Contacts of the helix formed by residues 84 - 94 (chain B) in PDB entry 6VSU
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 PHE 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B GLN* 4.9 2.2 - - + -
81B GLY* 2.9 24.4 + - - +
83B ALA* 1.3 86.1 - - + +
85B ALA* 1.3 64.3 + - - +
86B PRO* 3.6 3.1 - - - -
87B PRO* 3.5 13.6 - - - +
88B ARG* 3.7 19.1 + - + +
316B PRO* 3.9 12.1 - - + -
317B GLN* 3.5 37.7 - - + -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PRO 3.1 5.0 + - - +
84B PHE* 1.3 78.4 - - - +
86B PRO* 1.4 70.3 - - + +
88B ARG* 2.8 15.4 + - - +
89B ILE* 3.0 14.2 + - + +
158B GLY 3.3 20.0 - - - +
314B PHE* 3.3 42.8 - - + +
316B PRO* 3.7 10.0 - - - +
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Residues in contact with PRO 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLY* 4.1 0.2 - - - -
70B VAL 4.2 2.5 - - - +
71B PRO* 4.2 15.5 - - + -
82B PRO 4.0 5.4 - - - +
83B ALA 4.0 7.0 - - - +
84B PHE 3.6 1.3 - - - -
85B ALA* 1.4 93.5 - - + +
87B PRO* 1.3 71.8 - - + +
89B ILE* 3.3 3.6 + - + +
90B ARG* 3.2 30.4 + - - +
119B ASP* 3.6 20.0 - - - +
157B LEU* 3.5 42.3 - - + +
158B GLY 3.5 9.0 - - - +
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Residues in contact with PRO 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B PRO* 5.5 1.6 - - + -
83B ALA 5.2 1.1 - - - +
84B PHE* 3.5 15.0 - - - +
86B PRO* 1.3 100.5 - - + +
88B ARG* 1.3 66.4 + - - +
90B ARG* 3.4 13.8 + - + +
91B GLU* 3.2 20.8 + - - +
119B ASP* 3.8 15.9 - - - +
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PHE* 3.7 20.2 + - - +
85B ALA 2.8 11.2 + - - +
87B PRO* 1.3 76.1 - - - +
89B ILE* 1.3 64.7 + - - +
91B GLU* 3.4 20.3 + - - +
92B ALA* 3.2 21.5 + - - +
314B PHE* 3.8 16.8 - - + -
316B PRO* 4.0 23.4 - - + +
326B ALA* 4.1 9.3 - - + +
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ALA* 3.0 14.7 + - + +
86B PRO 3.8 5.2 - - - +
87B PRO 3.3 0.4 - - - -
88B ARG* 1.3 73.8 - - - +
90B ARG* 1.3 65.3 + - - +
92B ALA* 3.0 17.1 + - - +
93B ILE* 3.0 21.9 + - + +
157B LEU* 4.2 24.2 - - + -
158B GLY 4.1 18.2 - - - +
311B VAL* 4.7 10.5 - - + +
314B PHE* 3.6 27.8 - - + -
326B ALA 4.6 2.9 - - - -
329B ALA* 4.1 12.6 - - + -
330B ALA* 4.0 15.5 - - - +
333B VAL* 4.0 24.0 - - + -
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 4.8 5.8 - - + +
68B LEU 4.5 0.4 - - - -
69B GLY* 3.6 9.5 - - - +
86B PRO 3.2 24.3 + - - +
87B PRO* 3.6 11.2 - - - +
89B ILE* 1.3 77.4 - - - +
91B GLU* 1.3 64.8 + - - +
92B ALA 3.2 0.3 + - - -
93B ILE* 3.2 16.5 + - - -
94B TRP* 3.4 25.3 - - + +
116B ASP* 2.5 42.3 + - - +
118B GLY* 3.3 19.0 + - - -
119B ASP* 2.8 39.4 + - - -
157B LEU* 4.3 15.7 - - + +
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PRO 3.2 11.1 + - - +
88B ARG* 3.6 25.1 + - - +
89B ILE 3.3 0.2 - - - -
90B ARG* 1.3 80.5 - - - +
92B ALA* 1.3 56.6 + - - +
94B TRP* 3.3 4.1 + - - +
95B CYS* 3.0 27.0 + - + +
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ARG 3.2 10.2 + - - +
89B ILE 3.0 4.5 + - - +
91B GLU* 1.3 72.9 - - - +
93B ILE* 1.3 66.8 + - - +
94B TRP 3.3 0.3 + - - -
95B CYS* 3.3 16.4 + - - +
98B THR* 4.3 2.9 + - - +
326B ALA* 3.3 33.9 - - + +
327B MET* 3.7 32.0 - - - +
330B ALA* 3.4 10.6 - - + +
334B ARG* 5.3 0.9 + - - -
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 4.0 19.7 - - + -
89B ILE* 3.0 24.2 + - + +
90B ARG* 3.2 15.7 + - - +
92B ALA* 1.3 78.2 - - - +
94B TRP* 1.3 88.7 - - + +
98B THR* 3.6 4.9 + - - -
108B LEU* 4.9 2.7 - - + -
114B LEU* 4.4 8.3 - - + -
157B LEU* 5.4 0.2 - - + -
330B ALA* 3.7 24.7 - - + +
333B VAL* 3.9 24.9 - - + -
334B ARG* 3.3 38.9 + - + +
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Residues in contact with TRP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 6.1 1.4 - - - +
90B ARG* 3.4 28.7 + - + +
91B GLU* 3.3 7.1 + - - +
92B ALA 3.2 0.2 - - - -
93B ILE* 1.3 97.9 - - + +
95B CYS* 1.3 69.4 + - - +
96B GLY* 3.3 2.4 + - - -
98B THR* 4.7 0.2 - - - -
100B SER* 4.5 10.3 - - - -
108B LEU* 3.5 37.9 - - + -
109B LYS* 4.1 26.5 - - + -
114B LEU* 4.1 16.5 - - + +
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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