Contacts of the helix formed by residues 72 - 83 (chain A) in PDB entry 4DUB
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ASN* 3.5 15.0 + - - +
71A LEU* 1.3 75.9 - - - +
73A GLN* 1.3 65.8 + - - +
74A ALA* 3.4 11.8 + - - +
75A LEU* 3.2 27.2 + - - +
76A LYS* 2.9 20.9 + - - +
332A SER* 4.6 13.7 - - - -
354A MET* 5.4 8.7 - - - -
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Residues in contact with GLN 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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72A SER* 1.3 73.4 - - - +
74A ALA* 1.3 62.1 + - - +
76A LYS* 3.3 22.3 + - - +
77A PHE* 3.0 63.5 + - + -
188A LEU* 3.7 13.5 - - + -
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Residues in contact with ALA 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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72A SER* 3.2 10.6 + - - +
73A GLN* 1.3 76.7 - - - +
75A LEU* 1.3 61.1 + - + +
77A PHE* 3.3 6.0 + - - +
78A VAL* 2.8 33.7 + - - +
185A MET* 3.9 23.0 - - + +
188A LEU* 3.8 22.6 - - + +
437A LEU* 4.9 8.1 - - + -
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Residues in contact with LEU 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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69A LYS* 3.6 33.4 - - - +
70A ASN 4.4 2.9 - - - +
71A LEU* 3.9 21.5 - - + -
72A SER* 3.2 21.5 + - - +
74A ALA* 1.3 82.6 - - + +
76A LYS* 1.3 56.6 - - - +
78A VAL* 3.4 4.2 + - + +
79A ARG* 2.9 28.6 + - - +
87A PHE* 3.4 45.5 - - + +
88A THR* 3.6 10.0 - - + +
437A LEU* 5.0 8.7 - - + -
500A HEM 4.1 7.9 - - - +
501A LDP 6.3 0.4 - - + -
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Residues in contact with LYS 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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70A ASN* 5.7 0.4 + - - -
71A LEU* 3.8 28.1 + - + +
72A SER 2.9 17.4 + - - +
73A GLN* 3.3 28.9 + - - +
75A LEU* 1.3 75.8 - - - +
77A PHE* 1.3 62.9 + - + +
79A ARG* 3.3 23.0 + - - +
80A ASP* 3.6 10.9 + - - +
90A TRP* 4.2 23.4 - - - +
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Residues in contact with PHE 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 GLN* 3.0 49.0 + - + -
74A ALA 3.7 5.4 - - - +
76A LYS* 1.3 72.2 - - + +
78A VAL* 1.3 67.1 + - - +
80A ASP* 3.3 29.8 + - - +
81A PHE* 4.4 0.3 - - - -
184A ALA* 3.6 39.2 - - + +
187A LYS* 3.6 49.8 - - + +
188A LEU* 4.0 9.9 - - + -
205A PHE* 4.4 6.2 - - - -
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Residues in contact with VAL 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 ALA 2.8 25.7 + - - +
75A LEU* 3.8 7.4 - - + +
77A PHE* 1.3 73.6 - - - +
79A ARG* 1.3 57.6 + - - +
81A PHE* 3.0 30.0 + - + -
82A ALA* 2.9 32.2 + - + -
87A PHE* 4.9 9.4 - - + -
88A THR* 3.8 17.0 - - + -
181A LEU* 4.5 15.3 - - + -
184A ALA* 4.1 5.4 - - + -
185A MET* 3.6 22.2 - - + -
263A ALA* 5.6 2.5 - - + -
437A LEU* 4.6 10.5 - - + -
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Residues in contact with ARG 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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71A LEU* 4.3 12.3 - - + +
75A LEU 2.9 13.9 + - - +
76A LYS* 3.4 15.3 - - - +
77A PHE 3.2 0.8 - - - -
78A VAL* 1.3 76.7 - - - +
80A ASP* 1.3 62.3 + - - +
83A GLY* 2.7 47.4 + - - +
84A ASP* 4.2 9.7 - - - +
88A THR* 2.8 42.7 + - - +
89A SER* 3.7 4.8 + - - +
90A TRP* 4.3 4.3 - - - +
93A GLU* 2.8 42.6 + - - -
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Residues in contact with ASP 80 (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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76A LYS 3.6 9.2 + - - +
77A PHE* 3.3 27.9 + - - +
78A VAL 3.1 0.6 - - - -
79A ARG* 1.3 79.0 - - - +
81A PHE* 1.4 57.0 + - - +
187A LYS* 4.4 10.2 + - - -
205A PHE* 4.0 18.7 - - + -
209A ILE* 3.6 18.1 - - + +
256A TYR* 5.5 2.9 + - - -
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Residues in contact with PHE 81 (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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78A VAL* 3.0 34.9 + - + -
80A ASP* 1.4 74.4 - - - +
82A ALA* 1.3 64.0 + - + +
83A GLY 3.4 2.0 - - - -
177A MET* 4.9 1.3 - - + -
180A ALA* 3.6 31.2 - - + -
181A LEU* 3.8 32.8 - - + -
184A ALA* 4.3 5.2 - - + -
205A PHE* 4.1 13.0 - + - -
209A ILE* 3.8 23.3 - - + -
212A MET* 3.8 24.5 - - + -
213A ASN* 4.8 1.9 - - - +
256A TYR* 3.5 18.2 - - - -
259A ILE* 3.6 24.3 - - + +
263A ALA* 3.9 23.6 - - + -
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Residues in contact with ALA 82 (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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78A VAL* 2.9 29.2 + - + +
79A ARG 3.8 0.2 - - - -
81A PHE* 1.3 82.5 - - + +
83A GLY* 1.3 66.0 + - - +
85A GLY 3.2 12.8 + - - -
87A PHE* 6.0 0.4 - - + -
88A THR* 3.9 11.9 - - + +
256A TYR* 3.3 15.9 - - - +
259A ILE* 4.3 10.1 - - + -
260A THR* 3.7 24.1 + - + +
263A ALA* 5.7 1.6 - - + -
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Residues in contact with GLY 83 (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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79A ARG* 2.7 41.6 + - - +
81A PHE 3.4 2.8 - - - -
82A ALA* 1.3 71.1 - - - +
84A ASP* 1.3 56.6 + - - -
88A THR* 2.7 27.0 + - - +
256A TYR* 3.5 21.5 - - - -
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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