Contacts of the helix formed by residues 35 - 47 (chain F) in PDB entry 1DM0
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 ASN 35 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B TYR* 4.8 0.4 - - + -
34B TRP* 4.4 13.1 + - + -
37B GLN* 2.7 40.4 + - - +
38B SER* 4.5 7.3 + - - +
33F ARG 3.2 3.4 + - - -
34F TRP* 1.4 83.9 - - + +
36F LEU* 1.3 62.7 + - - +
37F GLN* 3.2 4.2 - - - +
38F SER* 3.4 17.3 + - - -
39F LEU* 3.1 30.8 + - - +
34J TRP* 5.5 1.4 - - - -
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Residues in contact with LEU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TYR* 3.9 26.9 - - + -
31F THR* 3.4 27.4 - - + +
33F ARG* 3.5 22.5 + - + +
34F TRP 3.2 3.8 + - - -
35F ASN* 1.3 78.7 - - - +
37F GLN* 1.3 56.7 + - - +
39F LEU* 3.5 5.3 + - + -
40F LEU* 2.9 36.6 + - + +
63F PHE* 3.7 18.2 - - + -
64F SER 3.7 22.7 - - - +
66F VAL* 4.0 16.8 - - + -
68F PHE* 4.6 9.4 - - + -
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Residues in contact with GLN 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F TYR* 3.4 26.4 + - - +
18F ASP* 4.1 14.9 + - - +
19F THR 5.0 0.3 - - - +
20F PHE* 3.1 47.2 - - + +
31F THR* 3.0 31.6 + - + -
32F ASN* 3.9 11.9 + - - +
33F ARG 4.1 10.5 - - - +
35F ASN* 5.1 0.9 - - - +
36F LEU* 1.3 73.5 - - - +
38F SER* 1.3 61.4 + - - +
40F LEU* 3.2 3.6 + - - +
41F LEU* 2.8 36.2 + - - +
34J TRP* 4.3 18.3 - - - -
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Residues in contact with SER 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LEU* 5.6 3.7 - - - +
14F TYR* 4.6 1.9 + - - -
35F ASN* 3.4 25.6 + - - -
37F GLN* 1.3 81.4 - - - +
39F LEU* 1.3 62.2 + - - -
41F LEU* 3.0 22.2 + - - +
42F SER* 3.3 12.8 + - - -
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Residues in contact with LEU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TYR* 4.2 23.1 - - + -
20B PHE* 4.2 13.9 - - + -
37B GLN* 4.2 4.9 - - + +
38B SER* 4.1 22.2 - - - +
41B LEU* 3.5 46.0 - - + +
35F ASN* 3.1 33.6 + - - +
36F LEU* 3.8 7.4 - - + +
38F SER* 1.3 79.3 - - - +
40F LEU* 1.3 62.0 + - - +
42F SER* 3.6 2.2 + - - -
43F ALA* 3.2 18.5 + - - +
68F PHE* 4.0 14.8 - - + -
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Residues in contact with LEU 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F VAL* 4.7 10.4 - - + +
20F PHE* 4.3 12.6 - - + -
22F VAL* 4.1 20.6 - - + -
24F VAL* 6.1 0.2 - - + -
31F THR* 4.7 1.3 - - + -
36F LEU* 2.9 30.1 + - + +
37F GLN* 3.6 5.6 - - - +
38F SER 3.0 0.4 - - - -
39F LEU* 1.3 75.6 - - - +
41F LEU* 1.3 60.3 + - - +
43F ALA* 3.2 8.5 + - + +
44F GLN* 2.9 25.8 + - - +
50F VAL* 4.7 12.1 - - + -
52F ILE* 5.4 3.8 - - + -
63F PHE* 3.5 33.9 - - + -
66F VAL* 4.2 13.5 - - + -
68F PHE* 4.1 17.7 - - + -
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Residues in contact with LEU 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LEU* 3.7 31.0 - - + -
68E PHE* 4.0 14.4 - - + -
12F THR* 3.5 26.0 - - + +
14F TYR* 3.0 40.8 - - + +
20F PHE* 3.7 16.2 - - + -
37F GLN 2.8 29.7 + - - +
38F SER* 3.0 8.3 + - - +
40F LEU* 1.3 72.1 - - - +
42F SER* 1.3 51.7 + - - +
44F GLN* 3.2 8.3 + - - +
45F ILE* 2.6 48.5 + - + +
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Residues in contact with SER 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ILE 4.3 14.2 + - - -
286A LEU* 4.4 18.8 + - - +
41B LEU* 4.0 17.2 - - - +
45B ILE* 5.0 1.8 - - - -
38F SER 3.3 9.8 + - - -
39F LEU* 3.8 8.6 - - - -
40F LEU 3.3 0.4 - - - -
41F LEU* 1.3 73.8 - - - +
43F ALA* 1.3 64.2 + - - +
45F ILE* 4.3 7.2 - - - +
46F THR* 2.9 31.3 + - - +
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Residues in contact with ALA 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 4.8 0.6 - - - +
9F VAL* 4.8 4.3 - - + -
39F LEU 3.2 11.0 + - - +
40F LEU* 3.2 12.6 + - + +
42F SER* 1.3 79.8 - - - +
44F GLN* 1.3 61.1 + - - +
46F THR* 4.3 1.3 - - - -
47F GLY* 3.1 4.9 + - - -
48F MET* 3.0 47.9 + - + +
50F VAL* 4.1 9.0 - - + -
68F PHE* 3.9 26.2 - - + -
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Residues in contact with GLN 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ARG* 5.2 1.6 + - - -
48E MET* 4.0 13.1 - - + +
68E PHE* 2.7 32.2 + - - +
69E ARG 3.6 14.8 + - - -
9F VAL* 3.7 38.7 + - + +
10F GLU 3.7 4.4 + - - -
11F TYR* 3.6 12.3 - - - +
12F THR* 2.8 26.8 + - + +
40F LEU 2.9 12.8 + - - +
41F LEU* 3.4 11.7 - - - +
43F ALA* 1.3 76.1 - - - +
45F ILE* 1.3 66.5 + - + +
46F THR 3.0 1.6 + - - -
47F GLY* 3.1 11.8 + - - -
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Residues in contact with ILE 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ARG* 4.4 4.6 + - - -
277A TRP* 3.8 13.0 - - - -
285A ILE* 3.2 38.1 - - + +
39E LEU* 4.9 13.9 - - + +
42E SER* 4.7 18.4 - - - +
43E ALA 5.9 0.2 - - - +
46E THR* 4.4 16.1 + - + +
48E MET* 4.1 29.8 - - + +
68E PHE* 5.8 4.9 - - + -
41F LEU* 2.6 44.7 + - + +
42F SER* 3.5 7.8 + - - +
44F GLN* 1.3 75.3 - - + +
46F THR* 1.3 57.6 + - + +
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Residues in contact with THR 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ARG* 4.1 2.7 + - - -
272A HIS 5.5 1.4 - - - +
275A ILE* 4.7 4.0 - - - +
277A TRP* 3.4 30.0 + - - -
282A LEU* 3.5 30.1 - - + -
285A ILE* 3.5 19.5 - - + -
286A LEU* 4.3 7.2 - - + -
45B ILE* 3.1 30.0 - - + +
42F SER* 2.9 21.6 + - - +
43F ALA 4.0 2.1 + - - -
45F ILE* 1.3 77.1 - - + +
47F GLY* 1.3 59.9 + - - +
48F MET* 4.0 4.3 - - - +
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Residues in contact with GLY 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ARG* 4.2 11.8 - - - +
272A HIS* 6.0 0.7 - - - -
273A ASN* 4.0 6.2 - - - +
275A ILE* 4.5 9.9 - - - +
8F LYS* 2.9 35.5 + - - -
43F ALA 3.1 2.8 + - - -
44F GLN 3.1 12.1 + - - -
45F ILE 3.5 0.2 - - - -
46F THR* 1.3 80.6 - - - +
48F MET* 1.3 61.0 + - - +
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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