Contacts of the helix formed by residues 11 - 24 (chain R) in PDB entry 2D2I
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 11 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192O ASP 5.7 0.2 - - - -
9R GLY 3.1 8.9 + - - -
10R PHE* 1.3 75.5 - - - +
12R ARG* 1.3 67.6 + - - +
13R ILE 3.4 2.5 - - - -
14R GLY 3.2 1.1 + - - -
15R ARG* 2.8 42.2 + - - +
6341R NAP 3.3 29.0 + - - -
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Residues in contact with ARG 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191O LEU* 4.6 15.7 - - + +
192O ASP* 3.6 27.8 + - - +
11R GLY* 1.3 72.4 - - - +
13R ILE* 1.3 65.3 + - - +
15R ARG* 3.2 22.3 - - - +
16R ASN* 2.9 41.3 + - - +
50R ASP* 2.7 42.7 + - - -
52R VAL* 4.0 11.7 - - - +
53R LEU* 4.7 1.2 - - - +
186R LEU* 3.8 11.9 - - + +
319R GLU* 2.8 46.3 + - + +
6341R NAP 2.8 40.0 + - - +
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Residues in contact with ILE 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12R ARG* 1.3 71.6 - - - +
14R GLY* 1.3 67.4 + - - +
17R PHE* 2.8 30.3 + - + +
98R SER* 4.2 8.3 - - - -
122R THR* 3.8 31.6 - - + +
319R GLU* 4.1 13.5 - - + +
322R TYR* 4.1 9.2 - - + -
323R SER* 3.8 20.9 - - - +
326R VAL* 4.8 2.9 - - + -
6341R NAP 3.0 74.2 + - + +
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Residues in contact with GLY 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7R ILE* 4.1 10.6 - - - +
9R GLY 3.6 20.1 + - - -
10R PHE* 4.0 8.5 - - - -
11R GLY 3.2 7.7 + - - -
13R ILE* 1.3 81.5 - - - +
15R ARG* 1.3 60.7 + - - +
17R PHE* 3.4 8.1 - - - +
18R LEU* 3.2 18.7 + - - +
96R ILE* 5.6 0.4 - - - -
98R SER* 3.7 13.0 + - - -
6341R NAP 4.6 0.4 + - - -
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Residues in contact with ARG 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192O ASP* 3.1 35.4 + - - +
193O ALA* 5.1 2.4 - - - +
194O SER 5.6 0.2 - - - +
10R PHE* 2.8 71.2 + - + +
11R GLY* 2.8 40.0 + - - +
12R ARG* 3.2 26.6 - - - +
14R GLY* 1.3 68.2 - - - -
16R ASN* 1.3 67.3 + - - +
17R PHE 3.2 0.9 - - - -
18R LEU* 3.0 5.2 + - - +
19R ARG* 2.9 26.5 + - - +
43R ALA* 5.9 0.2 - - - +
46R LEU* 3.2 51.1 + - - +
47R LEU* 4.1 8.6 - - + +
50R ASP* 4.8 4.2 + - - +
53R LEU* 5.5 2.2 - - + -
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Residues in contact with ASN 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12R ARG* 2.9 41.4 + - - +
13R ILE* 3.8 0.4 - - - +
15R ARG* 1.3 74.6 - - - +
17R PHE* 1.3 54.6 + - - +
19R ARG* 3.1 6.8 + - - +
20R CYS* 2.7 38.3 + - - -
50R ASP* 4.9 0.4 + - - -
53R LEU* 3.7 17.2 - - - +
319R GLU* 3.5 30.1 + - - +
320R TRP* 3.4 34.5 + - - +
323R SER* 3.3 21.5 - - - +
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Residues in contact with PHE 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5R VAL* 4.9 3.1 - - + -
7R ILE* 3.7 33.4 - - + -
13R ILE* 2.8 21.5 + - + +
14R GLY* 3.4 5.2 - - - +
16R ASN* 1.3 77.6 - - - +
18R LEU* 1.3 65.6 + - - +
20R CYS* 3.3 3.8 + - - +
21R TRP* 3.0 25.8 + - + +
29R LEU* 4.5 17.0 - - + -
31R VAL* 4.3 15.0 - - + -
96R ILE* 3.8 27.1 - - + -
323R SER* 3.8 12.2 - - - -
326R VAL* 3.1 36.3 - - + -
327R VAL* 3.5 30.8 - - + +
330R ALA* 4.5 0.9 - - + -
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Residues in contact with LEU 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7R ILE* 3.9 19.3 - - + -
10R PHE* 3.6 27.1 - - + -
14R GLY 3.2 8.7 + - - +
15R ARG* 3.0 9.9 + - - +
17R PHE* 1.3 81.9 - - - +
19R ARG* 1.3 58.2 + - - +
21R TRP* 3.2 18.1 + - + +
22R PHE* 2.9 64.0 + - + -
31R VAL* 4.5 2.2 - - + -
34R ILE* 4.3 5.4 - - + -
47R LEU* 3.9 22.9 - - + -
67R ILE* 5.8 0.2 - - + -
74R MET* 4.0 24.0 - - + -
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Residues in contact with ARG 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15R ARG* 2.9 15.5 + - - +
16R ASN* 3.6 7.9 - - - +
18R LEU* 1.3 77.2 - - - +
20R CYS* 1.3 63.7 + - - +
22R PHE* 3.3 2.9 + - - +
23R GLY* 3.1 19.2 + - - -
47R LEU* 3.3 21.6 + - + +
48R GLU 3.7 3.8 + - - -
50R ASP* 3.2 23.6 + - - +
53R LEU* 3.5 29.7 + - + +
54R GLY 2.8 26.5 + - - -
55R ARG 3.7 3.8 + - - -
56R PHE* 3.3 67.1 - - + +
320R TRP* 3.9 18.3 - - + -
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Residues in contact with CYS 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R ASN 2.7 23.2 + - - +
17R PHE 3.6 4.7 - - - +
19R ARG* 1.3 72.4 - - - +
21R TRP* 1.3 62.9 + - - +
23R GLY* 3.2 4.8 + - - -
24R ARG* 3.2 26.3 + - - +
320R TRP* 3.7 38.4 - - - -
323R SER* 3.9 5.6 - - - +
324R GLN* 3.2 48.0 + - - +
327R VAL* 3.9 10.1 - - + -
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Residues in contact with TRP 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17R PHE* 3.0 19.5 + + + +
18R LEU* 3.4 20.0 - - + +
20R CYS* 1.3 72.7 - - - +
22R PHE* 1.3 92.7 + + - +
24R ARG* 2.7 34.0 + - + +
27R THR* 2.8 37.9 + - + +
29R LEU* 3.5 34.5 - - + +
30R GLU* 3.7 12.3 - - - -
31R VAL* 3.7 43.3 - - + -
72R LYS* 3.4 32.5 - - + -
74R MET* 5.0 1.3 - - - -
327R VAL* 4.1 11.4 - - + +
331R GLU* 4.2 6.5 - - - -
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Residues in contact with PHE 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R LEU* 2.9 52.5 + - + +
19R ARG 3.8 4.3 - - - +
21R TRP* 1.3 90.5 - + - +
23R GLY* 1.3 61.1 + - - +
24R ARG 3.4 6.1 + - - +
56R PHE* 3.9 23.6 - + + -
69R VAL* 3.4 52.7 - - + -
70R ASN* 4.5 12.8 - - + +
72R LYS* 3.7 31.0 - - + +
74R MET* 4.1 10.3 - - + -
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Residues in contact with GLY 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19R ARG 3.1 13.3 + - - -
20R CYS 3.2 5.8 + - - -
21R TRP 3.0 1.2 - - - -
22R PHE* 1.3 74.9 - - - +
24R ARG* 1.3 66.9 + - - +
25R GLN* 3.5 2.4 + - - +
56R PHE* 6.0 0.2 - - - -
320R TRP* 6.3 1.3 - - - -
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Residues in contact with ARG 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R CYS 3.3 11.9 - - - +
21R TRP* 2.7 27.0 + - + +
22R PHE 3.8 6.1 - - - +
23R GLY* 1.3 81.3 - - - +
25R GLN* 1.3 85.3 + - - +
26R ASN* 3.7 18.3 + - - +
27R THR* 5.1 1.7 - - - +
324R GLN* 2.9 50.0 + - - +
325R ARG* 4.8 1.6 - - - +
327R VAL* 3.6 20.6 - - + +
328R ASP* 2.6 30.7 + - - -
331R GLU* 4.5 10.0 - - - +
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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