Contacts of the helix formed by residues 71 - 79 (chain A) in PDB entry 1RDC
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASP* 6.3 1.1 - - - -
48A GLU* 2.7 50.5 + - - +
69A THR* 3.3 19.9 + - - +
70A ASN* 1.3 73.3 - - - +
72A GLN* 1.3 65.3 + - - +
73A TYR* 3.1 0.3 + - - +
74A VAL* 3.2 24.0 + - - +
75A ARG* 3.0 24.2 + - - +
120A TRP* 5.7 0.2 - - - -
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Residues in contact with GLN 72 (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* 4.2 3.0 + - - +
70A ASN 3.0 9.5 + - - +
71A SER* 1.3 68.7 - - - +
73A TYR* 1.3 58.4 + - + +
75A ARG* 3.1 16.0 - - - +
76A GLN* 3.0 49.7 + - + +
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Residues in contact with TYR 73 (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 ASN* 3.2 51.8 - - + +
48A GLU* 3.6 14.8 + - - +
49A LEU* 4.1 9.4 - - + -
71A SER* 3.1 0.9 - - - -
72A GLN* 1.3 75.8 - - - +
74A VAL* 1.3 59.9 + - + +
76A GLN* 3.1 9.5 + - - +
77A GLY 2.9 27.4 + - - -
81A TRP* 3.8 30.5 - + - -
99A LYS* 3.7 14.9 + - - -
100A ASN* 2.8 29.2 + - - +
104A TRP* 2.9 40.2 + + - -
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Residues in contact with VAL 74 (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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9A THR* 6.1 0.7 - - - +
48A GLU* 4.0 22.9 - - + +
49A LEU* 4.1 21.8 - - + +
52A ALA* 5.3 10.3 - - + -
69A THR* 4.4 5.8 - - + +
71A SER* 3.2 27.8 + - - +
73A TYR* 1.3 75.6 - - + +
75A ARG* 1.3 55.6 + - - +
78A ILE* 2.9 48.1 + - + +
104A TRP* 4.1 8.1 - - - -
107A LEU* 5.4 2.7 - - + -
118A TRP* 4.2 14.6 - - + -
120A TRP* 3.7 14.1 - - + -
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Residues in contact with ARG 75 (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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71A SER 3.0 12.6 + - - +
72A GLN* 3.1 19.1 - - - +
74A VAL* 1.3 76.7 - - - +
76A GLN* 1.3 53.5 + - - +
78A ILE* 3.7 0.5 - - - +
79A THR* 2.4 56.0 + - - +
120A TRP* 3.4 52.8 - - + +
122A LYS* 3.0 43.6 - - - +
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Residues in contact with GLN 76 (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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72A GLN* 3.0 38.3 + - + +
73A TYR* 3.7 5.4 - - - +
75A ARG* 1.3 77.7 - - + +
77A GLY* 1.3 59.5 + - - +
78A ILE 3.2 0.9 - - - -
79A THR* 3.6 5.4 - - - +
80A GLN* 2.9 52.6 + - - +
81A TRP* 3.0 40.8 + - + +
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Residues in contact with GLY 77 (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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73A TYR 2.9 12.1 + - - -
76A GLN* 1.3 69.5 - - - +
78A ILE* 1.3 57.2 + - - +
81A TRP* 2.9 32.4 + - - -
82A ILE* 2.6 36.3 + - - +
85A TRP* 4.7 0.2 - - - -
104A TRP* 3.5 20.2 - - - -
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Residues in contact with ILE 78 (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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74A VAL* 2.9 34.2 + - + +
77A GLY* 1.3 76.7 - - - +
79A THR* 1.3 56.5 + - + +
82A ILE* 3.8 21.8 - - + +
83A HIS* 3.5 14.9 + - - -
104A TRP* 4.7 5.4 - - + -
107A LEU* 4.6 7.6 - - + -
111A LEU* 3.9 25.1 - - + -
118A TRP* 3.4 51.6 - - + +
120A TRP* 3.9 11.2 - - + -
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Residues in contact with THR 79 (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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75A ARG* 2.4 52.6 + - + +
76A GLN* 3.6 5.4 - - - +
78A ILE* 1.3 74.4 - - + +
80A GLN* 1.3 71.8 + - - +
83A HIS* 3.8 10.9 + - - -
120A TRP* 3.9 28.9 - - + +
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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