Contacts of the strand formed by residues 166 - 174 (chain E) in PDB entry 4PJE
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 PHE 166 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111E ILE* 6.6 0.2 - - + -
113E ASN* 5.6 7.4 - - + -
136E ASP* 4.5 7.4 - - + -
159E LEU* 5.1 0.4 - - + -
160E ASP* 3.5 3.4 + - - +
161E MET* 2.8 53.9 + - + +
164E MET* 3.9 19.5 - - + +
165E ASP* 1.3 78.7 - - - +
167E LYS* 1.3 68.2 + - - +
168E SER* 3.6 21.1 - - - -
139F LYS* 3.7 33.2 - - + -
194F ARG* 3.5 29.6 - - - -
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Residues in contact with LYS 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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14E GLU* 3.1 35.0 + - - +
80E MET* 3.7 27.4 - - + -
109E PRO* 4.2 18.2 - - + -
110E ASP 5.6 3.4 - - - +
111E ILE* 3.5 17.2 - - + +
158E VAL* 4.4 3.4 - - + -
159E LEU 3.3 7.9 - - - +
160E ASP* 3.4 37.3 + - + +
165E ASP* 5.0 11.5 + - - +
166E PHE* 1.3 89.4 - - - +
168E SER* 1.3 64.6 + - - +
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Residues in contact with SER 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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111E ILE* 4.2 5.4 - - - +
135E THR* 4.6 1.8 + - - -
136E ASP* 3.5 26.5 - - - +
157E CYS 3.6 0.9 - - - +
158E VAL* 3.5 5.0 - - - -
159E LEU* 2.9 54.1 + - - +
166E PHE* 3.6 7.8 - - - -
167E LYS* 1.3 77.5 - - - +
169E ASN* 1.3 64.7 + - - +
170E SER* 5.4 0.5 - - - -
194F ARG* 3.1 18.6 + - - -
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Residues in contact with ASN 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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109E PRO* 3.6 9.2 - - - +
111E ILE* 3.9 5.7 - - - +
135E THR* 3.2 6.1 + - - -
136E ASP* 3.0 27.8 + - - +
137E PHE* 3.1 46.2 + - + +
138E ASP 3.8 1.2 + - - -
139E SER* 3.3 32.5 + - - +
156E LYS* 4.6 12.4 + - + +
157E CYS 3.5 4.7 - - - +
158E VAL* 3.4 25.3 - - - +
168E SER* 1.3 73.7 - - - +
170E SER* 1.3 61.6 + - - +
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Residues in contact with SER 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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133E LEU* 3.8 12.8 - - - -
134E PHE 3.0 13.2 - - - -
135E THR* 3.8 11.2 - - - -
137E PHE* 3.8 4.2 - - - -
156E LYS* 3.2 5.0 - - - -
157E CYS 2.9 32.4 + - - +
159E LEU* 5.1 7.8 - - - +
168E SER* 5.4 0.7 - - - -
169E ASN* 1.3 77.3 - - - +
171E ALA* 1.3 60.2 + - - +
141F THR* 5.8 1.3 - - - +
192F ARG* 2.9 36.5 + - - +
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Residues in contact with ALA 171 (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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133E LEU* 3.7 4.3 - - - +
134E PHE* 2.8 32.6 + - + +
137E PHE* 4.3 0.2 - - - -
143E VAL* 3.8 31.2 - - + -
154E THR* 3.8 18.4 - - - +
155E ASP 4.2 4.0 - - - +
170E SER* 1.3 74.1 - - - +
172E VAL* 1.3 64.6 + - - +
186E PHE* 3.8 11.4 - - + -
192F ARG* 3.8 6.5 - - - +
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Residues in contact with VAL 172 (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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131E VAL* 3.7 28.7 - - + -
132E CYS 3.5 3.8 - - - +
133E LEU* 4.0 14.6 - - + -
152E TYR 3.8 0.7 - - - +
153E ILE* 3.5 3.5 - - - +
154E THR* 2.9 39.1 + - + +
171E ALA* 1.3 79.1 - - - +
173E ALA* 1.3 62.4 + - - +
174E TRP* 3.9 17.4 - - + -
186E PHE* 4.2 2.2 - - - -
143F VAL* 4.1 21.3 - - + -
145F LEU* 4.5 2.5 - - + -
190F SER* 4.2 9.0 - - - +
192F ARG* 3.8 25.1 - - + +
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Residues in contact with ALA 173 (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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131E VAL* 3.5 1.7 - - - +
132E CYS* 2.7 38.8 + - + +
152E TYR 3.2 9.0 - - - +
153E ILE* 4.0 13.9 - - + -
172E VAL* 1.3 74.0 - - - +
174E TRP* 1.4 63.1 + - - +
180E PHE* 3.9 6.7 - - + -
185E ALA* 3.9 17.9 - - + -
186E PHE* 3.6 25.6 - - + -
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Residues in contact with TRP 174 (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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131E VAL* 3.9 23.3 - - + +
151E VAL* 3.7 1.7 - - - +
152E TYR* 2.8 73.1 + + + -
154E THR* 3.6 26.9 - - + -
172E VAL* 3.9 7.2 - - + -
173E ALA* 1.4 78.4 - - - +
175E SER* 1.3 67.2 + - - +
180E PHE* 3.9 10.7 - - - -
145F LEU* 3.6 42.8 - - + +
147F THR* 4.3 11.4 - - + +
176F LEU* 3.9 19.5 - - + -
178F GLU* 5.5 1.0 + - - -
188F ALA* 3.5 31.4 - - + +
189F LEU* 5.5 0.2 - - - -
190F SER* 4.3 3.4 - - - -
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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