Contacts of the helix formed by residues 52 - 63 (chain A) in PDB entry 3DRB
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ASN* 3.9 31.9 + - + +
11A LYS* 5.0 1.9 + - - -
43A ARG 5.1 1.6 - - - -
45A LYS 3.8 15.3 - - - +
46A SER* 3.9 7.4 - - - -
50A GLY 3.6 11.2 - - - +
51A PHE* 1.3 76.8 - - - +
53A LEU* 1.3 65.7 + - - +
54A ASP* 3.6 9.3 + - - +
55A ASP* 2.9 30.6 + - - +
56A VAL* 3.0 24.1 + - - +
85A PHE* 3.6 9.9 - - - -
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Residues in contact with LEU 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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34A LEU* 4.3 5.8 - - + -
39A TYR* 3.6 37.2 - - + -
42A LEU* 3.7 35.0 - - + +
43A ARG* 4.0 13.6 + - + +
45A LYS 4.4 1.6 + - - -
52A THR* 1.3 74.8 - - - +
54A ASP* 1.3 62.6 + - - +
56A VAL* 3.1 7.7 + - + +
57A ILE* 3.0 29.8 + - + +
85A PHE* 3.5 32.7 - - + -
88A LEU* 3.9 31.0 - - + -
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Residues in contact with ASP 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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8A ASN* 4.5 5.0 + - - +
11A LYS* 2.7 43.9 + - - +
19A GLU* 5.0 1.0 - - - +
21A PRO* 5.8 0.2 - - - +
39A TYR* 2.6 38.9 + - - -
43A ARG* 5.8 3.7 - - - +
52A THR* 3.2 7.4 + - - +
53A LEU* 1.3 79.3 - - - +
55A ASP* 1.3 63.3 + - - +
57A ILE* 3.7 9.2 - - - +
58A GLN* 3.1 34.4 + - - +
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Residues in contact with ASP 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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50A GLY 3.8 4.7 - - - +
51A PHE* 3.4 40.0 - - + -
52A THR* 2.9 36.8 + - - +
54A ASP* 1.3 80.6 - - - +
56A VAL* 1.3 64.1 + - - +
58A GLN* 3.6 13.3 + - - +
59A THR 5.1 0.5 + - - -
75A VAL* 4.5 5.2 - - - +
145A HIS* 5.3 2.9 - - - -
205A SER* 5.5 3.6 - - - +
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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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51A PHE* 3.5 23.8 - - + -
52A THR 3.0 15.0 + - - +
53A LEU* 3.1 11.0 + - + +
55A ASP* 1.3 79.6 - - - +
57A ILE* 1.3 59.8 + - - +
59A THR* 4.7 1.6 + - - +
74A CYS* 3.1 9.8 - - + -
75A VAL* 3.0 42.3 + - - +
81A SER* 4.7 1.8 - - - +
85A PHE* 3.8 22.2 - - + -
88A LEU* 3.6 29.6 - - + -
89A PHE* 3.7 16.4 - - + -
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Residues in contact with ILE 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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21A PRO* 4.2 7.6 - - + -
30A MET* 3.6 27.8 - - + -
34A LEU* 3.8 25.1 - - + -
39A TYR* 4.2 17.7 - - + -
53A LEU* 3.0 25.7 + - + +
54A ASP* 3.7 11.4 - - - +
56A VAL* 1.3 77.6 - - - +
58A GLN* 1.3 68.6 + - - +
59A THR 3.3 2.7 - - - -
60A GLY* 2.9 14.8 + - - -
61A VAL* 3.0 26.3 + - + +
73A GLY 3.9 6.3 - - - -
88A LEU* 3.9 21.5 - - + -
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Residues in contact with GLN 58 (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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54A ASP* 3.1 23.9 + - - +
55A ASP* 3.6 9.6 + - - +
56A VAL 3.5 2.2 - - - -
57A ILE* 1.3 75.5 - - - +
59A THR* 1.3 64.1 + - - +
61A VAL* 3.0 16.8 + - - +
62A ASP* 2.8 51.9 + - - +
204A ALA 4.0 15.7 - - - +
205A SER* 5.8 1.1 - - - -
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Residues in contact with THR 59 (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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55A ASP 5.1 0.4 + - - -
56A VAL 4.7 1.8 + - - +
58A GLN* 1.3 78.6 - - - +
60A GLY* 1.3 59.8 + - - +
62A ASP 3.4 0.2 + - - -
63A ASN* 2.9 46.8 + - - +
73A GLY* 3.8 3.4 - - - +
74A CYS* 3.8 26.7 - - - +
75A VAL* 4.2 17.9 - - + -
201A LEU* 2.7 31.9 + - + +
204A ALA* 3.8 17.9 + - - +
205A SER* 4.1 10.0 - - - +
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Residues in contact with GLY 60 (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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26A HIS* 3.1 15.1 - - - -
28A ASN* 2.9 19.3 - - - +
30A MET* 3.4 10.3 - - - +
57A ILE 2.9 5.5 + - - -
59A THR* 1.3 75.5 - - - +
61A VAL* 1.3 60.5 + - - +
63A ASN 3.3 4.4 - - - +
73A GLY* 3.0 38.7 + - - -
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Residues in contact with VAL 61 (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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21A PRO* 3.8 32.5 - - + -
22A ASP 5.5 3.4 - - - +
23A LEU* 4.2 6.3 - - + -
26A HIS* 2.8 26.3 + - + +
30A MET* 4.1 6.5 - - + -
57A ILE* 3.0 35.8 + - + +
58A GLN* 3.0 17.7 + - - +
60A GLY* 1.3 76.1 - - - +
62A ASP* 1.3 67.3 + - - +
64A PRO* 5.0 0.3 - - - +
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Residues in contact with ASP 62 (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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58A GLN* 2.8 42.4 + - - +
59A THR 3.8 3.8 - - - +
61A VAL* 1.3 82.2 - - - +
63A ASN* 1.3 63.1 + - - +
64A PRO* 3.4 9.8 - - - +
204A ALA* 3.7 25.6 - - + +
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Residues in contact with ASN 63 (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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26A HIS* 4.3 0.2 - - - -
28A ASN* 3.1 19.2 - - - +
59A THR* 2.9 39.3 + - - +
60A GLY* 3.3 7.5 - - - +
62A ASP* 1.3 83.7 - - - +
64A PRO* 1.3 64.0 - - - +
65A GLY* 3.2 5.1 + - - +
71A THR* 4.4 3.4 + - - +
73A GLY* 5.6 0.2 - - - -
200A PRO* 3.2 38.2 + - - +
201A LEU* 3.4 29.8 - - + +
204A ALA* 3.7 8.1 - - - +
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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