Contacts of the helix formed by residues 47 - 57 (chain A) in PDB entry 1O4X
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 SER 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLY* 5.1 0.7 - - - -
46A PHE* 1.3 73.5 - - - +
48A GLN* 1.3 65.1 + - - +
49A THR* 3.5 11.3 + - - -
50A THR* 2.9 34.3 + - - -
51A ILE* 3.1 17.5 + - - +
325D G 2.8 47.3 + - - -
326D C 3.9 10.1 - - - -
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Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 1.6 73.0 + - + +
32A GLY* 4.1 20.5 - - - +
46A PHE 4.1 0.2 + - - -
47A SER* 1.3 73.2 - - - +
49A THR* 1.3 69.6 + - - +
51A ILE 3.2 0.3 + - - -
52A SER* 2.8 15.6 + - - -
310C C 3.6 27.4 + - + +
311C A 3.5 30.4 + - - +
327D A 4.8 1.4 + - - -
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Residues in contact with THR 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 4.0 0.7 - - - +
47A SER* 3.1 10.2 + - - -
48A GLN* 1.3 89.0 + - - +
50A THR* 1.3 57.7 + - - +
52A SER* 3.3 5.2 + - - -
53A ARG* 2.9 77.3 + - - +
312C T 3.2 20.5 + - + -
325D G 4.5 2.2 - - - +
326D C 3.0 30.3 + - - +
327D A 3.7 5.9 + - - -
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Residues in contact with THR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.2 19.7 - - + -
47A SER* 2.9 20.8 + - - -
49A THR* 1.3 80.5 - - - +
51A ILE* 1.3 59.9 + - + +
53A ARG* 3.3 9.6 + - - +
54A PHE* 2.8 29.2 + - + +
59A LEU* 4.5 4.4 - - + +
67A LEU* 4.0 25.6 - - + -
324D A 3.8 20.6 - - + +
325D G 3.0 15.5 + - - -
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Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 4.5 9.2 - - + -
24A ARG* 3.8 9.9 - - - +
31A GLN* 2.9 50.5 - - + +
34A VAL* 4.3 12.3 - - + -
35A GLY* 4.1 8.7 - - - +
38A MET* 5.5 0.2 - - + -
46A PHE* 4.3 15.7 - - + -
47A SER 3.1 14.4 + - - +
50A THR* 1.3 79.7 - - + +
52A SER* 1.3 59.3 + - - +
54A PHE* 3.3 3.6 + - + +
55A GLU* 3.0 38.3 + - + +
71A LEU* 4.2 30.7 - - + -
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Residues in contact with SER 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 2.3 41.7 + - - +
48A GLN* 2.8 17.2 + - - -
49A THR* 3.5 6.5 - - - -
51A ILE* 1.3 71.8 - - - +
53A ARG* 1.3 63.8 + - - +
55A GLU* 3.3 4.9 + - - +
56A ALA* 3.1 24.5 + - - +
58A ASN* 5.5 0.4 - - - -
310C C 3.7 7.0 + - - +
311C A 2.8 34.1 + - - -
312C T 5.5 1.1 - - - -
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR* 2.9 44.4 + - + +
50A THR* 3.3 9.2 + - - +
52A SER* 1.3 69.0 - - - +
54A PHE* 1.3 67.6 + - - +
56A ALA 3.3 0.3 + - - -
57A LEU* 2.9 3.6 + - - -
58A ASN* 2.8 48.5 + - + +
59A LEU* 3.6 34.9 - - + +
311C A 6.2 0.4 - - + -
312C T 3.6 21.3 + - + +
313C G 3.1 34.8 + - - -
314C C 4.6 1.4 - - - +
324D A 4.7 9.1 + - - -
325D G 3.5 24.0 + - - -
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Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 5.4 2.0 - - + -
16A PHE* 3.7 39.9 - + - -
17A ALA* 4.2 12.9 - - + +
20A PHE* 4.9 4.9 - + + -
50A THR* 2.8 19.2 + - + +
51A ILE* 3.6 6.1 - - + +
53A ARG* 1.3 77.4 - - - +
55A GLU* 1.3 68.1 + - + +
57A LEU* 3.0 17.5 + - - +
59A LEU* 3.9 3.5 - - + +
64A MET* 3.3 70.2 - - + +
67A LEU* 3.8 25.6 - - + -
68A LYS* 3.9 9.2 - - + -
71A LEU* 3.6 24.2 - - + -
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA* 4.1 18.1 - - - +
20A PHE* 3.5 32.0 - - + -
21A LYS* 3.6 34.4 + - + +
24A ARG* 3.1 50.2 + - - -
31A GLN* 4.1 3.5 - - - +
51A ILE* 3.0 22.8 + - + +
52A SER* 3.3 5.5 + - - +
54A PHE* 1.3 79.8 - - + +
56A ALA* 1.3 58.0 + - - +
57A LEU* 3.4 3.0 + - - +
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Residues in contact with ALA 56 (chain A).
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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52A SER 3.1 15.3 + - - +
53A ARG 4.0 0.2 - - - +
54A PHE 3.1 0.2 - - - -
55A GLU* 1.3 77.0 - - + +
57A LEU* 1.3 72.0 + - - +
58A ASN* 3.1 33.9 + - - +
276B LYS* 5.7 4.0 + - - +
311C A 4.3 14.6 - - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.9 6.7 - - + +
13A LEU* 4.5 6.7 - - + -
14A GLU* 3.5 43.3 - - + +
17A ALA* 3.7 25.1 - - + -
18A LYS* 6.4 2.0 - - - -
53A ARG 2.9 6.2 + - - -
54A PHE 3.0 7.1 + - - -
55A GLU 4.2 3.4 - - - +
56A ALA* 1.3 82.5 - - - +
58A ASN* 1.3 56.0 + - - +
59A LEU 3.1 19.2 + - - +
64A MET* 3.7 29.2 - - + -
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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