Contacts of the helix formed by residues 99 - 108 (chain B) in PDB entry 4IOP
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 TRP 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B LYS 3.3 2.5 + - - -
98B THR* 1.3 70.3 - - - +
100B LYS* 1.3 90.9 + - + +
102B SER* 3.1 4.9 + - - +
103B GLN* 3.0 53.7 + - + +
113B LEU* 3.6 13.8 - - + +
136B TRP* 3.1 58.0 - + + -
137B ILE 3.0 26.7 + - - -
138B GLY* 4.7 9.0 - - - -
139B LEU 4.1 1.0 + - - -
140B TYR* 4.4 26.9 - + + -
151B ILE* 4.8 8.7 - - + -
172B CYS* 3.5 30.8 - - + +
173B ALA 4.6 0.4 - - - -
185B CYS* 3.4 13.0 + - + +
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Residues in contact with LYS 100 (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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98B THR* 3.1 5.1 + - - -
99B TRP* 1.3 97.8 - - + +
101B GLU* 1.3 61.5 + - + +
103B GLN* 3.5 8.6 + - - +
104B ARG* 3.1 23.5 + - - +
185B CYS* 5.2 0.6 + - - +
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Residues in contact with GLU 101 (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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97B LYS* 3.7 29.4 - - + +
98B THR* 2.6 45.0 + - - +
100B LYS* 1.3 71.2 - - + +
102B SER* 1.3 56.8 + - - +
104B ARG* 2.9 42.2 + - - +
105B ASP* 2.7 34.1 + - - +
188B THR* 6.0 0.5 - - - +
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Residues in contact with SER 102 (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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93B SER* 5.6 0.3 + - - -
95B SER 5.5 0.5 + - - -
97B LYS* 3.5 25.7 + - - +
98B THR 3.1 0.4 + - - -
99B TRP 3.1 8.3 + - - -
101B GLU* 1.3 73.4 - - - +
103B GLN* 1.3 66.3 + - - +
104B ARG 2.7 5.6 + - - -
105B ASP* 2.8 21.3 + - - +
106B CYS* 2.8 18.2 + - - -
113B LEU* 4.2 16.6 - - - -
136B TRP* 3.8 11.9 - - - -
189B PHE 4.3 0.2 + - - -
191B GLY* 4.1 16.6 + - - -
193B CYS* 5.8 0.9 - - - -
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Residues in contact with GLN 103 (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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99B TRP* 3.0 43.8 + - + +
100B LYS* 3.6 12.6 + - - +
102B SER* 1.3 75.1 - - - +
104B ARG* 1.3 61.5 + - - +
106B CYS* 3.8 4.5 - - - +
107B THR* 3.4 21.1 + - - +
112B HIS* 5.1 1.6 - - + -
113B LEU* 3.8 25.2 + - + +
151B ILE* 3.2 36.4 - - + +
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Residues in contact with ARG 104 (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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100B LYS* 3.1 11.8 + - - +
101B GLU* 2.9 47.7 + - - +
102B SER 2.7 0.8 + - - -
103B GLN* 1.3 74.8 - - - +
105B ASP* 1.3 59.6 + - - +
106B CYS 3.0 1.1 - - - -
107B THR* 2.7 32.5 + - + +
108B GLN* 2.8 32.9 + - - +
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Residues in contact with ASP 105 (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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91B TRP* 5.6 10.6 - - + -
97B LYS* 2.5 43.1 + - - +
101B GLU* 2.7 28.3 + - - +
102B SER* 2.8 15.5 + - - +
104B ARG* 1.3 81.2 + - - +
106B CYS* 1.3 56.9 + - - +
108B GLN* 3.4 10.2 + - - +
109B LEU* 2.8 32.8 - - + +
193B CYS* 4.6 4.7 - - - -
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Residues in contact with CYS 106 (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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102B SER 2.8 17.9 + - - +
103B GLN 3.8 3.4 - - - +
105B ASP* 1.3 73.3 - - - +
107B THR* 1.3 64.2 + - - +
109B LEU* 3.1 12.5 + - - +
111B ALA* 2.8 35.9 + - - +
112B HIS* 3.5 10.5 - - - -
113B LEU* 3.3 32.5 - - - +
193B CYS* 2.0 50.7 - - + -
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Residues in contact with THR 107 (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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103B GLN* 3.4 12.8 + - - +
104B ARG* 2.7 21.6 + - + +
106B CYS* 1.3 70.9 - - - +
108B GLN* 1.3 62.4 + - - +
109B LEU 2.8 16.0 + - - -
110B GLN* 2.9 16.7 + - - +
111B ALA 3.1 12.9 + - - +
112B HIS* 5.3 1.4 - - - +
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Residues in contact with GLN 108 (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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104B ARG* 2.8 30.3 + - + +
105B ASP* 3.5 15.9 - - - +
106B CYS 3.2 0.6 - - - -
107B THR* 1.3 85.2 + - - +
109B LEU* 1.3 76.3 + - + +
110B GLN* 3.8 3.3 + - - -
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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