Contacts of the helix formed by residues 72 - 84 (chain A) in PDB entry 4QA7
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 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A HIS* 1.3 76.7 - - - +
73A ASP* 1.3 63.6 + - - +
74A ALA* 3.9 8.7 + - - +
75A TYR* 3.4 15.1 + - - +
76A LEU* 3.1 21.4 + - - +
146A LYS* 3.1 35.1 + - + +
147A ASP* 3.4 25.0 - - + +
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Residues in contact with ASP 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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64A MET* 4.8 13.3 - - - +
68A ALA* 4.3 18.6 - - - +
71A HIS 5.4 0.2 - - - +
72A THR* 1.3 71.0 - - - +
74A ALA* 1.3 60.5 + - - +
76A LEU* 4.5 5.2 - - - -
77A GLN* 2.8 54.3 + - - +
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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 THR* 4.1 7.6 - - - +
73A ASP* 1.3 80.0 - - - +
75A TYR* 1.3 59.8 + - - +
77A GLN* 4.2 7.3 - - - +
78A HIS* 3.2 22.9 + - - +
96A TYR* 3.7 22.3 + - + +
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Residues in contact with TYR 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 HIS* 3.8 30.7 - + + -
72A THR* 3.3 19.1 + - - +
73A ASP 3.2 0.4 - - - -
74A ALA* 1.3 77.2 - - - +
76A LEU* 1.3 65.1 + - + +
78A HIS* 3.2 4.2 + + + +
79A LEU* 2.9 51.4 + - + +
96A TYR* 3.5 48.2 - + + -
98A LEU* 5.0 1.8 - - + -
146A LYS 3.9 3.8 - - - +
147A ASP* 3.6 19.7 - - + -
148A GLU 4.0 3.1 - - - -
149A ALA* 3.5 23.8 + - + +
154A TYR* 2.5 35.3 + - - +
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Residues in contact with LEU 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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64A MET* 3.9 24.7 - - - -
67A MET* 3.8 32.3 - - + +
68A ALA* 3.8 36.1 - - + +
71A HIS* 3.8 20.0 - - + +
72A THR 3.1 19.3 + - - +
73A ASP* 3.9 5.4 - - - +
75A TYR* 1.3 82.9 - - + +
77A GLN* 1.3 61.6 + - - +
79A LEU* 3.2 11.8 + - + +
80A GLN* 3.1 23.8 + - - +
109A PHE* 3.7 10.8 - - + -
155A LEU* 4.3 9.6 - - + -
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Residues in contact with GLN 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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64A MET* 5.2 5.8 - - + -
73A ASP* 2.8 39.0 + - - +
74A ALA* 4.2 6.4 - - - +
76A LEU* 1.3 73.7 - - + +
78A HIS* 1.3 60.3 + - - +
80A GLN* 3.5 25.1 - - - +
81A LYS* 3.1 26.3 + - - +
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Residues in contact with HIS 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 3.2 20.7 + - - +
75A TYR* 3.2 6.0 + + - +
77A GLN* 1.3 74.3 - - - +
79A LEU* 1.3 66.3 + - - +
81A LYS* 3.3 7.9 - - - +
82A VAL* 3.2 28.0 + - + +
90A HIS* 3.5 36.1 + + - -
92A ASP 4.1 0.4 - - - -
93A SER* 3.1 42.2 + - - -
96A TYR* 3.6 34.0 - + + -
98A LEU* 3.9 16.0 - - + +
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Residues in contact with LEU 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 TYR* 2.9 47.1 + - + +
76A LEU* 3.2 18.8 + - + +
78A HIS* 1.3 79.1 - - + +
80A GLN* 1.3 57.7 - - - +
82A VAL* 3.3 5.4 - - + +
83A SER* 3.1 28.8 + - - -
98A LEU* 4.6 15.7 - - + -
108A ILE* 3.9 24.7 - - + +
109A PHE* 3.9 16.4 - - + +
112A ALA* 4.5 17.0 - - + -
154A TYR* 4.1 23.1 - - + +
155A LEU* 5.4 1.6 - - + -
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET* 3.4 31.3 - - - +
76A LEU 3.1 6.2 + - - +
77A GLN* 3.5 30.3 - - - +
79A LEU* 1.3 76.4 - - - +
81A LYS* 1.3 65.1 + - - +
83A SER* 3.7 2.5 - - - -
84A GLN* 3.3 40.0 + - + +
109A PHE* 3.5 36.1 - - + -
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Residues in contact with LYS 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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77A GLN 3.1 19.6 + - - +
78A HIS* 3.3 13.9 - - - +
79A LEU 3.1 0.2 - - - -
80A GLN* 1.3 81.2 - - - +
82A VAL* 1.3 69.0 + - + +
83A SER 3.1 0.4 + - - -
84A GLN* 3.7 8.7 + - - +
85A GLU* 3.9 21.1 - - - +
87A ASP* 6.0 1.3 - - - +
90A HIS* 4.6 22.4 - - + +
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Residues in contact with VAL 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 HIS* 3.5 32.8 - - + +
79A LEU* 3.3 18.2 - - + +
81A LYS* 1.3 81.1 - - + +
83A SER* 1.3 58.2 + - - +
84A GLN 3.5 0.7 - - - -
85A GLU 4.3 0.2 - - - -
86A GLY* 2.9 27.5 + - - -
87A ASP* 3.2 36.2 + - + +
90A HIS* 4.4 8.3 - - + -
93A SER* 4.0 8.1 - - - +
98A LEU* 3.9 22.0 - - + -
104A ALA* 4.2 9.0 - - + -
105A THR 3.7 2.6 - - - +
108A ILE* 4.9 2.7 - - + -
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU 3.1 17.9 + - - -
80A GLN* 3.9 4.0 - - - -
81A LYS 3.1 0.6 - - - -
82A VAL* 1.3 76.9 - - - +
84A GLN* 1.3 59.7 + - - +
85A GLU 3.0 10.4 + - - -
105A THR 3.9 8.3 - - - -
106A GLU* 3.5 5.9 - - - +
107A GLY* 2.9 28.9 + - - -
108A ILE* 3.0 22.8 + - - -
109A PHE* 3.0 27.9 + - - +
110A ASP* 4.3 2.4 + - - -
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Residues in contact with GLN 84 (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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80A GLN* 3.3 31.6 + - + +
81A LYS 3.7 5.8 + - - +
82A VAL 3.5 1.0 - - - -
83A SER* 1.3 76.2 - - - +
85A GLU* 1.3 62.5 + - + +
106A GLU* 4.6 7.1 - - - +
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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