Contacts of the helix formed by residues 45 - 56 (chain A) in PDB entry 1JID
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PRO* 4.2 4.3 - - - -
43A ASN 3.7 9.9 - - - +
44A PRO* 1.3 78.8 - - - +
46A ALA* 1.3 64.7 + - - +
47A THR* 3.5 9.1 + - - -
48A GLU* 2.9 39.7 + - - +
49A ILE* 3.0 24.6 + - - +
77A GLN 5.6 7.2 - - - +
118A ARG* 5.2 0.2 - - - +
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Residues in contact with ALA 46 (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 PRO* 3.7 13.9 - - + +
45A THR* 1.3 74.3 - - - +
47A THR* 1.3 57.2 + - - +
49A ILE* 3.2 4.2 + - - -
50A GLN* 2.9 27.2 + - - +
62A LEU* 3.5 16.6 - - + -
79A ARG 4.1 4.5 + - - +
80A GLY* 3.5 40.2 - - - +
81A ARG 3.9 0.9 - - - +
82A VAL* 3.3 15.7 - - + +
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Residues in contact with THR 47 (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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45A THR* 3.1 9.0 + - - -
46A ALA* 1.3 81.3 - - - +
48A GLU* 1.3 62.6 + - + +
50A GLN* 3.4 7.5 + - - +
51A ASP* 3.0 39.7 + - - +
62A LEU* 4.0 18.3 - - + +
64A LYS* 6.1 0.2 - - - -
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Residues in contact with GLU 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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44A PRO* 3.5 2.4 - - - +
45A THR* 2.9 38.0 + - - +
47A THR* 1.3 78.5 - - + +
49A ILE* 1.3 63.1 + - - +
51A ASP* 3.3 5.8 + - - +
52A VAL* 3.1 28.1 + - - +
112A ILE* 3.8 13.6 - - + +
115A LEU* 3.9 23.6 - - + +
117A THR* 4.9 4.3 + - - +
118A ARG* 2.9 50.2 + - - +
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Residues in contact with ILE 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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18A ILE* 4.1 23.8 - - + +
19A TYR 4.5 0.2 - - - -
20A PRO* 3.9 28.5 - - + -
23A LEU* 3.5 22.9 - - + -
44A PRO* 4.7 2.9 - - + -
45A THR 3.0 15.7 + - - +
46A ALA* 3.2 10.3 + - - +
48A GLU* 1.3 76.0 - - - +
50A GLN* 1.3 62.7 + - - +
52A VAL* 3.3 9.5 - - - +
53A CYS* 2.9 37.3 + - - +
82A VAL* 3.8 19.5 - - + -
108A ALA* 4.4 6.7 - - + -
112A ILE* 3.7 16.8 - - + -
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Residues in contact with GLN 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 ALA 2.9 16.3 + - - +
47A THR* 3.6 6.8 - - - +
49A ILE* 1.3 76.4 - - - +
51A ASP* 1.3 67.7 - - - +
53A CYS* 3.9 0.4 - - - -
54A SER* 2.8 34.1 + - - -
60A VAL* 3.9 15.8 + - + +
61A PHE* 3.8 10.9 - - - +
62A LEU* 3.5 46.9 - - + +
82A VAL* 3.8 18.8 - - + +
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Residues in contact with ASP 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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47A THR* 3.0 35.1 + - - +
48A GLU* 3.7 8.3 - - - +
49A ILE 3.2 0.2 - - - -
50A GLN* 1.3 88.5 - - - +
52A VAL* 1.3 57.2 + - - +
54A SER* 3.9 4.1 - - - -
55A ALA* 3.0 29.6 + - - +
115A LEU* 5.1 12.2 - - + +
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Residues in contact with VAL 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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48A GLU 3.1 13.7 + - - +
49A ILE* 3.3 12.6 - - - +
51A ASP* 1.3 76.0 - - - +
53A CYS* 1.3 65.8 + - - +
55A ALA* 3.5 7.6 + - - +
56A VAL 3.4 14.6 + - - -
107A TYR* 3.7 14.0 + - + -
108A ALA* 3.6 33.4 - - + -
111A MET* 3.8 29.2 - - + -
112A ILE* 4.0 15.0 - - + +
115A LEU* 3.8 25.8 - - + -
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Residues in contact with CYS 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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18A ILE* 4.8 2.0 - - - -
49A ILE* 2.9 34.5 + - - +
50A GLN* 4.0 2.2 - - - +
52A VAL* 1.3 76.7 - - - +
54A SER* 1.3 67.4 + - - +
56A VAL* 3.3 19.1 + - - +
58A LEU* 3.3 24.6 + - + +
60A VAL* 3.9 20.0 - - + -
82A VAL* 5.3 0.7 - - + -
84A VAL* 4.8 2.9 - - - -
104A VAL* 3.7 30.5 - - - -
107A TYR* 5.1 3.4 - - - -
108A ALA* 4.3 11.9 - - - -
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Residues in contact with SER 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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50A GLN* 2.8 26.7 + - - -
51A ASP* 3.9 4.5 - - - -
53A CYS* 1.3 73.6 - - - +
55A ALA* 1.3 63.3 + - - +
57A GLY* 3.1 14.9 + - - -
58A LEU 3.8 13.1 + - - +
60A VAL* 3.9 13.5 - - - +
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Residues in contact with ALA 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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51A ASP 3.0 19.5 + - - +
52A VAL* 3.7 9.0 - - - +
53A CYS 3.1 0.4 - - - -
54A SER* 1.3 79.2 - - - +
56A VAL* 1.3 56.3 + - - +
57A GLY 3.3 2.9 + - - -
107A TYR* 5.6 2.0 - - - +
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Residues in contact with VAL 56 (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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52A VAL 3.4 1.6 + - - +
53A CYS* 3.3 15.0 + - - +
54A SER 3.2 0.4 - - - -
55A ALA* 1.3 77.9 - - - +
57A GLY* 1.3 57.1 + - - +
58A LEU* 4.0 10.1 - - + -
95A LEU* 3.8 10.2 - - - +
97A GLN* 3.7 23.2 - - - +
98A PHE* 3.5 26.2 - - + -
107A TYR* 3.5 40.8 - - + +
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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