Contacts of the helix formed by residues 72 - 86 (chain A) in PDB entry 3MB8
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 GLY 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLY 3.4 1.2 + - - +
71A ILE* 1.3 77.0 - - - +
73A CYS* 1.3 60.4 + - - -
74A PRO* 3.4 4.6 - - - -
75A GLY* 3.7 1.6 + - - -
76A THR* 2.8 26.2 + - - -
187A MET* 3.6 11.2 - - - -
188A GLU* 2.7 19.5 + - - -
74B PRO* 3.6 22.4 - - - -
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Residues in contact with CYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY* 1.3 72.1 - - - -
74A PRO* 1.4 61.1 - - + +
76A THR* 3.3 7.5 + - - +
77A SER* 2.7 36.0 + - - -
120A THR* 3.5 32.3 - - - -
122A LEU* 3.7 24.4 - - + +
163A ASP* 4.5 2.7 - - - +
187A MET 3.5 12.9 + - - -
188A GLU* 3.8 10.3 - - - -
191A GLY* 3.6 25.1 - - - -
74B PRO* 4.4 1.4 - - - +
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Residues in contact with PRO 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY 3.5 4.0 - - - -
73A CYS* 1.4 93.7 - - + +
75A GLY* 1.3 61.5 - - - +
77A SER* 2.7 21.6 + - - +
78A ILE* 3.5 4.0 + - - +
163A ASP* 4.9 1.3 - - - +
71B ILE 5.3 0.2 - - - +
72B GLY* 3.7 19.3 - - - -
74B PRO* 3.7 26.0 - - + -
162B GLN 5.2 0.4 - - - +
163B ASP* 3.4 50.0 - - + +
187B MET* 3.7 21.1 - - + +
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Residues in contact with GLY 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU* 4.8 2.5 - - - -
52A TYR* 2.7 31.3 + - - -
69A HIS 3.6 10.8 - - - -
70A GLY* 6.1 0.2 - - - -
71A ILE 5.5 1.1 - - - -
72A GLY 3.7 4.1 + - - -
73A CYS 3.5 0.2 - - - -
74A PRO* 1.3 78.4 - - - +
76A THR* 1.3 62.8 + - - +
78A ILE* 3.4 7.5 + - - -
79A ALA 3.5 5.0 + - - -
71B ILE* 3.5 28.5 + - - -
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 4.4 1.3 - - + -
69A HIS* 2.9 42.9 + - + +
70A GLY 3.7 0.7 + - - -
72A GLY 2.8 22.6 + - - -
73A CYS* 3.5 9.0 - - - -
74A PRO 3.2 0.2 - - - -
75A GLY* 1.3 76.0 - - - +
77A SER* 1.3 65.3 + - - +
79A ALA* 3.1 3.5 + - - +
80A ILE* 3.0 32.7 + - + +
188A GLU* 3.6 5.6 - - + +
191A GLY 5.7 1.1 - - - -
192A VAL* 3.7 31.4 - - + +
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A CYS 2.7 18.8 + - - -
74A PRO* 2.7 18.3 + - - -
76A THR* 1.3 72.0 - - - +
78A ILE* 1.3 59.8 + - - +
80A ILE* 3.5 0.5 + - - +
81A GLU* 2.9 40.7 + - - +
122A LEU* 4.0 19.3 - - - -
195A LEU* 3.8 23.3 - - - +
164B TYR* 3.9 19.5 - - - +
165B PHE 4.4 1.2 + - - -
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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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12A HIS* 3.4 47.3 - - + +
13A ILE* 5.3 0.2 - - + -
52A TYR* 3.6 6.5 - - + +
74A PRO 3.5 6.3 + - - +
75A GLY 3.4 8.7 + - - +
76A THR 3.3 0.4 - - - -
77A SER* 1.3 83.9 + - - +
79A ALA* 1.3 62.8 + - - +
81A GLU* 3.9 0.3 - - - +
82A GLU* 3.0 31.9 + - - +
71B ILE* 3.9 38.4 - - + -
165B PHE* 3.6 34.1 - - + -
166B TYR* 4.5 8.3 - - + -
187B MET* 4.1 5.2 - - + -
280B IMH 4.4 0.7 - - - -
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Residues in contact with ALA 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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13A ILE* 4.0 15.7 - - + +
26A ILE* 5.9 1.1 - - + -
52A TYR* 3.7 25.8 - - + -
67A ILE* 5.2 3.4 - - + -
68A SER 4.8 2.0 - - - +
69A HIS* 4.3 14.8 - - + -
75A GLY 3.5 2.6 + - - +
76A THR 3.1 9.7 + - - +
78A ILE* 1.3 78.0 - - - +
80A ILE* 1.3 59.9 + - + +
82A GLU* 3.8 0.9 - - - +
83A LEU* 2.8 45.6 + - + +
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Residues in contact with ILE 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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26A ILE* 4.3 9.2 - - + -
76A THR* 3.0 36.5 + - + +
79A ALA* 1.3 78.1 - - + +
81A GLU* 1.3 58.3 + - - +
83A LEU* 3.7 7.9 - - + +
84A ALA* 2.8 30.4 + - + +
91A ILE* 4.1 21.7 - - + +
191A GLY 4.9 0.4 - - - +
192A VAL* 4.0 28.5 - - + +
195A LEU* 3.8 32.5 - - + +
196A CYS* 4.2 17.7 - - - +
199A ARG* 5.2 3.1 - - + -
201A ILE* 4.5 7.2 - - + -
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Residues in contact with GLU 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 SER* 2.9 29.1 + - - +
78A ILE 3.9 0.7 - - - +
80A ILE* 1.3 73.1 - - - +
82A GLU* 1.3 59.0 + - - +
84A ALA* 3.4 4.8 + - - +
85A TYR* 3.0 27.2 + - - +
195A LEU* 3.9 14.3 - - + +
199A ARG* 2.8 49.2 + - - -
166B TYR* 3.6 37.3 - - + +
168B ASN* 3.5 19.5 + - - +
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Residues in contact with GLU 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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10A GLN* 3.5 23.5 - - + +
11A PRO* 3.5 7.4 - - - +
12A HIS* 2.8 34.9 + - - -
13A ILE* 3.0 42.5 + - + +
78A ILE* 3.0 20.9 + - - +
79A ALA 4.0 0.7 - - - +
81A GLU* 1.3 73.5 - - - +
83A LEU* 1.3 65.5 + - - +
85A TYR* 3.4 4.0 + - - +
86A LEU* 3.1 28.2 + - - +
166B TYR* 2.5 35.6 + - + +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 3.9 18.4 - - + +
15A LEU* 4.8 0.7 - - + -
20A VAL* 4.2 23.9 - - + +
24A VAL* 4.0 18.6 - - + -
26A ILE* 4.1 10.3 - - + -
65A THR* 4.7 4.7 - - + -
67A ILE* 3.9 35.0 - - + -
79A ALA* 2.8 36.5 + - + +
80A ILE* 3.7 4.9 - - + +
82A GLU* 1.3 72.8 - - - +
84A ALA* 1.3 58.7 + - - +
86A LEU* 3.2 12.2 + - - +
87A GLY 3.2 0.9 + - - -
88A ALA* 3.0 31.5 + - + +
91A ILE* 4.4 11.2 - - + -
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Residues in contact with ALA 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 ILE 2.8 22.1 + - - +
81A GLU* 3.6 7.4 - - - +
83A LEU* 1.3 69.6 - - - +
85A TYR* 1.3 65.2 + - - +
87A GLY* 3.1 13.5 + - - -
88A ALA* 4.1 6.9 + - - +
199A ARG* 4.8 15.0 - - + +
201A ILE* 3.6 28.7 - - + +
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Residues in contact with TYR 85 (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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6A GLY* 3.9 22.2 - - - -
7A MET 5.1 5.9 + - - -
10A GLN* 3.3 38.4 - - - +
81A GLU 3.0 16.7 + - - +
82A GLU 3.6 5.4 - - - +
83A LEU 3.4 0.4 - - - -
84A ALA* 1.3 75.6 - - - +
86A LEU* 1.3 72.2 + - + +
87A GLY 3.5 0.7 + - - -
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Residues in contact with LEU 86 (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 GLU 5.6 2.2 - - - +
10A GLN* 3.7 17.7 - - + +
13A ILE* 4.2 5.2 - - + -
15A LEU* 3.4 35.0 - - + +
16A ARG* 4.0 2.0 - - - +
17A LYS* 3.7 42.1 - - + +
20A VAL* 3.8 37.8 - - + +
82A GLU 3.1 15.5 + - - +
83A LEU 3.6 5.2 - - - +
84A ALA 3.1 1.0 - - - -
85A TYR* 1.3 99.0 - - + +
87A GLY* 1.3 55.5 + - - +
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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