Contacts of the helix formed by residues 86 - 94 (chain B) in PDB entry 1IDB
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 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ASP 3.6 7.4 - - - -
28B ALA* 3.0 17.0 - - - -
30B ASP 3.2 16.9 + - - -
31B SER* 3.0 10.7 + - - -
84B ILE 3.9 0.4 - - - -
85B PHE* 1.3 75.9 - - - +
87B ARG* 1.3 58.4 + - - -
88B ASN* 2.9 12.4 + - - -
89B ILE 3.1 11.4 + - - -
90B LEU* 3.2 12.7 + - - +
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Residues in contact with ARG 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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5A LEU* 2.8 50.7 + - + +
6A TRP 3.0 21.8 + - - -
7A LYS* 3.4 11.0 - - - +
8A ARG* 3.6 21.6 - - - +
9A PRO* 4.0 7.4 - - - -
26B THR* 3.4 32.6 + - - +
27B GLY 5.7 0.4 - - - -
28B ALA 2.7 18.9 + - - +
29B ASP* 2.6 41.1 + - - +
86B GLY* 1.3 70.1 - - - -
88B ASN* 1.3 60.6 + - - +
89B ILE 3.4 0.2 - - - -
90B LEU* 3.9 9.4 - - + -
91B THR* 2.6 31.5 + - - -
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Residues in contact with ASN 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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29B ASP 3.3 12.0 + - - +
30B ASP* 3.4 29.7 - - - +
31B SER* 2.6 29.9 + - - +
73B ALA* 4.3 5.4 - - - +
74B THR* 3.0 32.8 + - - +
86B GLY 2.9 2.2 + - - -
87B ARG* 1.3 78.5 - - - +
89B ILE* 1.3 67.1 + - - +
91B THR* 4.3 3.0 - - - -
92B ALA* 3.5 16.8 + - - +
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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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31B SER* 3.4 25.8 - - - +
64B ILE* 3.8 19.3 - - + -
66B VAL* 4.7 1.1 - - + -
71B VAL* 4.5 10.3 - - + -
73B ALA* 4.2 11.7 - - + -
75B ILE* 4.3 4.9 - - + -
85B PHE* 3.6 49.8 - - + -
86B GLY 3.1 6.2 + - - +
88B ASN* 1.3 82.8 - - - +
90B LEU* 1.3 61.9 + - + +
91B THR 3.1 2.2 - - - -
92B ALA* 2.9 6.9 + - - +
93B LEU* 2.8 45.8 + - + +
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Residues in contact with LEU 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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5A LEU* 3.7 30.5 - - + -
97A LEU* 5.0 1.3 - - + -
24B LEU* 3.9 24.2 - - + -
25B ASP 3.9 32.8 - - - +
26B THR* 4.0 7.9 - - + +
85B PHE* 3.8 14.6 - - + +
86B GLY 3.2 16.3 + - - +
87B ARG* 4.3 2.5 - - - -
89B ILE* 1.3 79.1 - - + +
91B THR* 1.3 59.3 + - - +
93B LEU* 3.2 7.9 + - + -
94B GLY 3.0 4.5 + - - -
95B MET* 3.0 56.7 + - + +
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Residues in contact with THR 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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4A SER* 6.0 2.0 - - - -
5A LEU* 3.0 25.9 + - - +
6A TRP* 4.2 36.0 - - + +
87B ARG 2.6 23.7 + - - -
88B ASN* 4.3 3.6 - - - -
90B LEU* 1.3 74.4 - - - +
92B ALA* 1.3 65.0 + - - +
93B LEU 3.3 0.5 + - - -
94B GLY* 3.3 10.2 + - - +
95B MET 5.0 3.8 - - - +
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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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69B LYS* 5.1 1.6 + - - +
71B VAL* 4.2 27.2 - - + +
72B ARG 5.6 3.1 - - - +
73B ALA* 5.6 2.7 - - + -
88B ASN 3.5 11.9 + - - +
89B ILE* 2.9 12.8 + - - +
91B THR* 1.3 81.7 - - - +
93B LEU* 1.3 59.8 + - - +
94B GLY 3.5 0.2 + - - -
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Residues in contact with LEU 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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99A LEU* 3.3 11.4 - - + +
24B LEU* 5.6 1.6 - - + -
66B VAL* 4.3 23.8 - - + +
67B LEU* 4.2 25.1 - - + -
69B LYS* 2.8 58.5 + - + -
71B VAL* 4.0 17.0 - - + -
85B PHE* 5.4 1.8 - - + -
89B ILE* 2.8 33.2 + - + +
90B LEU* 3.2 10.7 + - + +
92B ALA* 1.3 76.6 - - - +
94B GLY* 1.3 60.5 + - - +
95B MET* 4.1 16.6 - - + -
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Residues in contact with GLY 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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98A ASN 4.0 1.7 - - - +
99A LEU* 3.5 16.5 - - - +
69B LYS* 5.0 0.2 - - - -
90B LEU 3.0 3.4 + - - -
91B THR* 3.3 7.9 + - - -
92B ALA 3.2 3.2 - - - -
93B LEU* 1.3 83.1 - - - +
95B MET* 1.3 64.5 + - - +
96B SER* 3.9 2.4 + - - -
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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