Contacts of the helix formed by residues 36 - 46 (chain D) in PDB entry 1ADO
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 THR 36 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D SER* 1.3 72.0 - - - +
37D GLY* 1.3 58.5 + - - +
39D ILE* 3.0 10.5 - - - +
40D ALA* 2.9 24.8 + - - +
50D ASN* 3.1 27.3 + - - +
55D ARG* 3.6 27.6 + - - +
79D PHE* 4.2 14.8 - - - -
81D GLU* 4.8 4.0 + - - -
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Residues in contact with GLY 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D SER* 3.2 5.4 + - - -
36D THR* 1.3 79.0 - - - +
38D SER* 1.3 61.0 + - - +
40D ALA* 3.3 16.9 - - - +
41D LYS* 3.6 16.5 + - - +
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Residues in contact with SER 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLU* 4.0 18.2 - - - -
35D SER* 2.9 20.2 + - - -
37D GLY* 1.3 70.8 - - - +
39D ILE* 1.3 67.0 + - - +
40D ALA 3.1 1.6 - - - -
41D LYS* 3.1 24.5 + - - +
42D ARG* 3.4 17.4 + - - +
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Residues in contact with ILE 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLU* 4.0 13.4 - - + +
35D SER 2.8 19.3 + - - +
36D THR* 3.0 27.8 - - - +
38D SER* 1.3 73.0 - - - +
40D ALA* 1.3 57.2 + - - +
42D ARG* 3.0 20.8 + - + +
43D LEU* 2.9 44.1 + - + +
50D ASN* 4.0 3.8 - - - +
55D ARG* 3.6 27.8 - - + -
58D TYR* 4.1 27.1 - - + -
59D ARG* 4.0 23.3 - - - +
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D THR 2.9 11.7 + - - +
37D GLY* 3.3 11.2 - - - +
38D SER 3.1 0.2 - - - -
39D ILE* 1.3 76.4 - - - +
41D LYS* 1.3 57.7 + - + +
42D ARG 3.2 0.3 + - - -
43D LEU* 3.2 2.9 + - - +
44D GLN* 2.8 34.0 + - - +
50D ASN* 3.1 36.4 - - + +
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Residues in contact with LYS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D GLY 3.7 15.7 - - - +
38D SER* 3.1 14.1 + - - +
40D ALA* 1.3 75.8 - - + +
42D ARG* 1.3 63.5 + - + +
44D GLN* 3.7 8.0 + - - +
45D SER* 3.4 21.1 + - - -
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLU* 2.9 45.4 + - - +
38D SER* 3.4 16.7 + - - +
39D ILE* 3.0 23.8 + - + +
41D LYS* 1.3 76.8 - - - +
43D LEU* 1.3 63.8 + - + +
45D SER* 2.5 26.4 + - - -
58D TYR* 5.4 2.7 + - + -
302D GLY* 5.4 0.8 - - - -
303D ARG* 4.7 21.9 - - - +
306D GLN* 3.9 15.4 + - - +
310D LEU* 3.5 24.2 - - + +
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D ILE* 2.9 38.1 + - + +
40D ALA* 3.8 2.9 - - - +
42D ARG* 1.3 71.2 - - + +
44D GLN* 1.3 65.5 + - - +
46D ILE* 3.1 15.1 + - + +
48D THR* 3.0 44.6 + - + +
49D GLU 4.1 2.9 - - - +
50D ASN* 3.6 37.9 - - + +
51D THR 4.6 0.7 - - - +
54D ASN* 4.6 8.7 - - + +
55D ARG* 4.1 9.6 - - + -
58D TYR* 5.1 3.8 - - + -
310D LEU* 4.9 3.6 - - + -
313D TRP* 3.8 34.1 - - + -
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Residues in contact with GLN 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ALA* 2.8 19.5 + - - +
41D LYS* 3.8 8.2 - - - +
43D LEU* 1.3 77.1 - - - +
45D SER* 1.3 63.5 + - - +
47D GLY* 2.9 15.3 + - - +
48D THR 3.9 6.2 + - - +
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LYS 3.4 10.8 + - - -
42D ARG* 2.5 24.2 + - - -
44D GLN* 1.3 79.5 - - - +
46D ILE* 1.3 61.1 + - - +
47D GLY 3.7 0.2 + - - -
310D LEU* 4.0 9.0 - - - +
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Residues in contact with ILE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU* 3.2 16.2 - - - +
45D SER* 1.3 79.7 + - - +
47D GLY* 1.3 59.8 + - - +
48D THR* 3.4 20.4 + - - +
310D LEU* 3.3 62.8 - - + +
311D LYS* 4.2 12.6 - - + +
313D TRP* 3.6 17.5 - - + -
314D GLY* 4.1 16.6 - - - +
315D GLY 3.8 7.2 - - - +
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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