Contacts of the helix formed by residues 4 - 22 (chain C) in PDB entry 3E20
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 THR 4 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C ALA* 1.3 76.3 + - - +
7C LYS* 3.5 35.5 - - + +
8C ALA* 3.4 21.1 - - - +
279C GLN* 5.3 11.7 + - - +
389C GLU* 5.6 1.0 - - - +
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Residues in contact with ALA 5 (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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4C THR* 1.3 87.3 + - - +
6C GLU* 1.3 69.6 + - + +
7C LYS 3.1 2.9 + - - -
8C ALA* 3.9 4.5 + - - +
9C ILE* 4.0 7.8 + - - +
388C LEU 5.5 1.9 - - - +
389C GLU* 4.9 8.7 - - - +
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Residues in contact with GLU 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 ALA* 1.3 83.6 - - + +
7C LYS* 1.3 59.0 + - - +
9C ILE* 3.0 29.6 - - + +
10C GLU* 3.6 11.1 - - - +
381C TYR* 3.3 23.8 + - - +
382C LYS* 3.5 29.9 + - - +
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Residues in contact with LYS 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C THR* 3.5 31.6 - - + +
5C ALA 3.1 0.2 - - - -
6C GLU* 1.3 76.0 - - - +
8C ALA* 1.3 59.0 + - - +
9C ILE 3.0 1.1 - - - -
10C GLU* 2.7 30.3 + - + +
11C ILE* 3.1 28.9 + - + +
114C PHE* 6.3 0.4 - - - -
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Residues in contact with ALA 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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4C THR* 3.4 19.0 + - - +
5C ALA 4.4 1.6 - - - +
7C LYS* 1.3 80.5 - - - +
9C ILE* 1.3 56.9 + - - +
11C ILE* 3.2 19.8 + - + +
12C TRP* 2.9 28.9 + - - +
389C GLU* 5.7 4.5 - - - +
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Residues in contact with ILE 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 ALA 4.0 4.7 + - - +
6C GLU* 3.0 39.6 - - + +
7C LYS 3.0 1.0 - - - -
8C ALA* 1.3 79.3 - - - +
10C GLU* 1.3 69.8 + - - +
12C TRP* 3.1 31.6 - - + +
13C LYS* 3.7 6.0 + - - +
378C ALA* 4.9 8.5 - - + +
381C TYR* 4.7 18.4 - - + +
388C LEU* 3.8 33.2 - - + +
389C GLU* 5.4 0.2 - - - -
390C PHE* 3.6 33.9 - - + +
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Residues in contact with GLU 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 GLU 3.6 15.6 - - - +
7C LYS* 2.7 10.2 + - - +
9C ILE* 1.3 88.5 - - - +
11C ILE* 1.3 57.2 + - + +
12C TRP 2.9 1.6 - - - -
13C LYS* 2.7 53.5 + - - +
14C ILE* 3.1 16.2 + - + +
114C PHE* 3.6 41.1 - - + -
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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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7C LYS* 3.5 30.3 - - + +
8C ALA* 3.5 23.1 - - + +
10C GLU* 1.3 76.8 - - + +
12C TRP* 1.3 62.8 + - - +
14C ILE* 3.3 10.1 + - - +
15C ARG* 3.0 24.2 + - + +
114C PHE* 6.5 0.7 - - + -
136C LEU 3.7 23.6 - - - +
137C LEU* 3.8 28.5 - - + -
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Residues in contact with TRP 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 ALA 2.9 13.2 + - - +
9C ILE 3.1 23.6 - - - +
11C ILE* 1.3 77.6 - - - +
13C LYS* 1.3 85.2 + - + +
15C ARG* 3.2 16.2 + - - +
16C ARG* 3.0 52.0 + - + +
321C ALA* 2.8 50.3 - - + -
374C SER* 2.9 26.9 - - - -
375C GLU* 5.1 4.2 - - + +
378C ALA* 4.0 11.1 - - + +
390C PHE* 3.4 47.9 - + + -
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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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9C ILE* 4.4 5.8 - - - -
10C GLU* 2.7 45.9 + - - +
12C TRP* 1.3 96.2 - - + +
14C ILE* 1.3 65.9 + - + +
16C ARG* 3.0 9.7 + - + +
17C LEU* 2.9 22.7 + - - +
375C GLU* 5.9 7.6 - - + -
378C ALA* 4.9 14.0 + - + +
379C GLU* 4.6 22.3 + - + +
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Residues in contact with ILE 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 GLU* 3.1 16.3 + - + +
11C ILE* 3.5 11.9 - - - +
13C LYS* 1.3 78.4 - - + +
15C ARG* 1.3 58.5 + - - +
17C LEU* 3.0 10.3 + - + +
18C VAL* 2.9 44.7 + - + +
111C PHE* 4.2 25.6 - - + -
113C PRO* 5.5 2.0 - - + -
114C PHE* 5.4 13.7 - - + -
133C LEU* 4.5 13.9 - - + -
136C LEU* 4.5 26.0 - - + +
137C LEU* 3.7 19.5 - - + -
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Residues in contact with ARG 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* 3.0 14.9 + - + +
12C TRP* 3.3 25.5 - - - +
14C ILE* 1.3 78.7 - - - +
16C ARG* 1.3 94.3 + - - +
18C VAL* 3.1 25.4 - - + +
19C LYS* 3.2 18.8 - - - +
137C LEU* 4.2 12.3 - - + +
321C ALA* 4.1 7.7 - - - +
322C ASP* 2.7 34.0 + - - -
392C SER* 5.7 2.6 + - - -
394C ARG* 5.2 15.6 - - - +
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Residues in contact with ARG 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 TRP* 3.0 44.1 + - + +
13C LYS* 3.0 13.0 + - + +
15C ARG* 1.3 89.8 - - - +
17C LEU* 1.3 67.8 + - - +
19C LYS* 3.3 28.3 - - - +
20C GLN* 3.3 25.0 + - - +
321C ALA 3.8 5.1 + - - -
322C ASP* 2.9 46.7 + - - +
323C LEU 5.6 2.2 + - - -
372C LEU* 5.0 16.0 - - - +
374C SER* 5.5 0.6 + - - -
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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 LYS 2.9 11.3 + - - +
14C ILE* 3.4 13.0 - - + +
16C ARG* 1.3 72.6 - - - +
18C VAL* 1.3 67.1 + - + +
19C LYS 2.9 3.8 - - - -
20C GLN* 2.7 41.7 + - + +
21C LEU* 3.0 39.9 + - + +
109C ILE* 4.8 19.3 - - + -
111C PHE* 3.8 38.6 - - + -
133C LEU* 4.8 6.1 - - + -
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Residues in contact with VAL 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 ILE* 2.9 27.5 + - + +
15C ARG* 3.1 24.5 - - + +
17C LEU* 1.3 73.0 - - - +
19C LYS* 1.3 65.1 + - + +
21C LEU* 3.9 0.9 - - - -
22C ILE* 3.2 34.1 + - + +
130C THR* 4.1 20.9 - - - +
133C LEU* 3.6 36.3 - - + -
134C ALA* 5.4 0.4 - - - +
137C LEU* 5.0 12.6 - - + -
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Residues in contact with LYS 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 ARG* 3.2 23.8 + - + +
16C ARG* 3.3 39.9 - - - +
17C LEU 2.7 1.4 + - - -
18C VAL* 1.3 84.0 - - + +
20C GLN* 1.3 56.6 + - + +
22C ILE* 3.8 10.7 - - + +
23C ASN* 3.2 31.8 + - - +
322C ASP* 3.3 24.0 + - - +
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Residues in contact with GLN 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 ARG* 3.5 13.2 + - - +
17C LEU* 2.7 51.8 + - + +
19C LYS* 1.3 74.9 - - + +
21C LEU* 1.3 64.7 + - + +
23C ASN* 3.3 9.3 - - - +
24C CYS* 3.2 23.4 + - - +
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Residues in contact with LEU 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* 3.0 43.2 + - + +
19C LYS 3.5 0.2 - - - -
20C GLN* 1.3 76.3 - - + +
22C ILE* 1.3 61.4 + - - +
23C ASN 2.9 4.3 + - - -
24C CYS* 3.1 27.9 + - - +
93C TYR* 3.6 44.4 - - + -
107C LEU* 4.4 16.2 - - + -
109C ILE* 4.5 6.7 - - + -
128C PHE* 3.8 33.8 + - + +
130C THR* 3.9 19.1 - - + -
133C LEU* 4.5 1.1 - - + -
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Residues in contact with ILE 22 (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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18C VAL* 3.2 20.8 + - + +
19C LYS* 3.8 11.0 - - - +
21C LEU* 1.3 75.0 - - - +
23C ASN* 1.3 64.5 + - - +
24C CYS 4.2 3.6 - - - +
25C HIS* 6.0 0.3 - - - +
127C LYS* 6.3 3.6 - - - -
128C PHE 4.4 11.4 - - - +
130C THR* 3.1 32.5 - - + +
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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