Contacts of the helix formed by residues 40 - 51 (chain D) in PDB entry 5L08
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 ASP 40 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D GLU* 6.1 1.3 - - - +
19D LEU* 3.7 12.3 - - - +
38D ILE* 3.3 7.4 - - - +
39D LYS* 1.3 81.3 - - - +
41D ALA* 1.3 63.3 + - - +
42D LEU* 2.9 13.2 + - - +
43D MET* 2.7 39.2 + - - +
44D LEU 3.2 9.0 + - - -
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Residues in contact with ALA 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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11D GLY* 3.8 36.6 - - - +
14D LEU* 3.9 19.3 - - + -
19D LEU* 4.1 14.3 - - + +
22D LEU* 5.8 0.9 - - + -
40D ASP* 1.3 75.4 - - - +
42D LEU* 1.3 59.2 + - + +
44D LEU* 3.2 4.6 + - - +
45D PHE* 2.9 40.6 + - + -
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Residues in contact with LEU 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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4D SER 4.8 6.1 - - - +
7D LEU* 3.5 21.8 - - + +
8D TYR* 3.8 51.1 - - + +
11D GLY* 4.4 5.6 - - - -
12D GLU* 5.4 1.3 - - + +
40D ASP* 2.9 11.3 + - - +
41D ALA* 1.3 83.2 - - + +
43D MET* 1.3 61.0 + - + +
45D PHE* 3.2 21.0 + - + +
46D GLN* 2.9 42.8 + - + +
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Residues in contact with MET 43 (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 PRO* 4.0 24.0 - - + +
38D ILE* 3.8 15.3 - - + -
39D LYS* 3.9 15.5 - - + +
40D ASP* 2.7 33.5 + - - +
42D LEU* 1.3 73.4 - - + +
44D LEU* 1.3 61.2 + - - +
46D GLN* 3.4 20.7 + - - +
47D ARG* 3.2 49.5 + - - +
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Residues in contact with LEU 44 (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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19D LEU* 4.2 9.2 - - + -
22D LEU* 3.7 42.0 - - + +
23D LYS* 5.1 3.6 - - + +
26D SER* 4.5 21.1 - - - +
30D ILE* 4.9 3.8 - - + -
38D ILE* 3.6 31.3 - - + +
40D ASP 3.2 7.6 + - - +
41D ALA* 3.2 10.8 + - - +
43D MET* 1.3 78.3 - - - +
45D PHE* 1.3 71.9 + - + +
47D ARG* 3.0 5.9 + - - +
48D LEU* 3.0 47.4 + - + +
65D LEU* 5.4 3.8 - - + -
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Residues in contact with PHE 45 (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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7D LEU* 4.0 47.8 - - + -
10D ILE* 6.2 0.4 - - + -
11D GLY* 4.7 3.8 - - - -
14D LEU* 4.4 13.0 - - + -
22D LEU* 5.5 1.8 - - + -
41D ALA* 2.9 36.7 + - + -
42D LEU* 3.2 21.7 + - + +
44D LEU* 1.3 90.2 - - + +
46D GLN* 1.3 52.8 + - + +
48D LEU* 3.1 7.3 + - + +
49D GLN* 2.7 46.3 + - - +
54D LEU* 3.5 30.4 - - + +
62D LEU* 4.1 21.5 - - + -
65D LEU* 6.2 0.4 - - + -
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Residues in contact with GLN 46 (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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42D LEU* 2.9 25.9 + - + +
43D MET* 3.5 32.2 - - - +
45D PHE* 1.3 77.7 - - + +
47D ARG* 1.3 83.4 + - - +
49D GLN* 3.2 18.3 + - - +
50D GLU* 3.0 27.3 + - + +
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Residues in contact with ARG 47 (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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30D ILE* 4.0 21.3 - - + -
34D LYS* 4.0 28.7 + - - +
37D PRO* 5.8 3.2 - - - +
38D ILE* 4.0 19.8 - - + +
43D MET* 3.2 42.9 + - - +
44D LEU 3.0 6.6 + - - +
46D GLN* 1.3 95.3 + - - +
48D LEU* 1.3 57.7 + - - +
50D GLU* 2.9 46.5 + - - +
51D LYS* 3.0 32.1 + - - +
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Residues in contact with LEU 48 (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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26D SER* 5.2 2.9 - - - -
29D TYR* 5.0 2.5 - - + -
30D ILE* 3.8 25.1 - - + -
44D LEU* 3.0 38.4 + - + +
45D PHE* 3.1 4.0 + - - +
47D ARG* 1.3 74.3 - - - +
49D GLN* 1.3 55.7 + - - +
51D LYS* 4.3 2.0 - - - +
52D ARG 2.8 11.4 + - - -
53D MET* 2.7 40.7 + - + -
54D LEU* 3.1 43.4 + - + +
61D PHE* 3.6 32.1 - - + -
65D LEU* 4.5 6.7 - - + -
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Residues in contact with GLN 49 (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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4D SER* 4.3 25.9 + - - +
7D LEU* 5.3 2.4 - - - +
45D PHE* 2.7 23.9 + - - +
46D GLN* 3.5 23.1 - - - +
48D LEU* 1.3 74.3 - - - +
50D GLU* 1.3 64.8 + - + +
52D ARG* 3.1 11.5 + - - +
54D LEU* 3.0 31.7 + - + +
55D GLU* 3.5 24.7 - - + +
56D GLU 5.8 0.4 - - - +
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Residues in contact with GLU 50 (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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46D GLN* 3.0 13.4 + - - +
47D ARG* 2.9 53.4 + - - +
49D GLN* 1.3 76.7 - - + +
51D LYS* 1.3 59.4 + - + +
52D ARG* 2.7 32.4 + - - -
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Residues in contact with LYS 51 (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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29D TYR* 5.0 5.6 - - + +
30D ILE* 3.7 22.2 - - + -
31D PRO* 4.9 15.0 - - - +
34D LYS* 5.8 5.7 - - - +
47D ARG 3.0 19.5 + - - +
48D LEU 4.0 2.9 - - - +
50D GLU* 1.3 83.3 - - - +
52D ARG* 1.3 84.4 + - - +
53D MET* 3.1 27.3 + - + +
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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