Contacts of the helix formed by residues 81 - 91 (chain B) in PDB entry 4I7Z
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 LEU 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A VAL* 3.9 21.1 - - + -
133A VAL* 3.6 29.6 - - + -
151A VAL* 5.8 6.5 - - + -
77B PRO* 4.0 22.0 - - + -
78B GLU 2.9 12.2 + - - +
80B TYR* 1.3 100.0 - - + +
82B TYR* 1.3 60.9 + - - +
83B PRO* 3.4 2.5 - - - -
84B VAL* 3.6 24.4 + - + +
85B PHE* 2.9 30.7 + - + +
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Residues in contact with TYR 82 (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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76B LEU* 3.7 25.7 - - + +
77B PRO* 3.3 33.0 + - + -
78B GLU* 3.5 8.5 - - - -
79B TRP* 2.8 34.0 + - + +
81B LEU* 1.3 78.4 - - - +
83B PRO* 1.3 61.2 - - + +
85B PHE* 3.1 3.1 + - - +
86B GLN* 2.8 26.5 + - - +
144B GLY* 3.4 29.6 - - - +
147B ALA* 3.4 20.1 - - + +
148B THR* 3.9 16.0 - - + +
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Residues in contact with PRO 83 (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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79B TRP 3.7 6.7 - - - +
80B TYR* 4.3 5.6 - - - +
81B LEU* 3.6 5.2 - - - -
82B TYR* 1.3 96.7 - - + +
84B VAL* 1.3 63.2 + - + +
86B GLN* 3.3 3.1 + - - +
87B ILE* 3.1 29.8 + - + +
140B THR* 3.7 42.6 - - + +
143B LEU* 4.0 19.4 - - + +
144B GLY* 4.1 4.0 - - - +
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Residues in contact with VAL 84 (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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80B TYR 5.5 2.5 - - - +
81B LEU* 3.6 28.2 + - + +
82B TYR 3.4 0.2 - - - -
83B PRO* 1.3 81.5 - - + +
85B PHE* 1.3 63.3 + - - +
87B ILE* 3.3 12.5 + - + +
88B LEU* 3.1 21.9 + - + +
101B MET* 3.6 43.3 - - + +
104B VAL* 5.1 17.7 - - + -
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Residues in contact with PHE 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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150A ILE* 5.3 19.7 - - + -
75B ILE 4.3 16.8 - - - -
76B LEU* 4.8 6.5 - - + -
77B PRO* 4.1 29.8 - - + -
81B LEU* 2.9 20.9 + - + +
82B TYR 3.4 2.9 - - - +
84B VAL* 1.3 77.2 - - - +
86B GLN* 1.3 66.2 + - - +
88B LEU* 3.4 12.2 + - + +
89B ARG* 3.3 54.7 + - + +
147B ALA* 4.0 29.2 - - + -
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Residues in contact with GLN 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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82B TYR 2.8 14.6 + - - +
83B PRO 3.3 5.4 + - - +
85B PHE* 1.3 74.7 - - - +
87B ILE* 1.3 53.0 + - - +
89B ARG* 3.2 18.3 + - - +
90B SER* 2.6 49.1 + - - -
143B LEU* 3.4 47.1 - - + +
146B GLY* 4.1 3.8 - - - -
147B ALA* 3.4 9.8 + - + -
154B THR* 2.5 44.6 + - - +
155B LEU* 3.7 11.8 - - + +
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Residues in contact with ILE 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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83B PRO* 3.1 19.6 + - + +
84B VAL* 3.5 13.0 - - + +
85B PHE 3.3 0.2 - - - -
86B GLN* 1.3 76.8 - - - +
88B LEU* 1.3 66.0 + - - +
90B SER* 3.1 5.5 + - - -
91B VAL* 3.0 30.8 + - + +
97B GLY* 4.4 7.4 - - - +
100B LEU* 4.0 45.5 - - + +
101B MET* 5.0 4.9 - - + +
104B VAL* 5.4 8.1 - - + -
143B LEU* 3.9 26.9 - - + -
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Residues in contact with LEU 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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150A ILE* 5.5 10.1 - - + -
154A VAL* 3.5 36.8 - - + -
84B VAL* 3.1 14.5 + - + +
85B PHE* 3.4 12.7 + - + +
87B ILE* 1.3 83.2 - - - +
89B ARG* 1.3 65.9 + - + +
91B VAL* 3.8 11.6 - - - +
94B LYS* 5.9 4.1 - - - +
97B GLY* 5.2 9.3 - - - -
98B VAL* 5.3 4.9 - - + +
101B MET* 3.5 28.0 - - + -
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Residues in contact with ARG 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 PHE* 3.3 43.3 + - + +
86B GLN* 3.2 17.2 + - - +
88B LEU* 1.3 82.2 - - + +
90B SER* 1.3 66.7 + - - +
91B VAL 4.5 2.1 - - - +
146B GLY 3.2 6.9 + - - -
147B ALA 3.3 13.0 + - - -
149B PHE 2.8 28.7 + - - -
150B PRO* 4.3 1.0 - - - +
151B LEU* 4.1 39.8 - - + +
154B THR* 2.8 26.7 + - - -
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Residues in contact with SER 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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86B GLN* 2.6 42.4 + - - +
87B ILE* 3.1 7.1 + - - -
89B ARG* 1.3 80.1 - - - +
91B VAL* 1.3 69.3 + - - +
92B PRO* 3.2 11.4 - - - +
143B LEU* 5.8 0.7 - - - +
151B LEU* 4.6 9.6 - - - -
154B THR* 5.1 1.1 - - - -
155B LEU* 4.7 18.8 - - - +
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Residues in contact with VAL 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 ILE* 3.0 23.1 + - + +
88B LEU 3.8 12.2 - - - +
89B ARG 4.5 1.6 - - - +
90B SER* 1.3 84.6 + - - +
92B PRO* 1.4 72.3 - - + +
93B ASN 3.3 25.4 - - - +
94B LYS* 5.0 2.3 - - - +
96B LEU* 3.8 24.5 - - + -
97B GLY* 4.0 11.0 - - - +
100B LEU* 3.8 22.2 - - + -
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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