1.3 81.5 - - - +
20C LYS* 1.3 59.8 + - - +
21C ASP 3.1 2.7 - - - -
22C LEU* 2.9 22.1 + - + +
23C ILE* 2.9 26.9 + - + +
28C TRP* 5.1 2.9 - - + -
37C LEU* 4.5 18.8 - - + -
48C VAL* 3.4 33.9 - - + -
50C LEU* 4.6 5.6 - - + -
72C LEU* 3.7 26.7 - - + -
247C LEU* 4.2 14.1 - - + -
249C TYR* 4.7 3.6 - - + +
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Residues in contact with LYS 20 (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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16C LEU* 2.9 16.2 + - + +
17C GLU* 3.3 28.8 + - - +
19C LEU* 1.3 77.8 - - - +
21C ASP* 1.3 85.9 + - - +
23C ILE 3.5 17.1 - - - +
24C ASN* 5.4 0.2 - - - -
72C LEU* 4.4 12.8 - - + +
73C THR* 4.8 12.4 + - + +
76C SER* 3.3 30.7 + - - +
80C LYS* 2.9 31.9 - - - +
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Residues in contact with ASP 21 (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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17C GLU 4.5 4.5 + - - +
18C ALA 5.5 2.0 - - - +
19C LEU 3.1 0.4 - - - -
20C LYS* 1.3 109.6 - - - +
22C LEU* 1.3 61.1 + - + +
23C ILE 5.3 0.2 - - - -
42C SER* 4.8 4.9 + - - -
214C PHE* 4.8 12.4 - - + -
217C LYS* 2.5 50.2 + - + +
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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