Contacts of the helix formed by residues 197 - 205 (chain E) in PDB entry 1B06
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 197 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96E LYS* 5.8 1.0 + - - +
98E GLY 3.4 26.4 + - - +
99E GLY 3.2 16.2 + - - -
100E LYS 3.8 12.8 - - - +
101E PRO* 3.5 35.2 - - + -
102E GLY 5.1 2.0 + - - +
105E LEU* 3.7 23.9 - - + +
109E ILE* 4.8 3.8 - - + -
116E PHE* 3.5 32.3 - + - -
119E PHE* 4.4 5.4 - + - -
138E LEU* 6.2 1.6 - - + -
167E LEU* 4.0 33.2 - - + -
192E TRP* 4.0 14.4 + + - -
195E VAL* 3.4 25.4 + - + +
196E ASN* 1.3 69.4 + - - +
198E ASP* 1.3 59.6 + - - +
200E ALA* 3.7 7.4 - - + +
201E GLU* 2.9 30.0 + - - +
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Residues in contact with ASP 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LYS* 2.9 33.9 + - - +
196E ASN* 3.2 9.7 + - - +
197E TRP* 1.3 75.1 - - - +
199E ASP* 1.3 66.7 + - - +
201E GLU* 3.4 5.9 + - - +
202E LYS* 3.0 42.7 + - - +
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Residues in contact with ASP 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ASN* 3.1 33.2 - - - +
90E ASN* 2.9 20.6 - - - +
196E ASN* 3.1 19.2 + - + +
198E ASP* 1.3 80.1 - - - +
200E ALA* 1.3 60.6 + - - +
202E LYS* 3.2 12.9 + - - +
203E ARG* 2.7 61.5 + - - +
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Residues in contact with ALA 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E ASN* 4.3 3.6 - - - +
105E LEU* 3.8 19.3 - - + -
166E ILE* 3.5 37.0 - - + +
167E LEU* 4.9 4.0 - - + -
196E ASN 3.1 9.1 + - - +
197E TRP* 3.7 19.5 - - + +
199E ASP* 1.3 81.2 + - - +
201E GLU* 1.3 61.0 + - - +
203E ARG* 3.3 3.7 + - - +
204E LEU* 3.2 18.2 + - - +
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Residues in contact with GLU 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E GLY 3.5 12.0 - - - +
103E GLY* 3.7 6.6 - - - -
104E ALA* 3.2 14.6 + - - -
105E LEU* 3.0 35.7 + - + +
197E TRP 2.9 17.2 + - - +
198E ASP* 3.8 6.1 - - - +
199E ASP 3.3 0.2 - - - -
200E ALA* 1.3 77.6 - - - +
202E LYS* 1.3 57.8 + - + +
204E LEU* 3.3 6.3 + - - +
205E GLN* 2.9 58.6 + - + +
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Residues in contact with LYS 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LYS* 5.8 0.8 - - - +
198E ASP* 3.0 34.6 + - - +
199E ASP* 3.2 14.5 + - - +
201E GLU* 1.3 79.5 - - - +
203E ARG* 1.3 61.5 + - + +
205E GLN* 3.5 8.0 + - + +
206E LYS* 3.3 29.8 + - - +
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Residues in contact with ARG 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C GLU* 5.4 3.2 + - - -
86E ILE* 3.7 41.2 - - - +
89E ASN* 4.1 14.5 - - - +
90E ASN* 4.6 1.1 - - - -
165E VAL 3.3 27.5 + - - +
166E ILE* 4.0 17.5 - - + -
199E ASP* 2.7 60.7 + - - +
200E ALA 3.6 5.6 - - - +
202E LYS* 1.3 76.2 - - + +
204E LEU* 1.3 60.9 + - - +
206E LYS* 3.3 25.3 - - - +
207E TYR* 2.9 32.8 - - + -
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Residues in contact with LEU 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ALA* 3.8 15.7 - - + +
105E LEU* 3.4 42.6 - - + +
108E LEU* 4.2 13.2 - - + -
140E TYR* 3.8 37.0 - - + -
147E LEU* 4.7 4.9 - - + -
166E ILE* 3.7 14.3 - - + +
200E ALA 3.2 11.0 + - - +
201E GLU* 3.6 9.0 - - - +
203E ARG* 1.3 80.0 - - - +
205E GLN* 1.3 64.8 + - - +
207E TYR* 3.0 14.8 + - - +
208E LEU* 3.2 24.3 + - + +
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Residues in contact with GLN 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ALA* 3.7 19.0 - - - +
201E GLU* 2.9 46.5 + - + +
202E LYS* 3.8 8.3 - - + +
203E ARG 3.4 0.2 - - - -
204E LEU* 1.3 75.3 - - - +
206E LYS* 1.3 62.0 + - - +
207E TYR 3.2 0.9 + - - -
208E LEU* 3.5 26.5 + - - +
210E LYS* 4.8 4.0 - - - +
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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