Contacts of the helix formed by residues 39 - 48 (chain D) in PDB entry 3LOC
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 39 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D GLY 4.7 4.5 - - - +
38D THR* 1.3 85.5 - - - +
40D LEU* 1.3 66.4 + - - +
41D GLU* 4.3 11.4 - - + +
42D GLN* 2.9 39.0 + - + +
43D ILE* 3.4 3.3 + - - +
61D LYS* 5.4 1.3 - - - +
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Residues in contact with LEU 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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39D ARG* 1.3 73.1 - - - +
41D GLU* 1.3 57.8 + - - +
43D ILE* 3.1 18.9 + - + +
44D ALA* 2.8 31.1 + - - +
51D LYS* 4.1 25.7 - - + +
54D LEU* 4.1 20.4 - - + +
55D LEU* 3.6 33.4 - - + -
61D LYS* 3.5 48.8 - - + +
64D LEU* 4.5 3.6 - - + -
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Residues in contact with GLU 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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39D ARG* 3.2 8.7 - - + +
40D LEU* 1.3 79.2 - - - +
42D GLN* 1.3 54.8 + - + +
44D ALA* 3.7 6.7 - - - +
45D GLU* 2.9 31.5 + - - +
51D LYS* 4.1 31.5 - - + +
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Residues in contact with GLN 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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29D THR* 4.0 15.0 - - + +
33D PHE* 3.1 38.3 - - - -
37D GLY 3.6 7.1 - - - +
38D THR* 3.4 11.3 - - - -
39D ARG* 2.9 43.9 + - + +
41D GLU* 1.3 77.8 - - - +
43D ILE* 1.3 63.3 + - - +
45D GLU* 3.4 5.3 + - - +
46D LEU* 3.1 23.6 + - - +
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Residues in contact with ILE 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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22D ILE* 3.9 11.7 - - + +
25D ALA* 3.8 5.4 - - + -
26D ALA* 3.7 34.8 - - + +
29D THR* 3.9 19.7 - - - -
30D PHE* 3.9 20.2 - - + -
38D THR* 3.7 24.2 - - + -
39D ARG 3.4 1.1 + - - +
40D LEU* 3.1 16.8 + - + +
42D GLN* 1.3 79.3 - - - +
44D ALA* 1.3 53.7 + - - +
46D LEU* 3.2 4.6 + - - +
47D ALA* 2.8 34.2 + - + +
54D LEU* 3.7 15.9 - - + -
64D LEU* 4.0 15.0 - - + -
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Residues in contact with ALA 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 LEU 2.8 16.8 + - - +
41D GLU* 3.7 7.9 - - - +
43D ILE* 1.3 77.0 - - - +
45D GLU* 1.3 55.5 + - - +
47D ALA 3.7 0.2 - - - -
48D GLY* 2.9 22.9 + - - -
49D VAL* 2.9 39.5 + - + +
50D SER 4.1 0.9 - - - -
51D LYS* 3.8 25.6 - - + +
54D LEU* 3.9 5.5 - - + +
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Residues in contact with GLU 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 GLU 2.9 17.9 + - - +
42D GLN* 3.8 5.1 - - - +
43D ILE 3.2 0.2 - - - -
44D ALA* 1.3 73.8 - - - +
46D LEU* 1.3 67.1 + - - +
48D GLY* 3.2 12.9 + - - -
49D VAL 4.9 0.4 - - - -
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Residues in contact with LEU 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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25D ALA* 3.6 34.3 - - + +
28D ASP* 4.0 19.1 - - + +
29D THR* 3.6 10.5 - - - +
42D GLN 3.1 16.8 + - - +
43D ILE* 3.7 3.6 - - - +
45D GLU* 1.3 78.9 + - - +
47D ALA* 1.3 61.5 + - - +
48D GLY 3.3 0.7 + - - -
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Residues in contact with ALA 47 (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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21D ALA* 4.0 21.8 - - + +
22D ILE* 4.2 10.1 - - + -
25D ALA* 3.6 18.1 - - + +
43D ILE* 2.8 19.6 + - + +
46D LEU* 1.3 77.0 - - - +
48D GLY* 1.3 61.6 + - - +
49D VAL* 3.9 26.6 - - + +
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Residues in contact with GLY 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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18D LYS* 4.7 3.5 + - - -
44D ALA 2.9 5.4 + - - -
45D GLU* 3.2 8.6 + - - -
46D LEU 3.2 5.0 - - - -
47D ALA* 1.3 78.9 - - - +
49D VAL* 1.3 61.4 + - - +
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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