Contacts of the helix formed by residues 75 - 86 (chain A) in PDB entry 1V8O
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 PRO 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ASP 4.4 1.8 - - - +
74A PRO* 1.3 84.1 - - + +
76A LEU* 1.3 64.8 + - - +
77A ASP* 2.7 14.6 + - + -
78A GLU* 2.9 30.9 + - + +
79A VAL* 3.3 10.5 + - - +
97A TYR* 3.8 21.8 - - + +
62B LYS* 4.0 18.8 - - - +
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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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74A PRO 3.2 6.2 + - - -
75A PRO* 1.3 70.1 - - - +
77A ASP* 1.3 61.4 + - - +
79A VAL* 4.7 0.7 - - - -
80A MSE 3.2 27.5 + - + +
90A PHE* 3.8 24.0 - - + -
36B ILE* 4.2 14.2 - - + +
40B GLY* 4.0 12.3 - - - -
43B LEU* 4.8 1.6 - - + -
58B SER* 3.5 37.0 - - - +
61B LEU* 3.3 34.1 - - + -
62B LYS* 4.8 12.0 - - + +
65B MSE 3.9 23.1 - - - -
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO* 3.9 4.9 - - + +
76A LEU* 1.3 81.7 - - - +
78A GLU* 1.3 72.7 + - + +
80A MSE 3.6 13.0 - - - +
81A ARG* 3.7 6.1 + - - +
54B TRP* 5.0 2.1 - - - -
58B SER* 4.0 16.1 + - - -
59B ARG* 3.5 29.2 + - - +
62B LYS* 3.5 43.2 + - + +
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Residues in contact with GLU 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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75A PRO* 2.9 28.6 + - + +
77A ASP* 1.3 81.0 - - + +
79A VAL* 1.3 64.1 + - - +
81A ARG* 3.2 13.7 + - - +
82A VAL* 3.1 22.9 + - - +
97A TYR* 3.2 48.3 + - + +
62B LYS* 6.1 0.4 - - - -
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO* 3.4 36.3 - - + -
75A PRO 3.3 7.3 + - - +
76A LEU 4.1 1.1 - - - +
78A GLU* 1.3 71.9 - - - +
80A MSE 1.3 56.3 + - - +
82A VAL* 3.0 7.5 + - - +
83A ALA* 2.8 32.9 + - - +
90A PHE* 3.4 50.3 - - + +
93A ALA* 3.7 4.5 - - + -
94A SER* 3.6 23.1 - - - +
97A TYR* 4.3 10.1 - - + -
37B TYR* 6.1 0.2 - - + -
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Residues in contact with MSE 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 LEU* 3.2 18.8 + - + +
77A ASP 3.6 6.3 - - - +
79A VAL* 1.3 77.2 - - - +
81A ARG* 1.3 59.4 + - - +
83A ALA* 3.6 3.0 - - - +
84A VAL* 2.9 59.0 + - + +
90A PHE* 3.9 13.4 - - + -
40B GLY 4.3 1.3 - - - +
43B LEU* 4.2 7.0 - - + -
44B TRP* 3.6 37.5 - - + -
47B ALA* 4.0 7.2 - - + -
54B TRP* 3.3 42.4 - - + +
58B SER* 3.5 25.6 - - - -
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Residues in contact with ARG 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 ASP 3.7 4.8 + - - +
78A GLU* 3.2 18.3 + - - +
79A VAL 3.1 0.4 - - - -
80A MSE 1.3 77.9 - - - +
82A VAL* 1.3 75.6 + - - +
84A VAL* 4.2 0.2 - - - +
85A GLU* 3.0 66.4 + - - +
86A ARG* 6.2 0.2 - - - +
54B TRP* 3.8 25.0 - - + -
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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 GLU 3.1 10.6 + - - +
79A VAL 3.0 7.8 + - - +
81A ARG* 1.3 85.7 - - - +
83A ALA* 1.3 58.2 + - - +
85A GLU* 4.8 2.9 - - - -
86A ARG* 2.8 69.7 + - - +
88A LEU* 4.1 2.4 - - + +
93A ALA* 3.9 23.3 - - + +
96A ALA* 4.1 10.5 - - + -
97A TYR* 3.9 26.7 - - + -
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Residues in contact with ALA 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 VAL 2.8 16.4 + - - +
80A MSE 3.6 7.0 - - - +
82A VAL* 1.3 78.0 - - - +
84A VAL* 1.3 62.4 + - - +
87A GLY* 3.0 5.7 + - - -
88A LEU* 2.8 46.4 + - - +
89A THR 3.8 4.0 - - - +
90A PHE* 4.3 4.9 - - + -
93A ALA* 3.5 17.1 - - + +
44B TRP* 3.9 17.2 + - + -
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Residues in contact with VAL 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 MSE 2.9 45.4 + - + +
81A ARG 4.2 1.6 - - - +
83A ALA* 1.3 77.5 - - - +
85A GLU* 1.3 68.9 + - + +
87A GLY* 3.4 6.4 + - - -
44B TRP* 4.6 8.3 - - + +
47B ALA* 4.6 7.6 - - + -
54B TRP* 4.0 34.3 - - + +
112D GLU* 4.8 5.4 - - - +
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Residues in contact with GLU 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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81A ARG* 3.0 67.4 + - + +
82A VAL* 4.2 2.3 - - - +
84A VAL* 1.3 86.4 - - + +
86A ARG* 1.3 64.7 + - + +
87A GLY 3.2 2.4 + - - -
54B TRP* 5.8 4.1 - - + -
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Residues in contact with ARG 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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82A VAL* 2.8 53.3 + - - +
85A GLU* 1.3 75.7 + - + +
87A GLY* 1.3 65.3 + - - +
88A LEU* 3.3 13.5 + - + +
96A ALA* 4.3 7.3 + - - +
97A TYR* 6.3 0.2 - - - +
100A GLU* 2.6 45.6 + - - -
116A LYS* 2.9 54.5 + - + +
118A LYS* 4.6 8.6 - - - +
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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