Contacts of the helix formed by residues 5 - 21 (chain C) in PDB entry 1E8O
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 GLN 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C THR* 1.3 73.0 + - - +
7C TRP 3.4 2.9 - - - +
8C GLU* 3.4 33.1 + - - +
9C GLU* 2.3 51.3 + - - +
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Residues in contact with THR 6 (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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5C GLN* 1.3 87.5 - - - +
7C TRP* 1.3 59.1 + - - +
9C GLU* 3.9 2.4 - - - +
10C PHE* 2.8 32.2 + - + +
51C TYR* 3.9 27.6 - - + -
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Residues in contact with TRP 7 (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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5C GLN* 3.4 0.6 - - - +
6C THR* 1.3 78.0 - - - +
8C GLU* 1.3 70.8 + - + +
10C PHE* 3.4 29.5 - + - +
11C SER* 3.0 32.8 + - - -
40C VAL* 4.9 2.0 - - + -
51C TYR* 3.3 48.9 - + - +
61C LYS* 3.4 67.7 - - + +
62C ILE* 3.8 15.5 - - + -
65C PHE* 3.7 32.5 - + + -
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Residues in contact with GLU 8 (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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5C GLN 3.3 22.9 + - - +
7C TRP* 1.3 85.4 - - + +
9C GLU* 1.3 66.8 + - - +
11C SER* 3.0 18.6 + - - +
12C ARG* 3.7 6.9 + - - +
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Residues in contact with GLU 9 (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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5C GLN* 2.3 41.0 + - - +
6C THR* 3.9 2.9 - - - +
8C GLU* 1.3 75.4 - - - +
10C PHE* 1.3 66.2 + - - +
12C ARG* 2.6 71.8 + - + +
13C ALA* 3.2 2.3 + - + +
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Residues in contact with PHE 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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6C THR* 2.8 24.9 + - + +
7C TRP* 3.4 35.9 - + - +
9C GLU* 1.3 73.4 - - - +
11C SER* 1.3 64.1 + - - +
13C ALA* 3.0 20.6 + - + +
14C ALA* 3.0 20.0 + - + +
40C VAL* 4.2 14.4 - - + -
42C VAL* 4.9 3.8 - - + -
49C LEU* 3.8 39.5 - - + -
50C VAL 4.0 8.5 - - - -
51C TYR* 3.6 30.5 - - + -
65C PHE* 4.3 15.5 - + - -
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Residues in contact with SER 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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7C TRP* 3.0 23.1 + - - -
8C GLU* 3.0 17.5 + - - +
10C PHE* 1.3 84.2 - - - +
12C ARG* 1.3 65.5 + - - +
14C ALA* 3.0 7.6 + - - +
15C GLU* 2.8 31.6 + - - +
65C PHE* 4.3 20.0 - - - -
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Residues in contact with ARG 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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8C GLU 4.1 6.1 - - - +
9C GLU* 2.6 68.2 + - + +
11C SER* 1.3 78.3 + - - +
13C ALA* 1.3 81.3 + - + +
15C GLU* 2.9 6.4 + - - +
16C LYS* 2.9 23.3 + - + +
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Residues in contact with ALA 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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9C GLU* 4.3 4.5 - - + +
10C PHE* 3.0 13.8 + - + +
12C ARG* 1.3 85.7 - - + +
14C ALA* 1.3 59.2 + - - +
16C LYS* 3.0 31.5 - - + +
17C LEU* 3.1 13.5 + - - +
49C LEU* 3.6 23.0 - - + +
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Residues in contact with ALA 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 PHE* 3.0 19.9 + - + +
11C SER* 3.4 4.7 - - - +
13C ALA* 1.3 71.5 - - - +
15C GLU* 1.3 58.0 + - - +
16C LYS 2.9 4.9 - - - -
17C LEU* 2.9 9.3 + - - +
18C TYR* 2.9 27.5 + - - +
42C VAL* 4.0 22.8 - - + +
49C LEU* 4.1 7.8 - - + +
65C PHE* 3.3 32.3 - - + -
69C LEU* 5.7 0.9 - - - -
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Residues in contact with GLU 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 SER* 2.8 25.0 + - - +
12C ARG* 3.5 6.1 - - - +
14C ALA* 1.3 72.3 - - - +
16C LYS* 1.3 52.9 + - - +
18C TYR* 4.0 9.2 - - - -
19C LEU* 2.8 42.6 + - + +
65C PHE* 3.9 22.7 - - + -
68C GLN* 3.3 30.1 + - - +
69C LEU* 4.3 10.3 - - + +
72C LEU* 5.3 10.0 - - + +
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Residues in contact with LYS 16 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C ARG* 2.9 12.0 + - + +
13C ALA* 3.0 21.3 - - + +
15C GLU* 1.3 79.5 - - - +
17C LEU* 1.3 62.9 + - + +
19C LEU* 3.4 7.5 + - - +
20C ALA* 2.9 31.4 + - + +
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Residues in contact with LEU 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 ALA 3.1 13.1 + - - +
14C ALA* 2.9 8.4 + - - +
16C LYS* 1.3 84.9 - - + +
18C TYR* 1.3 66.3 + - - +
19C LEU 3.1 0.6 + - - -
20C ALA* 3.4 10.5 + - + +
21C ASP 3.4 21.3 + - - +
25C ALA* 4.4 9.3 - - + +
42C VAL* 4.1 21.5 - - + +
43C THR 4.8 0.2 - - - -
44C ASP* 4.6 9.4 - - + +
47C VAL* 3.8 44.6 - - + +
49C LEU* 3.9 21.8 - - + -
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Residues in contact with TYR 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 ALA 2.9 15.5 + - - +
15C GLU* 4.3 9.4 - - - +
16C LYS 3.4 0.2 - - - -
17C LEU* 1.3 78.0 - - - +
19C LEU* 1.3 67.7 + - + +
21C ASP 5.0 0.2 - - - -
22C PRO* 2.9 67.7 - - + +
25C ALA* 5.0 12.1 - - + -
42C VAL* 5.4 4.0 - - + +
69C LEU* 4.4 15.9 - - + -
72C LEU* 3.0 55.5 + - + -
73C MET* 3.0 48.9 - - + +
32D LYS* 3.8 7.4 + - - +
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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 GLU* 2.8 30.5 - - + +
16C LYS* 3.4 6.7 + - - +
17C LEU 3.1 0.6 - - - -
18C TYR* 1.3 89.2 - - + +
20C ALA* 1.3 65.6 + - - +
21C ASP 3.0 3.1 + - - -
22C PRO* 3.5 11.3 - - - +
72C LEU* 4.8 11.0 - - + -
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Residues in contact with ALA 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 LYS* 2.9 21.2 + - + +
17C LEU* 3.7 15.5 - - + +
19C LEU* 1.3 74.8 - - - +
21C ASP* 1.3 65.3 + - + +
22C PRO* 4.6 0.2 - - - +
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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 LEU 3.4 8.1 + - - +
18C TYR 3.5 2.2 - - - -
19C LEU 3.0 0.6 + - - -
20C ALA* 1.3 83.6 - - + +
22C PRO* 1.3 64.3 - - - +
23C MET* 2.9 32.0 + - - +
24C LYS* 3.3 45.6 + - + +
25C ALA* 3.6 9.9 + - - +
44C ASP* 5.7 3.1 - - - +
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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