Contacts of the strand formed by residues 164 - 170 (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 PRO 164 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C GLU* 3.3 15.5 - - + +
139E TYR* 3.3 7.4 - - - -
140E TYR* 3.3 50.1 + - + +
142E ASN* 4.2 9.0 - - - +
162E GLU 3.6 5.6 - - - +
163E LEU* 1.3 84.8 - - - +
165E VAL* 1.3 63.4 + - - +
166E ILE* 4.2 3.2 - - + +
207E TYR* 3.5 56.3 - - + +
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Residues in contact with VAL 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ALA* 5.0 2.5 - - + -
162C GLU* 2.8 28.7 + - + +
83E LEU* 4.9 11.4 - - + -
86E ILE* 4.0 25.8 - - + -
137E VAL* 3.4 30.5 - - + -
138E LEU 3.8 3.8 - - - -
139E TYR* 4.1 12.8 - - + -
159E HIS* 5.9 0.7 - - + +
164E PRO* 1.3 74.4 - - - +
166E ILE* 1.3 62.4 + - - +
167E LEU 3.8 10.5 - - - +
168E ILE* 4.0 16.2 - - + -
203E ARG* 3.3 26.9 + - - +
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Residues in contact with ILE 166 (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* 3.4 16.4 - - - +
105E LEU* 4.3 20.9 - - + -
138E LEU* 2.8 25.2 + - + +
139E TYR 4.2 2.2 - - - +
140E TYR* 3.8 32.8 - - + +
147E LEU* 4.7 5.4 - - + -
164E PRO* 4.5 7.6 - - + +
165E VAL* 1.3 80.0 - - - +
167E LEU* 1.3 60.2 + - + +
200E ALA* 3.5 36.0 - - + +
203E ARG* 4.0 11.1 - - + +
204E LEU* 3.7 31.6 - - + +
207E TYR* 5.2 0.4 - - + -
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Residues in contact with LEU 167 (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* 3.4 18.6 - - - +
119E PHE* 4.0 29.4 - - + -
123E PHE* 4.1 17.3 - - + -
136E THR 4.8 0.2 - - - -
137E VAL* 3.4 5.2 - - - +
138E LEU* 2.9 39.9 + - + -
165E VAL* 4.2 1.3 - - - -
166E ILE* 1.3 81.5 - - + +
168E ILE* 1.3 65.5 + - - +
191E TRP* 4.0 18.2 - - + -
192E TRP* 4.6 2.0 - - + -
195E VAL* 3.6 27.8 - - + -
197E TRP* 4.0 23.8 - - + -
200E ALA* 4.9 2.7 - - + -
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Residues in contact with ILE 168 (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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83E LEU* 4.0 26.2 - - + +
86E ILE* 4.0 15.5 - - + -
87E TYR* 3.9 31.9 - - + -
90E ASN* 2.9 23.7 + - - +
91E MET* 5.7 0.2 - - - +
123E PHE* 5.2 0.2 - - - -
135E TRP* 3.5 31.0 - - + -
136E THR 3.5 4.7 - - - +
137E VAL* 3.6 26.7 - - + -
165E VAL* 4.0 9.2 - - + -
167E LEU* 1.3 78.2 - - - +
169E VAL* 1.3 68.1 + - - +
191E TRP* 3.6 15.4 + - - -
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Residues in contact with VAL 169 (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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87E TYR* 4.5 1.1 - - - -
123E PHE* 3.4 33.2 - - + -
127E ALA* 5.4 0.2 - - + -
135E TRP* 3.3 10.9 - - - +
136E THR* 3.1 34.2 + - - +
168E ILE* 1.3 72.7 - - - +
170E ASP* 1.3 67.5 + - - +
171E GLU* 3.5 2.8 + - + +
187E TYR* 4.0 9.9 - - - +
188E LEU* 4.1 22.2 - - + -
191E TRP* 3.4 48.2 - - + +
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Residues in contact with ASP 170 (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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33E HIS* 2.7 12.5 + - - -
84E HIS* 3.4 2.4 + - - -
87E TYR* 3.6 26.3 - - + +
134E GLY 3.9 0.5 - - - +
135E TRP* 3.4 29.3 - - + -
169E VAL* 1.3 73.0 - - - +
171E GLU* 1.3 63.6 + - - +
172E PHE* 3.0 21.7 + - - +
174E HIS* 4.3 0.2 - - - -
175E ALA* 3.7 11.5 - - + +
187E TYR* 2.7 31.7 + - - -
326E FE 2.0 34.3 - - - -
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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