Contacts of the helix formed by residues 73 - 84 (chain G) in PDB entry 4U7B
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 GLU 73 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G LYS* 5.3 7.2 - - + -
72G TYR* 1.3 93.2 - - - +
74G ASP* 1.3 67.1 + - - +
75G ALA* 3.4 13.1 - - + +
76G GLU* 3.1 36.0 + - + +
77G LEU* 3.6 2.3 + - - +
106G ARG* 3.9 2.0 - - - +
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Residues in contact with ASP 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G LYS* 4.1 15.1 + - - +
73G GLU* 1.3 74.2 - - - +
75G ALA* 1.3 57.7 + - - +
76G GLU 3.4 0.2 + - - -
77G LEU* 3.5 3.2 + - - +
78G GLN* 3.1 21.4 + - - -
106G ARG* 2.9 28.6 + - - +
109G GLU* 5.4 4.2 - - - +
110G MET* 3.3 42.5 + - + +
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Residues in contact with ALA 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G GLU* 3.4 8.6 - - + +
74G ASP* 1.3 76.0 - - - +
76G GLU* 1.3 64.1 + - - +
78G GLN* 3.8 10.8 - - + +
79G ALA* 3.2 22.2 + - - +
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Residues in contact with GLU 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G ARG 4.5 3.5 - - - +
72G TYR* 3.4 22.9 - - + +
73G GLU* 3.1 48.3 + - + +
74G ASP 3.2 0.2 - - - -
75G ALA* 1.3 80.1 - - - +
77G LEU* 1.3 61.1 + - - +
79G ALA* 3.5 8.5 - - - +
80G LEU* 3.3 22.8 - - + +
96G LEU* 4.8 14.7 - - + +
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Residues in contact with LEU 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G TYR* 4.1 18.2 - - + -
73G GLU 3.6 7.0 + - - +
74G ASP 3.5 9.1 + - - +
75G ALA 3.3 0.2 - - - -
76G GLU* 1.3 77.3 - - - +
78G GLN* 1.3 56.7 + - - +
80G LEU* 2.7 35.6 + - + +
81G LEU* 3.2 34.1 + - + -
92G LEU* 4.7 13.2 - - + -
96G LEU* 3.9 21.9 - - + +
103G VAL* 4.3 13.9 - - + -
106G ARG* 4.3 16.2 - - + -
107G LEU* 4.2 18.8 - - + -
110G MET* 4.5 9.9 - - + -
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Residues in contact with GLN 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G ASP 3.1 11.9 + - - +
75G ALA* 4.0 10.8 - - + +
76G GLU 3.5 0.2 - - - -
77G LEU* 1.3 78.1 - - - +
79G ALA* 1.3 61.2 + - - +
81G LEU* 3.3 13.0 + - - +
82G ASP* 2.8 50.8 + - - +
110G MET* 3.6 20.8 - - + +
112G LYS* 2.6 33.3 + - - +
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Residues in contact with ALA 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G ALA 3.2 13.4 + - - +
76G GLU* 3.5 13.2 - - - +
77G LEU 3.1 0.2 + - - -
78G GLN* 1.3 76.3 - - - +
80G LEU* 1.3 64.8 + - + +
82G ASP* 3.3 11.7 + - - +
83G GLU* 3.1 27.1 + - + +
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Residues in contact with LEU 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76G GLU* 3.3 16.6 - - + +
77G LEU* 2.7 17.7 + - - +
79G ALA* 1.3 75.7 - - + +
81G LEU* 1.3 55.1 + - - +
83G GLU* 3.4 9.7 - - + +
84G ASP 3.1 21.0 + - - -
87G GLN* 3.2 15.5 + - - +
92G LEU* 3.9 34.1 - - + +
95G GLN* 3.7 28.3 - - + +
96G LEU* 3.4 33.0 - - + -
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Residues in contact with LEU 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G LEU* 3.2 25.8 + - + +
78G GLN* 3.8 15.7 - - - +
79G ALA 3.3 0.4 - - - -
80G LEU* 1.3 73.5 - - - +
82G ASP* 1.3 65.8 + - - +
83G GLU 3.2 0.4 - - - -
84G ASP 3.9 5.2 - - - +
85G ASP* 3.2 47.8 + - - +
87G GLN* 5.7 0.7 - - + +
92G LEU* 4.0 33.9 - - + -
107G LEU* 4.1 13.0 - - + -
110G MET* 5.2 0.9 - - + -
112G LYS* 3.9 29.4 - - + -
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Residues in contact with ASP 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G GLN* 2.8 40.2 + - - +
79G ALA* 3.3 11.6 + - - +
81G LEU* 1.3 76.2 - - - +
83G GLU* 1.3 65.2 + - - +
85G ASP* 4.6 4.3 - - - +
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Residues in contact with GLU 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G ALA* 3.1 18.5 + - + +
80G LEU* 3.4 12.8 - - + +
82G ASP* 1.3 81.1 - - + +
84G ASP* 1.3 63.8 + - + +
85G ASP* 4.9 1.3 - - - +
87G GLN* 5.2 0.9 - - - +
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Residues in contact with ASP 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G LEU 3.1 5.8 + - - +
81G LEU* 3.5 6.5 - - - +
83G GLU* 1.3 84.3 - - + +
85G ASP* 1.3 69.6 + - - +
86G ALA* 3.0 17.2 + - - +
87G GLN* 3.3 44.1 + - - +
91G GLN* 5.1 2.1 - - - +
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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