Contacts of the helix formed by residues 43 - 53 (chain D) in PDB entry 1A4Y
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 43 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.8 15.8 - - - +
15D SER* 3.5 22.4 + - - +
16D ASP* 2.2 47.7 + - - +
19D TRP* 3.6 40.0 - - + +
37D CYS 4.9 1.4 + - - -
38D GLY 4.6 9.3 + - - -
39D LEU* 3.8 26.5 - - + +
40D THR* 3.6 27.2 + - - +
42D ALA* 1.3 78.0 - - + +
44D CYS* 1.3 56.2 + - - +
45D LYS 3.3 0.2 - - - -
46D ASP* 3.3 11.3 + - - +
47D ILE* 2.9 32.1 + - - +
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Residues in contact with CYS 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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39D LEU* 5.5 0.2 - - - -
40D THR 3.2 19.7 + - - -
41D GLU* 3.5 13.9 - - - +
42D ALA 3.0 0.2 - - - -
43D ARG* 1.3 77.9 - - - +
45D LYS* 1.3 60.5 + - - +
47D ILE* 3.5 11.5 - - - +
48D SER* 2.9 28.4 + - - -
67D LEU* 3.4 26.7 - - - -
71D GLY* 3.6 35.9 - - - +
74D CYS* 4.1 7.0 - - + +
75D VAL* 3.9 11.7 - - + +
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Residues in contact with LYS 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* 3.4 22.7 - - - +
42D ALA* 3.0 19.1 - - - +
44D CYS* 1.3 74.2 - - - +
46D ASP* 1.3 69.2 + - - +
48D SER* 3.4 6.1 + - - +
49D SER* 3.2 27.2 + - - -
74D CYS* 4.5 19.5 - - - -
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Residues in contact with ASP 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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19D TRP* 2.9 28.2 + - + +
23D LEU* 3.6 28.9 - - + +
42D ALA 3.9 10.8 - - - +
43D ARG* 3.3 10.4 + - - +
44D CYS 3.2 0.2 - - - -
45D LYS* 1.3 81.7 - - - +
47D ILE* 1.3 61.5 + - - +
49D SER* 3.4 7.1 + - - -
50D ALA* 3.2 23.4 + - - +
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Residues in contact with ILE 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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19D TRP* 3.7 19.7 - - + -
26D LEU* 4.2 16.6 - - + +
34D LEU* 4.7 4.7 - - + -
39D LEU* 3.6 31.0 - - + -
43D ARG* 2.9 25.1 + - + +
44D CYS* 3.5 14.4 - - - +
45D LYS 3.2 0.2 - - - -
46D ASP* 1.3 77.7 - - - +
48D SER* 1.3 63.3 + - - +
50D ALA* 3.4 1.6 + - - +
51D LEU* 2.9 50.9 + - + +
60D LEU* 5.2 2.9 - - + -
62D LEU* 4.7 11.7 - - + -
75D VAL* 4.0 19.3 - - + -
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Residues in contact with SER 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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44D CYS 2.9 15.6 + - - -
45D LYS* 3.8 6.7 - - - -
46D ASP 3.4 0.2 - - - -
47D ILE* 1.3 77.6 - - - +
49D SER* 1.3 62.2 + - - +
51D LEU* 4.3 1.8 - - - -
52D ARG* 3.1 36.5 + - - -
74D CYS* 2.5 32.7 + - - -
75D VAL* 4.2 3.4 - - - -
77D GLN* 3.9 1.1 + - - +
78D GLY* 2.9 29.6 + - - -
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Residues in contact with SER 49 (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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45D LYS 3.2 17.2 + - - -
46D ASP* 3.6 8.1 - - - -
48D SER* 1.3 74.5 - - - +
50D ALA* 1.3 64.0 + - - +
52D ARG* 3.6 19.5 + - - +
53D VAL* 3.5 22.3 - - - +
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Residues in contact with ALA 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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23D LEU* 4.0 8.1 - - + +
26D LEU* 3.7 28.8 - - + +
27D GLN* 3.7 28.6 - - + +
46D ASP 3.2 12.9 + - - +
47D ILE 4.0 1.6 - - - +
49D SER* 1.3 77.2 - - - +
51D LEU* 1.3 67.0 + - - +
53D VAL* 3.3 16.5 + - - +
54D ASN* 3.3 12.8 + - - +
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Residues in contact with LEU 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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26D LEU* 4.3 14.8 - - + +
32D VAL* 5.3 2.9 - - + -
47D ILE* 2.9 40.0 + - + +
48D SER* 3.7 5.2 - - - +
49D SER 3.3 0.2 - - - -
50D ALA* 1.3 79.2 - - - +
52D ARG* 1.3 59.1 + - - +
54D ASN* 3.0 27.7 + - - +
57D LEU* 3.4 37.0 - - + +
60D LEU* 3.4 34.8 - - + -
75D VAL* 4.3 9.9 - - + +
78D GLY 3.9 9.8 - - - +
79D LEU* 3.9 15.6 - - + +
81D THR* 5.2 0.5 + - - -
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Residues in contact with ARG 52 (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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48D SER* 3.1 38.3 + - - +
49D SER* 3.6 22.2 + - - +
51D LEU* 1.3 76.5 - - - +
53D VAL* 1.3 64.9 + - + +
54D ASN 3.3 2.2 + - - -
77D GLN* 4.4 26.9 + - - +
78D GLY* 3.2 24.8 + - - +
80D GLN* 5.9 1.2 - - - +
81D THR* 3.5 37.4 + - + +
83D SER* 4.3 5.0 + - - -
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Residues in contact with VAL 53 (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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27D GLN* 3.5 34.1 - - + +
49D SER 3.5 15.7 - - - +
50D ALA 3.3 13.0 + - - +
51D LEU 3.2 1.0 - - - -
52D ARG* 1.3 85.5 - - + +
54D ASN* 1.3 58.3 + - - +
55D PRO* 3.4 10.8 - - - +
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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