Contacts of the helix formed by residues 10 - 18 (chain B) in PDB entry 1DM9
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 ARG 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B GLU 4.2 0.9 - - - +
9B VAL* 1.3 76.6 - - - +
11B LEU* 1.3 60.0 + - - +
12B ASP* 2.6 39.7 + - - +
13B LYS* 3.3 8.7 + - + +
14B TRP* 2.9 26.9 + - - +
28B ARG* 4.2 2.0 - - - +
45B PRO* 3.5 9.0 - - - +
46B SER* 3.4 35.4 - - - +
47B LYS 3.4 7.0 - - - -
48B ILE* 4.5 7.0 - - + -
49B VAL* 4.0 0.2 - - - -
73B GLU* 5.2 0.6 + - - -
992B SO4 2.7 42.3 + - - -
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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
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10B ARG* 1.3 71.8 - - - +
12B ASP* 1.4 65.2 + - - +
14B TRP* 4.8 1.6 - - + -
15B LEU* 2.9 42.7 + - + +
31B ILE* 3.6 26.2 - - + -
36B VAL* 4.5 9.9 - - + -
38B TYR* 4.2 10.5 - - + -
43B SER* 3.6 32.3 - - - +
44B LYS 4.1 1.8 - - - +
45B PRO 3.4 3.8 + - - +
47B LYS* 2.7 22.9 + - + +
49B VAL* 3.5 21.5 - - + +
55B LEU* 4.1 28.0 - - + -
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Residues in contact with ASP 12 (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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10B ARG* 2.6 48.6 + - - +
11B LEU* 1.4 77.9 - - - +
13B LYS* 1.3 80.2 + - - +
15B LEU 3.3 0.3 + - - -
16B TRP* 3.1 19.8 + - - +
24B ARG* 3.9 26.5 - - - +
27B ALA* 3.6 12.4 - - - +
28B ARG* 3.4 28.7 - - - +
31B ILE* 3.8 12.9 - - + +
45B PRO* 3.3 8.3 + - + +
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Residues in contact with LYS 13 (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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9B VAL* 4.1 15.7 - - + -
10B ARG* 3.3 15.7 + - + +
12B ASP* 1.3 85.5 + - - +
14B TRP* 1.3 58.6 + - - +
16B TRP* 3.2 26.8 + - + +
17B ALA* 2.8 26.2 + - - +
24B ARG* 3.2 43.9 - - - +
73B GLU* 3.6 39.9 + - + +
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Residues in contact with TRP 14 (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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9B VAL* 4.1 6.9 - - + +
10B ARG 2.9 16.9 + - - +
11B LEU* 3.7 3.8 - - + +
13B LYS* 1.3 77.6 - - - +
15B LEU* 1.3 63.6 + - + +
17B ALA* 3.0 7.0 + - + +
18B ALA* 2.7 37.5 + - + +
20B PHE* 3.7 28.9 - + - -
49B VAL* 3.7 26.9 - - + -
55B LEU* 3.2 34.3 - - + -
66B VAL* 4.8 0.9 - - + -
68B VAL* 3.9 18.3 - - + +
70B ALA 2.9 22.7 + - - -
71B ILE* 4.2 15.7 - - + -
72B THR 4.4 9.6 - - - -
84B LEU* 3.5 38.4 - - + +
85B TYR* 4.1 11.7 - - + -
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Residues in contact with LEU 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 31.5 + - + +
12B ASP 3.6 4.0 - - - +
14B TRP* 1.3 97.4 - - + +
16B TRP* 1.3 60.7 + - - +
18B ALA 3.4 1.2 + - - -
19B ARG 3.2 3.3 + - - -
20B PHE* 3.0 34.3 + - + +
21B TYR* 3.9 9.5 + - + -
27B ALA* 3.8 15.7 - - + -
31B ILE* 3.6 32.5 - - + -
36B VAL* 4.2 14.4 - - + -
55B LEU* 4.3 8.3 - - + -
57B LEU* 3.7 28.0 - - + -
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Residues in contact with TRP 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 ASP 3.1 13.2 + - - +
13B LYS* 3.5 36.3 - - + +
15B LEU* 1.3 73.0 - - - +
17B ALA* 1.3 74.4 + - - +
19B ARG 2.9 14.9 + - - -
21B TYR 3.8 8.3 - - - -
22B LYS 3.1 28.5 + - - -
23B THR* 3.5 17.0 - - - +
24B ARG* 3.7 28.4 - - + +
27B ALA* 4.6 1.0 - - - +
73B GLU 3.8 15.3 - - - -
74B GLN* 5.3 0.7 - - - -
75B ARG* 3.0 64.4 + - + +
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Residues in contact with ALA 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 LYS 2.8 17.2 + - - +
14B TRP* 3.0 5.8 + - + +
16B TRP* 1.3 83.3 - - + +
18B ALA* 1.3 59.3 + - - +
19B ARG* 3.3 6.8 + - - +
72B THR* 3.9 25.1 - - + +
73B GLU 4.5 1.6 - - - -
74B GLN 3.6 22.8 - - - +
75B ARG* 3.8 21.3 - - - +
76B ARG 4.3 2.9 + - - -
81B ALA* 4.4 1.9 - - - +
84B LEU* 3.5 10.4 - - + +
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Residues in contact with ALA 18 (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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14B TRP* 2.7 32.6 + - + +
15B LEU 3.4 0.2 + - - -
16B TRP 3.1 0.2 - - - -
17B ALA* 1.3 72.0 - - - +
19B ARG* 1.3 71.2 + - - +
20B PHE* 3.3 29.0 + - + -
81B ALA* 3.7 10.7 - - - +
84B LEU* 3.4 20.2 - - + -
85B TYR* 4.0 17.7 + - + -
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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