Contacts of the strand formed by residues 179 - 185 (chain E) in PDB entry 3WBR
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 ARG 179 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D ARG* 3.7 37.5 - - - +
153D TRP* 3.5 22.4 - - + -
174D ASN* 4.3 15.2 - - - +
145E SER* 3.3 6.1 - - - -
146E ASP* 2.9 32.3 + - + +
177E ASP 3.9 0.2 + - - -
178E GLU* 1.3 78.2 + - - +
180E CYS* 1.3 60.8 + - - +
195E ASP* 3.1 38.4 + - + +
196E ILE* 3.5 13.4 + - - +
197E HIS* 3.1 33.5 - - - +
198E CYS* 3.3 8.8 - - - +
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Residues in contact with CYS 180 (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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153D TRP* 4.1 4.9 - - - -
104E TRP* 3.3 38.1 - - + -
141E PHE* 3.8 14.1 - - + -
144E LEU 3.9 3.1 - - - -
145E SER* 3.9 8.7 - - - -
179E ARG* 1.3 76.0 - - - +
181E ALA* 1.3 61.5 + - - +
195E ASP* 3.3 2.8 - - - -
196E ILE* 2.8 36.3 + - - +
198E CYS* 2.0 48.7 - - - -
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Residues in contact with ALA 181 (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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153D TRP* 4.1 1.7 - - + -
168D TRP* 4.0 12.3 - - + -
141E PHE* 3.6 5.9 - - - -
142E LEU* 3.0 32.8 + - + +
144E LEU* 3.0 49.4 + - + +
180E CYS* 1.3 73.2 - - - +
182E ILE* 1.3 65.3 + - - +
193E TRP* 5.5 0.7 - - + -
194E ASN 3.2 9.0 - - - +
195E ASP* 4.5 0.4 - - - +
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Residues in contact with ILE 182 (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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139E SER* 3.5 11.0 - - - +
140E TYR 3.0 10.8 - - - +
141E PHE* 3.5 28.3 - - + +
142E LEU* 4.1 5.7 - - - +
181E ALA* 1.3 72.5 - - - +
183E ILE* 1.3 58.9 + - - +
184E ASN* 3.4 26.6 + - - +
192E GLY 3.8 0.2 - - - +
193E TRP* 3.2 8.3 - - - +
194E ASN* 2.8 50.4 + - + +
196E ILE* 3.7 33.9 - - + -
202E GLN* 3.5 22.4 - - + +
201H PRO* 4.4 6.5 - - + -
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Residues in contact with ILE 183 (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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121E ILE* 5.2 0.7 - - + -
127E GLN* 4.1 19.5 - - - +
130E ILE* 4.8 7.0 - - + -
131E ILE* 3.8 28.9 - - + -
134E LEU* 3.9 13.7 - - + -
140E TYR* 2.7 48.3 + - + +
142E LEU* 3.6 26.4 - - + +
182E ILE* 1.3 73.3 - - - +
184E ASN* 1.3 64.6 + - - +
191E TRP* 3.8 10.8 - - + -
192E GLY 3.3 14.6 - - - +
193E TRP* 4.4 5.2 - - + +
205E ILE* 3.8 19.1 - - + -
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Residues in contact with ASN 184 (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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169D HIS* 3.1 26.8 + - - -
138E SER 3.9 5.6 - - - +
139E SER* 3.1 29.7 + - - +
182E ILE* 3.4 21.8 - - - +
183E ILE* 1.3 73.2 - - - +
185E PHE* 1.3 64.5 + - - +
186E ARG* 4.5 5.0 + - - +
191E TRP* 3.2 16.7 - - - -
192E GLY 3.0 29.3 + - - -
194E ASN* 4.7 8.5 + - - +
201H PRO* 4.0 13.0 - - + +
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Residues in contact with PHE 185 (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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136E ARG* 3.4 76.9 + - + +
138E SER 4.5 1.8 + - - -
184E ASN* 1.3 80.1 - - - +
186E ARG* 1.3 86.0 + - - +
187E SER* 4.7 4.9 - - - -
188E SER 5.3 0.7 - - - -
190E GLU* 3.5 38.1 - - + -
191E TRP* 3.3 34.4 - + + -
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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