Contacts of the strand formed by residues 177 - 187 (chain E) in PDB entry 4WFH
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 LEU 177 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117E ALA* 4.6 6.3 - - + -
118E LYS 4.8 0.7 - - - +
120E THR* 4.2 18.2 - - + +
147E GLY* 3.9 28.5 - - - +
148E TYR 3.8 6.3 - - - +
149E PHE* 3.7 23.1 - - + -
173E LEU* 3.5 6.5 - - - -
174E GLN* 2.7 37.1 + - - +
175E SER 4.1 7.2 - - - +
176E ASP* 1.3 89.3 - - + +
178E TYR* 1.3 63.0 + - - +
179E THR* 5.1 0.2 - - - -
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Residues in contact with TYR 178 (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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113E THR* 4.5 15.6 - - + +
147E GLY 2.8 24.9 + - - -
148E TYR* 2.9 48.5 + - + +
149E PHE* 3.6 30.3 - + - -
150E PRO* 5.0 0.4 - - + -
151E GLU* 3.7 43.9 - - + +
171E ALA* 3.9 14.4 - - + -
172E VAL* 3.3 10.8 - - - -
173E LEU* 3.9 30.2 - - + +
177E LEU* 1.3 73.2 - - - +
179E THR* 1.3 62.3 + - - +
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Residues in contact with THR 179 (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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177D THR* 6.0 4.0 - - + -
144E LEU* 4.0 17.9 - - + -
145E VAL 3.4 5.8 - - - +
146E LYS* 3.4 33.8 - - + +
147E GLY* 3.8 1.9 + - - -
148E TYR* 4.2 0.7 - - - -
170E PRO 4.1 0.7 - - - +
171E ALA* 3.2 4.7 - - - -
172E VAL* 2.9 43.0 + - + +
174E GLN* 3.7 22.8 + - - +
177E LEU 4.7 0.2 + - - -
178E TYR* 1.3 80.0 + - - +
180E LEU* 1.3 66.3 + - - +
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Residues in contact with LEU 180 (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 LEU* 3.8 4.1 - - - +
145E VAL* 2.8 50.1 + - + +
148E TYR* 3.6 20.6 - - - +
151E GLU* 5.2 1.6 - - - +
153E VAL* 3.7 19.5 - - + +
155E VAL* 4.3 7.0 - - + -
168E THR* 3.8 16.4 - - + -
169E PHE* 3.4 24.0 - - - +
170E PRO 4.0 2.9 - - - +
171E ALA* 3.9 11.4 - - + +
179E THR* 1.3 80.3 - - - +
181E SER* 1.3 80.7 + - - +
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Residues in contact with SER 181 (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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132D VAL* 4.7 3.9 - - - +
134D PHE* 3.9 25.4 - - - -
175D SER* 4.3 12.8 + - - -
177D THR* 4.8 4.3 + - - -
127E LEU* 4.6 2.9 - - - -
143E CYS 3.0 18.2 - - - -
144E LEU* 4.1 12.7 - - - +
168E THR* 3.7 3.5 - - - +
169E PHE* 3.0 33.5 + - - +
180E LEU* 1.3 81.0 - - - +
182E SER* 1.3 62.0 + - - +
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Residues in contact with SER 182 (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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134D PHE* 4.0 4.0 - - - -
142E GLY* 3.1 5.4 - - - -
143E CYS 2.8 33.6 + - - -
155E VAL* 3.7 25.2 + - - +
157E TRP* 3.3 23.0 + - - -
166E VAL* 3.9 3.6 - - - +
167E HIS 3.2 9.0 + - - -
168E THR* 2.9 25.8 + - - -
169E PHE* 4.8 0.2 - - - -
181E SER* 1.3 74.5 - - - +
183E SER* 1.3 59.5 + - - +
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Residues in contact with SER 183 (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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134D PHE* 3.3 32.7 - - - -
136D ASN* 3.2 23.2 + - - -
140E THR* 4.3 3.7 - - - +
141E LEU 3.4 6.3 - - - -
157E TRP* 4.3 0.9 - - - -
165E GLY 4.5 1.4 + - - -
166E VAL* 3.2 10.0 - - - +
167E HIS* 2.7 47.2 + - - +
169E PHE* 4.4 5.0 - - - -
182E SER* 1.3 73.7 - - - +
184E VAL* 1.3 62.8 + - - +
185E THR* 5.1 0.3 + - - -
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Residues in contact with VAL 184 (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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139E VAL 4.0 0.7 - - - +
140E THR* 3.5 2.4 - - - +
141E LEU* 2.9 51.2 + - + +
157E TRP* 3.7 37.9 - - + +
162E LEU* 3.8 31.2 - - + -
164E SER 4.5 0.7 - - - +
165E GLY 3.2 5.8 - - - +
166E VAL* 3.8 18.4 - - + -
183E SER* 1.3 75.1 - - - +
185E THR* 1.3 67.0 + - - +
186E VAL* 4.1 8.3 + - + +
196E VAL* 4.6 6.3 - - + -
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Residues in contact with THR 185 (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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136D ASN* 4.6 8.3 + - - +
137D ASN* 5.6 3.7 + - - -
138E MET* 3.7 35.4 - - + +
139E VAL 3.4 9.9 - - - +
140E THR* 3.0 22.5 + - - +
162E LEU* 5.1 0.2 - - - +
164E SER 4.3 3.1 - - - +
165E GLY* 2.9 27.9 + - - -
167E HIS* 5.9 0.9 - - - -
183E SER* 5.1 0.2 + - - -
184E VAL* 1.3 74.4 - - - +
186E VAL* 1.3 69.7 + - - +
187E PRO* 4.8 0.2 - - - +
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Residues in contact with VAL 186 (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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138E MET* 3.5 7.4 - - - -
139E VAL* 2.7 59.8 + - + +
141E LEU* 4.6 10.1 - - + -
162E LEU* 3.9 35.7 - - + -
184E VAL* 4.1 8.5 - - + +
185E THR* 1.3 79.6 - - - +
187E PRO* 1.3 76.4 - - + +
190E SER* 4.7 7.2 - - - -
191E TRP* 4.3 14.1 - - + -
196E VAL* 5.1 6.3 - - + -
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Residues in contact with PRO 187 (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 SER* 3.7 1.6 - - - +
138E MET* 3.7 24.4 - - + -
186E VAL* 1.3 92.8 - - + +
188E SER* 1.3 54.2 + - - +
189E SER* 3.1 16.4 - - - +
190E SER* 2.7 46.2 + - - +
191E TRP 3.7 2.1 + - - -
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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