Contacts of the strand formed by residues 186 - 195 (chain F) in PDB entry 4PJ7
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 TYR 186 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F GLY 2.9 24.6 + - - -
148F PHE* 2.7 51.1 + + + +
149F TYR* 3.6 19.9 - + - -
151F ASP* 3.8 40.8 + - + -
174F PRO* 3.9 20.6 - - + -
175F LEU 3.3 20.0 - - - +
176F LYS* 3.8 31.2 - - + -
177F GLU* 4.0 3.4 - - - -
182F ASN 5.5 1.7 + - - -
184F SER 3.4 18.3 + - - -
185F ARG* 1.4 71.6 - - - +
187F ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E TRP* 3.5 31.2 - - + -
145F ALA 3.2 5.6 - - - -
146F THR* 3.9 4.5 - - + -
148F PHE* 4.0 2.0 - - - -
171F ASP* 5.2 0.5 - - - +
174F PRO* 3.4 5.2 - - - +
175F LEU* 3.0 49.0 + - + +
177F GLU* 3.8 15.3 - - + +
186F TYR* 1.3 76.2 - - - +
188F LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E TRP* 5.4 1.6 - - - -
143F CYS 3.7 0.7 - - - +
144F LEU* 3.4 4.1 - - - +
145F ALA* 2.7 44.4 + - + +
146F THR* 5.5 0.2 - - - +
148F PHE* 4.1 15.7 - - + -
153F VAL* 4.1 21.5 - - + +
155F LEU* 4.0 22.1 - - + +
170F THR* 3.9 17.9 - - + -
171F ASP* 3.6 38.4 - - + +
172F PRO 5.3 0.4 - - - +
173F GLN 4.2 0.2 - - - -
174F PRO* 3.9 24.9 - - + -
187F ALA* 1.3 75.0 - - - +
189F SER* 1.3 64.1 + - - +
210F VAL* 6.1 0.2 - - + -
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Residues in contact with SER 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E THR* 3.1 17.0 + - - +
172E VAL* 4.3 7.2 - - - +
174E TRP* 4.6 0.7 - - - -
142F VAL* 5.0 0.7 - - - -
143F CYS 3.2 5.2 - - - -
144F LEU* 3.6 24.2 - - - -
155F LEU* 4.6 1.1 - - - -
170F THR* 3.6 5.8 - - - +
171F ASP* 2.7 50.0 + - - -
188F LEU* 1.3 73.2 - - - +
190F SER* 1.3 62.7 + - - +
191F ARG* 2.8 21.3 + - - -
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Residues in contact with SER 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F VAL* 3.4 5.9 - - - +
143F CYS* 2.9 32.0 + - - +
155F LEU* 3.5 23.1 - - - -
157F TRP* 2.8 31.8 + - - -
168F VAL* 4.0 0.3 - - - +
169F CYS 3.3 9.8 + - - -
170F THR* 2.9 20.6 + - - -
189F SER* 1.3 76.1 - - - +
191F ARG* 1.3 66.8 + - - +
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Residues in contact with ARG 191 (chain F).
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* 4.4 2.0 - - + -
154E THR* 2.8 25.7 + - - -
155E ASP 3.4 9.1 + - - -
157E CYS* 4.1 6.7 - - - +
159E LEU* 4.4 12.6 - - + -
170E SER* 3.2 37.2 + - - +
171E ALA* 3.6 5.7 - - - +
172E VAL* 3.6 19.8 - - + +
140F THR* 3.9 20.9 - - + -
141F LEU 3.4 4.3 - - - -
142F VAL* 4.4 3.8 - - + -
157F TRP* 4.0 2.6 + - - -
167F GLY 3.6 1.5 - - - +
168F VAL* 3.2 5.7 - - - -
169F CYS* 2.9 50.5 + - - +
171F ASP* 2.8 25.2 + - - +
189F SER* 2.8 24.2 + - - -
190F SER* 1.3 78.4 + - - +
192F LEU* 1.3 58.6 + - - +
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Residues in contact with LEU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F ALA 3.5 2.3 - - - +
140F THR* 3.4 1.5 - - - -
141F LEU* 2.8 41.9 + - + +
157F TRP* 3.6 45.3 - - + +
159F VAL* 3.9 23.6 - - + -
164F VAL* 3.9 11.0 - - + -
166F SER 4.0 9.0 - - - +
167F GLY 3.3 5.6 - - - +
168F VAL* 3.6 22.2 - - + -
191F ARG* 1.3 72.3 - - - +
193F ARG* 1.3 62.1 + - - +
194F VAL* 4.2 16.6 - - + -
206F PHE* 3.9 16.8 - - + -
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Residues in contact with ARG 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E THR* 3.9 8.5 + - - +
136E ASP* 2.5 40.4 + - - -
159E LEU* 3.7 30.5 - - + +
161E MET* 3.5 21.7 - - - +
166E PHE* 3.6 8.9 - - - -
168E SER* 3.3 22.8 + - - -
132F GLU* 2.8 31.4 + - - +
136F THR* 4.1 4.0 + - - -
138F LYS* 3.6 38.7 - - - +
139F ALA 3.3 3.4 - - - -
140F THR* 3.1 24.3 + - + +
166F SER 4.9 0.3 - - - +
167F GLY* 2.7 21.9 + - - -
191F ARG 4.2 0.6 - - - -
192F LEU* 1.3 71.7 - - - +
194F VAL* 1.3 66.0 + - - +
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Residues in contact with VAL 194 (chain F).
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* 3.7 8.7 - - - -
138F LYS* 3.4 4.5 - - - +
139F ALA* 2.7 43.4 + - + +
141F LEU* 4.4 7.2 - - + -
159F VAL* 5.6 1.8 - - + -
166F SER 5.9 0.4 - - - +
192F LEU* 4.2 20.2 - - + -
193F ARG* 1.3 81.0 - - - +
195F SER* 1.3 65.9 + - - +
198F PHE* 4.2 24.5 - - + -
199F TRP* 4.2 16.6 - - + -
206F PHE* 4.2 20.2 - - + -
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Residues in contact with SER 195 (chain F).
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* 3.9 6.2 - - - +
164E MET* 4.6 21.9 - - - +
137F GLN 3.9 10.1 - - - -
138F LYS* 4.3 1.6 - - - +
139F ALA 4.4 0.4 - - - -
194F VAL* 1.3 78.4 - - - +
196F ALA* 1.3 64.6 + - - +
197F THR* 3.3 16.4 - - - +
198F PHE* 3.3 22.6 + - - +
199F TRP* 3.0 21.5 + - - +
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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