Contacts of the helix formed by residues 82 - 92 (chain A) in PDB entry 1VBF
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 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.9 7.2 - - - -
79A THR* 3.4 7.6 + - - -
80A GLY 3.2 4.8 + - - -
81A ILE* 1.3 79.5 - - - +
83A TYR* 1.3 63.9 + - - +
84A TYR 3.5 2.5 - - - -
85A THR* 3.0 20.7 + - - -
86A ALA* 2.9 22.0 + - - +
108A ALA* 4.5 0.2 - - - -
112A LEU* 3.9 19.0 - - - +
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Residues in contact with TYR 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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20A PHE* 3.1 36.0 - - - -
23A VAL* 4.1 16.8 + - + -
25A ARG* 3.4 50.1 - - + +
28A PHE* 3.6 24.2 - + + -
38A TYR* 4.5 2.3 + - - -
56A LEU* 3.7 20.4 - - + +
81A ILE* 3.4 26.7 + - + +
82A GLY* 1.3 73.9 - - - +
84A TYR* 1.3 86.9 + + + +
86A ALA* 3.0 14.7 + - - +
87A LEU* 3.1 34.6 + - + +
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Residues in contact with TYR 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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25A ARG* 4.0 4.7 + - - -
53A THR* 3.8 20.2 - - - -
54A THR* 2.8 34.2 + - - -
55A ALA 3.7 0.9 + - - -
56A LEU* 3.6 17.2 - - - +
59A GLY* 3.2 30.5 - - - -
60A ILE* 4.0 5.6 - - + -
63A LEU* 3.8 24.2 - - + +
76A GLU* 4.0 7.0 - - - +
79A THR 5.8 4.2 + - - +
81A ILE* 6.0 1.3 - - + -
82A GLY 3.5 0.4 - - - -
83A TYR* 1.3 103.3 - + + +
85A THR* 1.3 59.1 + - - +
87A LEU* 3.5 4.2 + - - +
88A ILE* 2.8 31.9 + - - +
141A TRP* 3.7 32.5 - + + -
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Residues in contact with THR 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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76A GLU* 2.6 33.1 + - - +
79A THR* 3.9 8.3 + - - +
82A GLY* 3.0 22.2 + - - -
84A TYR* 1.3 78.5 - - - +
86A ALA* 1.3 57.9 + - - +
88A ILE* 3.1 7.4 + - - +
89A ALA* 2.9 27.7 + - - +
95A VAL* 4.0 17.4 - - + +
97A SER* 4.0 10.5 - - - -
112A LEU* 4.5 8.1 - - + -
118A ILE* 3.8 23.8 - - + -
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Residues in contact with ALA 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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23A VAL* 4.1 7.4 - - + -
28A PHE* 3.5 30.5 - - + -
82A GLY 2.9 6.4 + - - +
83A TYR 3.2 10.1 - - - +
85A THR* 1.3 74.1 - - - +
87A LEU* 1.3 66.3 + - - +
89A ALA* 3.1 15.0 + - - +
90A GLU* 3.1 19.2 + - - +
112A LEU* 4.5 1.5 - - + +
115A TYR* 3.7 25.4 - - + +
118A ILE* 4.6 3.4 - - - -
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Residues in contact with LEU 87 (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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16A LEU* 4.6 9.6 - - + -
19A ALA* 3.6 39.6 - - + +
20A PHE* 3.6 9.4 - - + +
23A VAL* 3.7 17.3 - - + -
60A ILE* 4.2 10.3 - - + -
63A LEU* 4.0 22.4 - - + -
83A TYR* 3.1 46.7 + - + +
84A TYR* 3.8 7.6 - - - +
85A THR 3.3 0.2 - - - -
86A ALA* 1.3 77.7 - - - +
88A ILE* 1.3 59.6 + - - +
90A GLU* 3.4 6.4 + - - +
91A ILE* 3.0 27.7 - - - +
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Residues in contact with ILE 88 (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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63A LEU* 3.6 31.6 - - + -
66A LEU* 5.2 0.2 - - + -
68A LEU* 4.2 8.5 - - + -
74A VAL* 4.2 23.1 - - + -
76A GLU* 4.4 18.6 - - + +
84A TYR* 2.8 24.9 - - + +
85A THR* 3.1 8.0 + - - +
86A ALA 3.1 0.8 - - - -
87A LEU* 1.3 79.8 - - - +
89A ALA* 1.3 52.9 + - - +
91A ILE* 3.0 6.6 + - - -
92A VAL* 2.8 47.7 + - + +
95A VAL* 3.5 23.3 - - + -
139A VAL* 4.8 7.6 - - + -
141A TRP* 5.6 0.4 - - + -
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Residues in contact with ALA 89 (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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85A THR 2.9 7.7 + - - +
86A ALA 3.1 4.9 + - - +
88A ILE* 1.3 76.4 - - - +
90A GLU* 1.3 62.1 + - - +
91A ILE 3.2 0.2 - - - -
92A VAL 3.6 3.4 - - - +
95A VAL* 4.2 5.3 - - + +
115A TYR* 4.2 9.6 - - + -
117A ASN* 3.1 43.5 + - - +
118A ILE* 3.5 33.9 - - + -
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ALA* 3.8 14.1 - - + -
22A LYS* 3.7 25.1 - - - +
23A VAL* 3.8 24.7 - - + -
86A ALA 3.1 16.4 + - - +
87A LEU 3.5 10.1 - - - +
88A ILE 3.1 0.2 - - - -
89A ALA* 1.3 78.2 - - - +
91A ILE* 1.3 59.1 + - - +
114A TYR* 5.9 1.0 - - - -
115A TYR* 3.7 20.9 - - + -
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Residues in contact with ILE 91 (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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15A GLU* 3.4 37.2 - - + +
16A LEU* 3.6 33.4 - - + +
19A ALA* 4.1 4.7 - - + -
68A LEU* 3.9 48.9 - - + +
69A HIS 4.3 1.8 - - - +
70A LYS* 3.3 27.4 - - - +
87A LEU* 3.0 20.9 - - + +
88A ILE 3.0 3.9 + - - +
90A GLU* 1.3 83.4 - - - +
92A VAL* 1.3 63.1 - - + +
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Residues in contact with VAL 92 (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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68A LEU* 3.9 18.6 - - + -
69A HIS 3.3 17.3 - - - +
70A LYS* 5.1 0.2 - - - -
71A GLY 4.3 0.9 - - - -
72A GLN* 2.6 44.4 - - + +
74A VAL* 3.8 21.8 - - + -
88A ILE* 2.8 24.7 + - + +
89A ALA 3.6 3.1 - - - +
91A ILE* 1.3 80.3 - - + +
93A ASP* 1.3 70.3 + - - +
94A LYS 3.5 14.4 - - - +
95A VAL* 4.4 2.0 - - + -
117A ASN* 2.9 14.8 + - - -
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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