Contacts of the strand formed by residues 157 - 163 (chain E) in PDB entry 3V62
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 SER 157 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155E SER* 3.1 22.5 + - - -
156E ASP* 1.3 82.1 - - - +
158E ILE* 1.3 69.2 + - - +
170E VAL 4.2 0.2 - - - +
171E ALA* 4.0 6.9 - - - +
172E ASP 4.9 0.3 + - - -
206E THR* 3.6 18.0 - - - +
207E PHE 3.2 9.0 - - - -
209E ALA 4.2 0.9 - - - +
253E LYS* 3.5 23.0 + - - +
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Residues in contact with ILE 158 (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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148E VAL* 4.1 17.3 - - + +
151E LEU* 3.9 31.4 - - + +
152E SER* 3.8 24.0 - - - +
155E SER 5.3 0.4 - - - +
157E SER* 1.3 79.2 - - - +
159E ASN* 1.3 73.2 + - - +
160E ILE* 4.1 9.1 + - + -
169E PHE* 4.7 7.4 - - + -
170E VAL 3.5 6.7 - - - +
171E ALA* 4.5 1.1 - - + -
205E LEU 3.9 0.3 - - - +
206E THR* 3.3 4.2 - - - -
207E PHE* 2.9 33.8 + - - +
209E ALA* 3.8 20.0 - - + -
212E LEU* 4.0 23.6 - - + -
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Residues in contact with ASN 159 (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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158E ILE* 1.3 74.5 - - - +
160E ILE* 1.3 73.7 + - - +
161E MET* 3.9 10.1 - - - +
168E LYS* 3.3 2.3 - - - +
169E PHE* 3.1 8.3 - - - -
170E VAL* 2.9 48.8 + - + +
204E ASP* 3.4 25.7 + - - +
205E LEU 3.2 11.9 + - - -
206E THR* 2.7 25.8 + - + +
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Residues in contact with ILE 160 (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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137E LEU* 5.6 2.2 - - + -
144E PHE* 5.4 4.3 - - + -
158E ILE* 4.6 7.0 - - + -
159E ASN* 1.3 79.4 - - - +
161E MET* 1.3 64.3 + - - +
162E ILE* 4.3 13.9 - - + -
167E ILE* 3.8 16.2 - - + -
168E LYS 3.4 2.0 - - - -
169E PHE* 3.8 37.0 - - + -
203E VAL 4.4 0.4 - - - -
204E ASP* 3.2 3.5 + - - -
205E LEU 2.9 31.8 + - - +
207E PHE* 3.8 30.5 - - + -
212E LEU* 5.5 4.3 - - + -
227E ILE* 5.3 4.7 - - + -
229E LEU* 4.4 17.7 - - + -
237E PHE* 4.9 13.9 - - + -
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Residues in contact with MET 161 (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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159E ASN* 3.9 9.4 - - - +
160E ILE* 1.3 78.1 - - - +
162E ILE* 1.3 65.3 + - - +
163E THR* 5.1 11.7 - - + -
166E THR* 3.4 6.2 - - - +
167E ILE* 3.4 1.7 - - - -
168E LYS* 2.9 73.4 + - + +
203E VAL 3.1 11.2 - - - +
204E ASP* 2.7 37.2 - - + +
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Residues in contact with ILE 162 (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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135E SER* 3.7 30.1 - - - +
137E LEU* 4.1 11.7 - - + -
160E ILE* 4.6 5.6 - - + -
161E MET* 1.3 78.0 - - - +
163E THR* 1.3 75.5 + - - +
166E THR 3.5 3.8 - - - +
167E ILE* 4.1 18.8 - - + -
197E LEU* 3.5 28.0 - - + -
199E MET* 4.0 5.2 - - + -
202E PRO* 3.4 6.8 - - - +
203E VAL* 2.7 37.6 + - + +
229E LEU* 3.2 34.8 - - + -
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Residues in contact with THR 163 (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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161E MET* 5.1 14.4 - - + -
162E ILE* 1.3 83.9 - - - +
164E LYS* 1.3 57.7 + - - +
165E GLU* 2.7 15.4 + - - -
166E THR* 3.0 43.0 + - + +
197E LEU* 3.7 9.0 - - - +
199E MET* 3.9 8.9 - - - +
202E PRO* 5.1 8.1 - - + -
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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