Contacts of the helix formed by residues 35 - 46 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34D TRP* 4.6 9.3 - - - -
33G ARG* 3.2 0.7 - - - +
34G TRP* 1.3 79.5 + - - +
36G LEU* 1.3 59.9 + - - +
37G GLN 3.0 6.8 + - - -
38G SER* 4.2 4.5 + - - -
39G LEU* 3.4 21.0 + - - +
14H TYR* 2.7 30.1 + - + +
18H ASP* 4.2 0.5 - - - +
34H TRP* 3.5 29.5 - - - +
37H GLN* 4.0 15.9 - - - +
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Residues in contact with LEU 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G THR* 4.0 20.6 - - + +
33G ARG* 3.5 17.5 + - + +
34G TRP 3.3 0.6 - - - -
35G ASN* 1.3 77.9 - - - +
37G GLN* 1.3 58.9 + - - +
38G SER 3.4 0.2 - - - -
39G LEU* 3.9 7.0 - - + -
40G LEU* 2.9 46.1 + - + +
63G PHE* 4.5 5.8 - - + -
64G SER 4.5 4.7 - - - +
66G VAL* 4.2 22.2 - - + -
68G PHE* 4.0 27.8 - - + -
14H TYR* 4.0 45.1 - - + -
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Residues in contact with GLN 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G TYR* 3.6 21.7 - - - -
18G ASP 3.3 24.5 + - - -
19G THR* 4.7 0.4 - - - +
20G PHE* 3.2 60.1 - - + +
31G THR 5.3 0.6 + - - -
33G ARG 4.3 4.3 + - - +
34G TRP* 3.3 30.5 + - - +
35G ASN 3.0 1.8 - - - -
36G LEU* 1.3 79.3 - - - +
38G SER* 1.3 62.1 + - - +
41G LEU* 3.4 16.8 + - - +
35K ASN* 3.7 18.4 - - - +
39K LEU* 4.2 13.8 - - + +
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Residues in contact with SER 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G TRP 5.3 0.9 + - - -
35G ASN 4.2 5.6 + - - -
37G GLN* 1.3 74.9 - - - +
39G LEU* 1.3 72.5 + - - +
40G LEU 3.1 1.8 - - - -
41G LEU* 4.4 2.2 - - - +
42G SER* 2.8 30.9 + - - -
39K LEU* 4.5 14.9 - - - +
287L MET* 4.6 27.4 - - - -
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Residues in contact with LEU 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G ASN 3.4 18.4 - - - +
36G LEU* 3.6 19.1 - - + +
38G SER* 1.3 76.5 - - - +
40G LEU* 1.3 57.5 + - - +
42G SER* 3.8 2.4 - - - -
43G ALA* 3.0 27.7 + - - +
68G PHE* 3.7 21.7 - - + -
14H TYR* 4.9 1.1 - - + -
20H PHE* 4.3 25.6 - - + -
37H GLN* 4.3 19.1 - - + +
38H SER* 4.6 6.3 - - - -
41H LEU* 3.6 18.1 - - + +
287L MET* 3.4 31.9 - - + -
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Residues in contact with LEU 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 4.5 7.4 - - + +
12G THR* 4.5 2.4 - - + +
20G PHE* 4.2 22.4 - - + -
22G VAL* 3.8 30.7 - - + -
31G THR* 4.4 4.5 - - + -
36G LEU* 2.9 38.4 + - + +
39G LEU* 1.3 74.7 - - - +
41G LEU* 1.3 63.3 + - - +
43G ALA* 3.4 6.6 + - - +
44G GLN* 3.3 22.5 + - - +
50G VAL* 4.9 11.0 - - + -
52G ILE* 5.8 0.4 - - + -
63G PHE* 4.1 15.3 - - + -
66G VAL* 4.2 21.8 - - + -
68G PHE* 4.2 17.9 - - + -
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Residues in contact with LEU 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G THR* 3.3 13.2 - - - +
20G PHE* 4.6 5.8 - - + -
37G GLN 3.4 15.2 + - - +
38G SER* 3.1 5.1 + - - +
40G LEU* 1.3 77.0 - - - +
42G SER* 1.3 60.0 + - - +
44G GLN* 3.0 30.3 + - - +
45G ILE* 2.9 44.7 + - + +
39K LEU* 4.3 32.1 - - + +
42K SER* 4.4 8.5 - - - -
48K MET* 3.7 23.1 - - + -
68K PHE* 3.6 25.6 - - + -
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Residues in contact with SER 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G SER* 2.8 16.1 + - - -
39G LEU 3.8 2.5 - - - -
41G LEU* 1.3 74.2 - - - +
43G ALA* 1.3 55.1 + - - +
44G GLN 2.9 8.5 + - - -
45G ILE* 4.3 9.9 - - - +
46G THR* 2.9 32.7 + - - +
41H LEU* 4.8 0.9 - - - -
45H ILE* 4.3 7.7 - - - +
283L GLY* 3.1 14.9 + - - -
286L LEU* 4.9 3.1 - - - +
287L MET* 2.9 41.0 + - - +
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Residues in contact with ALA 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 4.6 5.7 + - + +
39G LEU 3.0 19.3 + - - +
40G LEU* 3.8 7.4 - - - +
41G LEU 3.2 0.6 - - - -
42G SER* 1.3 75.0 - - - +
44G GLN* 1.3 59.1 + - - +
46G THR 4.2 2.2 - - - -
47G GLY 4.2 0.2 + - - -
48G MET* 3.5 51.5 + - + +
50G VAL* 4.3 9.0 - - + -
68G PHE* 3.8 26.2 - - + -
41H LEU* 5.4 0.4 - - + +
45H ILE* 5.6 0.2 - - - -
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Residues in contact with GLN 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.9 35.1 - - + +
10G GLU 4.6 0.9 - - - +
11G TYR* 3.9 5.4 - - - -
12G THR* 3.0 34.7 + - - +
40G LEU 3.3 11.0 - - - +
41G LEU* 3.0 23.8 - - - +
42G SER 2.9 0.6 - - - -
43G ALA* 1.3 80.6 - - - +
45G ILE* 1.3 62.2 + - + +
46G THR 3.0 5.0 + - - -
47G GLY* 3.9 7.4 + - - -
48K MET* 4.4 6.7 - - - +
68K PHE* 3.5 22.0 - - - +
69K ARG* 3.9 12.4 - - - +
268L ARG* 5.0 3.3 + - - -
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Residues in contact with ILE 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LEU* 2.9 33.7 + - + +
42G SER* 4.0 11.2 - - - +
44G GLN* 1.3 79.1 - - - +
46G THR* 1.3 66.1 + - + +
47G GLY 3.8 0.4 - - - -
42K SER* 4.3 13.0 - - - -
46K THR* 4.1 29.2 - - + +
48K MET* 3.2 34.5 - - + -
268L ARG* 3.1 31.0 + - - +
270L ILE* 4.9 2.2 - - + -
279L SER* 4.0 13.8 + - - +
283L GLY* 4.4 8.3 - - - +
286L LEU* 5.0 4.5 - - + -
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Residues in contact with THR 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G SER 2.9 21.5 + - - +
43G ALA 4.6 0.2 - - - -
44G GLN 3.0 0.4 - - - -
45G ILE* 1.3 84.9 - - + +
47G GLY* 1.3 57.1 + - - +
48G MET* 3.1 21.8 + - - +
45H ILE* 4.0 26.3 - - + +
266L ARG* 3.6 26.1 + - - +
279L SER* 3.9 12.1 - - - +
280L SER* 4.4 8.2 + - - -
283L GLY* 3.6 28.0 - - - -
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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