Contacts of the strand formed by residues 155 - 161 (chain E) in PDB entry 4F2N
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 GLY 155 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151E ASN* 4.0 3.1 - - - -
153E GLY 4.0 1.2 + - - -
154E SER* 1.3 77.9 - - - +
156E TRP* 1.3 65.5 + - - -
173E THR 3.3 11.9 - - - -
175E ASN 3.6 10.8 - - - -
192E VAL* 2.9 30.8 + - - +
193E TRP* 3.3 19.6 - - - +
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Residues in contact with TRP 156 (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 GLN* 2.9 20.6 + - - -
107E ASN* 3.4 54.2 - - + +
108E HIS* 3.5 31.9 - + - -
111E PHE* 3.9 11.9 - - + -
151E ASN* 3.1 6.7 + - - +
155E GLY* 1.3 74.7 - - - -
157E THR* 1.3 64.2 + - - +
158E TRP* 3.3 26.3 - + + +
172E SER* 3.4 0.3 - - - -
173E THR* 2.9 38.4 + - - +
175E ASN 3.1 21.3 + - - -
177E GLY 4.2 0.7 - - - -
189E THR* 3.4 19.1 - - + +
190E ALA 3.5 6.1 - - - -
191E ASP* 3.4 46.2 - - + -
192E VAL* 4.4 0.7 - - - -
193E TRP* 3.6 4.9 - - - +
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Residues in contact with THR 157 (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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144E PHE* 3.4 46.8 - - + +
147E ALA* 4.0 9.2 - - + -
148E GLY* 3.3 21.0 - - - -
151E ASN* 3.6 6.1 + - - -
156E TRP* 1.3 74.9 - - - +
158E TRP* 1.3 63.6 + - - +
170E ILE* 4.1 5.4 - - + -
171E ASP 3.6 2.5 - - - +
172E SER* 2.9 21.9 + - - +
189E THR* 3.2 2.9 + - - -
190E ALA* 2.8 37.2 + - - -
192E VAL* 4.5 2.8 - - - +
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Residues in contact with TRP 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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106E PHE* 4.4 5.8 - + - -
107E ASN* 3.3 35.0 - - + -
110E PHE* 4.0 10.5 - + - -
144E PHE* 3.9 5.4 - - - -
156E TRP* 3.3 30.1 - + + +
157E THR* 1.3 75.1 - - - +
159E LEU* 1.3 59.5 + - - +
160E CYS* 3.7 16.2 - - - -
169E LEU 3.6 0.2 - - - +
170E ILE* 3.2 9.4 - - - +
171E ASP* 2.7 47.3 + - - +
173E THR* 3.0 28.9 + - + +
177E GLY 3.9 5.6 - - - -
179E PRO* 3.4 28.7 - - + -
186E PRO* 3.5 34.1 - - + -
188E PHE 3.4 6.3 - - - -
189E THR* 3.3 31.0 - - + -
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Residues in contact with LEU 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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130E ILE* 4.3 19.3 - - + -
134E PHE* 3.7 22.7 - - + -
140E PHE* 3.6 40.8 - - + -
144E PHE* 4.0 2.3 - - + -
158E TRP* 1.3 73.4 - - - +
160E CYS* 1.3 60.4 + - - +
168E LEU* 4.2 11.0 - - + -
169E LEU 3.5 14.1 - - - +
170E ILE* 4.6 0.2 - - + -
186E PRO* 3.8 1.9 - - - +
187E ILE* 2.9 52.6 + - + +
188E PHE* 2.9 28.8 + - + +
218E TRP* 5.2 1.6 - - + -
221E VAL* 4.8 3.1 - - + -
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Residues in contact with CYS 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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158E TRP* 3.7 26.0 - - - -
159E LEU* 1.3 76.4 - - - +
161E VAL* 1.3 67.5 - - - +
168E LEU* 3.2 10.0 - - - +
169E LEU* 2.9 44.6 + - + +
171E ASP* 4.6 4.9 - - - -
179E PRO* 3.8 26.9 - - - -
184E LEU* 4.2 15.0 - - + -
185E ARG 3.3 7.4 - - - +
186E PRO* 4.0 9.9 - - - -
187E ILE* 4.3 0.7 - - - +
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Residues in contact with VAL 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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160E CYS* 1.3 74.7 - - - +
162E ASP* 1.3 76.2 + - - +
163E PRO* 3.6 4.6 - - + +
166E LYS* 4.4 3.6 - - - -
167E GLU 3.4 6.7 - - - +
168E LEU* 3.7 22.4 - - + -
184E LEU* 3.8 2.1 - - - +
185E ARG* 2.8 38.6 + - + +
187E ILE* 4.0 13.7 - - + +
225E TYR* 3.9 19.1 - - + -
228E ALA* 4.0 24.0 - - + +
229E THR* 3.8 23.6 - - + -
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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