Contacts of the helix formed by residues 9 - 23 (chain B) in PDB entry 2DOU
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 VAL 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B SER* 1.3 80.0 - - - +
10B PHE* 1.3 69.4 + - + +
11B LEU 3.1 1.6 - - - -
12B VAL* 3.5 10.8 - - - +
13B VAL* 3.4 23.0 + - - +
326B LEU* 3.4 39.9 - - + -
341B PRO* 4.2 11.2 - - + -
343B ARG* 3.5 27.8 - - + -
344B GLY* 4.4 17.0 - - - -
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Residues in contact with PHE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B SER* 4.1 15.5 - - - -
9B VAL* 1.3 81.1 - - + +
11B LEU* 1.3 59.3 + - - +
13B VAL* 4.2 5.8 - - + +
14B ASP* 2.8 33.7 + - - +
31B SER 5.9 0.9 - - - -
122B PRO* 3.9 21.1 - - + -
340B ALA* 4.0 22.2 - - + -
341B PRO* 3.9 29.8 - - + -
344B GLY* 3.3 39.7 - - - -
345B PHE* 4.2 9.6 - + - -
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B SER* 3.5 28.0 - - - +
10B PHE* 1.3 75.7 - - - +
12B VAL* 1.3 73.1 + - + +
14B ASP* 3.1 7.0 + - - +
15B GLU* 2.9 19.0 + - - +
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B SER 4.4 5.6 - - - +
9B VAL* 3.5 22.4 - - + +
11B LEU* 1.3 83.7 - - + +
13B VAL* 1.3 57.0 + - + +
14B ASP 2.7 0.9 + - - -
15B GLU* 2.5 25.1 + - - +
16B ALA* 2.8 13.3 + - + -
326B LEU* 4.9 9.6 - - + -
330B LEU* 3.7 29.6 - - + -
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL 3.4 16.7 + - - +
10B PHE* 4.2 5.4 - - - +
12B VAL* 1.3 79.9 - - - +
14B ASP* 1.3 62.8 + - - +
16B ALA* 3.6 10.4 - - - -
17B LYS* 3.0 24.2 + - + +
31B SER* 5.2 5.4 - - - +
326B LEU* 4.3 4.3 - - + -
329B GLY 5.0 1.6 - - - +
330B LEU* 4.0 22.7 - - + +
333B VAL* 4.2 16.9 - - + +
338B ALA* 5.0 7.0 - - + -
339B LEU 3.7 21.3 - - - +
341B PRO* 3.9 24.9 - - + -
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Residues in contact with ASP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE 2.8 24.5 + - - +
11B LEU* 3.1 8.1 - - - +
12B VAL 2.7 4.4 + - - -
13B VAL* 1.3 70.9 - - - +
15B GLU* 1.3 63.4 + - - +
17B LYS* 3.1 24.6 + - - +
18B ARG* 3.0 25.6 + - - +
32B ILE* 5.4 5.7 - - - +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU 2.9 10.0 + - - +
12B VAL* 2.5 16.0 + - - +
14B ASP* 1.3 68.3 + - - +
16B ALA* 1.3 52.9 + - - +
17B LYS 2.7 15.6 + - - -
18B ARG* 2.8 18.4 + - - +
19B LYS* 2.8 16.1 + - - +
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 2.8 18.6 + - + +
13B VAL* 3.6 4.9 - - - +
15B GLU* 1.3 70.4 - - - +
17B LYS* 1.3 55.8 + - - +
19B LYS* 4.1 11.5 - - - +
20B ALA* 3.8 9.2 + - - +
330B LEU* 4.0 26.2 - - + -
333B VAL* 2.9 24.8 - - + +
334B GLU* 3.9 10.5 - - - +
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL* 3.0 18.3 + - - +
14B ASP* 3.3 23.4 + - - +
15B GLU 2.7 6.3 + - - -
16B ALA* 1.3 75.1 - - - +
18B ARG* 1.3 58.5 + - + +
19B LYS 3.0 4.9 - - - -
20B ALA* 3.4 2.0 + - - +
21B ARG* 2.9 63.6 + - + +
27B LEU* 3.6 23.9 - - + +
29B ASP* 3.0 34.8 + - - -
31B SER* 4.3 4.4 + - - -
32B ILE* 4.2 15.2 - - - +
333B VAL* 3.8 8.5 - - + -
338B ALA* 4.3 8.7 - - + -
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASP* 3.0 16.2 + - - +
15B GLU* 2.8 11.1 + - - +
17B LYS* 1.3 80.2 - - + +
19B LYS* 1.3 58.5 + - - +
21B ARG* 3.9 9.5 - - - +
22B GLU* 3.4 20.1 + - - +
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLU 2.8 14.4 + - - +
16B ALA* 4.2 9.4 - - - +
18B ARG* 1.3 75.5 - - - +
20B ALA* 1.3 65.8 + - - +
21B ARG 3.1 1.3 - - - -
22B GLU* 3.1 7.7 + - - +
23B ARG* 3.0 24.3 + - - +
334B GLU* 6.0 1.1 - - - +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA 3.8 16.0 + - - +
17B LYS 3.4 5.2 + - - +
19B LYS* 1.3 79.4 - - - +
21B ARG* 1.3 59.9 + - - +
23B ARG* 3.4 28.5 + - - +
24B GLY 3.3 3.3 + - - -
25B VAL* 2.8 38.4 + - + +
27B LEU* 4.5 4.7 - - + -
333B VAL* 4.0 18.2 - - + +
334B GLU* 4.3 4.9 + - - +
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS* 2.9 61.3 + - + +
18B ARG* 3.9 9.0 - - - +
19B LYS 3.1 0.2 - - - -
20B ALA* 1.3 74.2 - - - +
22B GLU* 1.3 58.4 + - - +
24B GLY* 2.5 30.5 + - - -
25B VAL 4.2 10.0 + - - +
27B LEU* 2.7 49.3 + - + +
29B ASP* 3.6 14.1 + - - +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG 3.4 12.2 + - - +
19B LYS* 3.1 12.2 + - - +
21B ARG* 1.3 76.3 - - - +
23B ARG* 1.3 55.2 + - - +
24B GLY* 2.6 13.5 + - - -
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LYS 3.0 11.1 + - - +
20B ALA* 3.6 21.1 - - - +
21B ARG 3.1 0.2 - - - -
22B GLU* 1.3 77.2 - - - +
24B GLY* 1.3 60.3 + - - +
25B VAL* 3.3 17.4 + - - +
334B GLU* 2.5 36.4 + - - +
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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