Contacts of the helix formed by residues 180 - 194 (chain E) in PDB entry 5JLH
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 ALA 180 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E HIS* 5.5 0.7 - - + +
155E GLY 3.8 5.8 - - - +
156E ASP 2.7 31.6 - - - +
157E GLY 3.2 14.4 - - - +
159E THR* 4.7 2.7 - - - -
179E LEU* 1.3 80.4 - - - +
181E GLY* 1.3 60.9 + - - +
182E ARG* 3.7 4.9 - - + +
183E ASP* 3.1 16.3 + - - +
184E LEU* 3.1 26.7 + - - +
260E LEU* 5.2 2.6 - - - +
302E THR* 4.6 5.4 - - - -
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Residues in contact with GLY 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E GLY 3.3 12.2 + - - -
156E ASP* 3.7 6.7 - - - +
180E ALA* 1.3 73.8 - - - +
182E ARG* 1.3 56.5 + - - +
184E LEU* 3.2 4.9 + - - +
185E THR 2.9 13.9 + - - -
212E LYS* 2.5 26.2 + - - -
302E THR* 3.9 17.6 - - - -
401E ADP 3.4 17.7 - - - -
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Residues in contact with ARG 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E SER* 5.8 0.2 - - - -
68E TYR* 3.5 25.7 - - + +
71E GLU* 2.8 52.6 + - - +
72E HIS* 5.4 3.0 + - + -
156E ASP* 3.2 35.5 + - - +
157E GLY 5.7 0.2 - - - +
180E ALA* 3.1 3.7 - - + +
181E GLY* 1.3 76.4 - - - +
183E ASP* 1.3 67.7 + - - +
185E THR* 3.2 9.7 + - - -
186E ASP* 2.9 34.5 + - - +
205E ARG* 3.3 37.4 - - - +
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Residues in contact with ASP 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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72E HIS* 3.9 28.1 - - - -
178E ASP 3.9 6.2 - - - +
179E LEU* 3.6 22.8 + - + -
180E ALA* 3.1 16.0 + - - +
182E ARG* 1.3 85.6 + - - +
184E LEU* 1.3 58.7 + - + +
186E ASP* 3.2 12.2 + - - +
187E TYR* 2.9 28.1 + - - +
266E LEU* 4.2 22.8 - - + +
268E MET* 5.2 3.8 - - + +
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Residues in contact with LEU 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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179E LEU* 6.3 0.2 - - + -
180E ALA 3.1 15.5 + - - +
181E GLY* 3.5 7.4 - - - +
183E ASP* 1.3 73.3 - - - +
185E THR* 1.3 59.6 + - - +
187E TYR* 3.2 5.9 + - + +
188E LEU* 2.7 29.6 + - - +
212E LYS* 4.0 6.3 - - + -
256E CYS* 3.3 36.6 - - - +
257E PRO* 4.5 4.0 - - + -
259E ALA* 3.6 20.9 - - + -
260E LEU* 3.9 26.9 - - + -
266E LEU* 5.0 4.7 - - + -
302E THR* 3.8 11.7 - - - +
305E TYR* 3.3 35.0 - - + +
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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
----------------------------------------------------------
156E ASP* 5.5 0.2 + - - -
181E GLY 2.9 7.1 + - - -
182E ARG* 3.3 13.1 - - - -
184E LEU* 1.3 76.4 - - - +
186E ASP* 1.3 65.0 + - - +
188E LEU* 3.0 7.9 + - - +
189E MET* 3.0 23.6 + - - +
205E ARG* 3.9 29.8 - - + +
208E VAL* 3.7 25.0 - - + +
209E ARG* 4.1 12.5 - - + +
212E LYS* 2.5 33.3 + - - +
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Residues in contact with ASP 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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283A LYS* 5.2 11.8 + - - +
182E ARG* 2.9 19.8 + - - +
183E ASP* 3.2 14.1 + - - +
185E THR* 1.3 77.4 - - - +
187E TYR* 1.3 61.2 + - - +
189E MET* 3.4 16.1 - - - +
190E LYS* 3.3 19.9 + - - +
205E ARG* 3.3 38.3 + - - -
266E LEU* 6.3 0.2 - - + -
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Residues in contact with TYR 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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183E ASP 2.9 9.3 + - - +
184E LEU* 3.4 10.8 - - + +
186E ASP* 1.3 75.1 - - - +
188E LEU* 1.3 62.2 + - - +
190E LYS* 3.1 33.0 + - - +
191E ILE* 2.9 53.9 + - + +
255E ARG* 4.0 27.5 - - + -
256E CYS* 4.1 22.9 - - - -
259E ALA* 4.9 4.0 - - + -
265E PHE* 4.1 39.4 - - + +
266E LEU* 3.6 34.2 - - + +
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Residues in contact with LEU 188 (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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184E LEU 2.7 20.4 + - - +
185E THR* 3.0 7.2 + - - +
187E TYR* 1.3 73.5 - - - +
189E MET* 1.3 67.4 + - - +
191E ILE* 3.0 29.2 + - + +
192E LEU* 3.0 33.4 + - + +
208E VAL* 3.9 20.6 - - + +
211E ILE* 4.4 8.5 - - + -
212E LYS* 3.8 34.5 - - + +
216E CYS* 4.3 8.3 - - - -
249E ILE* 6.4 2.2 - - + -
252E GLU* 4.1 9.4 - - + +
253E ARG* 5.5 0.9 - - - -
256E CYS* 3.5 27.1 - - + -
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Residues in contact with MET 189 (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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185E THR 3.0 14.2 + - - +
186E ASP* 3.4 28.3 - - - +
188E LEU* 1.3 78.3 - - - +
190E LYS* 1.3 61.6 + - - +
192E LEU* 3.5 14.3 + - - +
193E THR* 3.3 20.0 + - - +
197E TYR 4.9 0.3 - - - +
199E PHE* 2.9 40.4 + - + +
200E THR* 4.7 9.4 - - - +
201E THR 5.3 0.2 - - - +
205E ARG* 3.8 35.2 - - + -
208E VAL* 4.3 15.9 - - + +
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Residues in contact with LYS 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 4.3 27.5 - - + +
171A PRO* 4.5 25.6 + - - +
172A HIS* 4.6 16.6 - - - +
174A ILE 5.3 2.9 - - - +
186E ASP 3.3 13.5 + - - +
187E TYR* 3.1 40.0 + - - +
188E LEU 3.0 0.6 - - - -
189E MET* 1.3 78.2 - - - +
191E ILE* 1.3 64.9 + - - +
193E THR* 2.3 32.8 + - - -
194E GLU* 4.1 0.9 + - - +
265E PHE 5.0 6.2 + - - -
266E LEU* 5.9 1.6 - - - +
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Residues in contact with ILE 191 (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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187E TYR* 2.9 43.8 + - + +
188E LEU* 3.0 34.5 + - + +
190E LYS* 1.3 79.4 - - - +
192E LEU* 1.3 61.3 + - - +
193E THR 3.2 0.2 - - - -
194E GLU* 3.0 52.4 - - - +
252E GLU* 3.5 29.0 - - + +
255E ARG* 3.8 24.7 - - - +
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Residues in contact with LEU 192 (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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188E LEU* 3.0 50.0 + - + +
189E MET* 3.8 9.4 - - - +
190E LYS 3.3 0.2 - - - -
191E ILE* 1.3 76.7 - - - +
193E THR* 1.3 55.8 + - - +
194E GLU 3.0 0.7 - - - -
195E ARG* 2.7 33.3 + - - +
196E GLY 3.4 3.1 + - - -
197E TYR* 3.6 27.7 + - + +
199E PHE* 3.5 36.6 - - + -
208E VAL* 4.1 7.6 - - + -
211E ILE* 4.9 9.6 - - + -
247E ILE* 4.9 4.9 - - + -
249E ILE* 4.9 2.0 - - + -
252E GLU* 2.9 33.0 - - - +
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Residues in contact with THR 193 (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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109A LEU* 3.8 32.9 + - + +
111A PRO* 3.4 17.5 - - - +
176A ARG* 5.5 4.0 - - - -
189E MET 3.3 17.3 - - - +
190E LYS* 2.3 28.8 + - - +
192E LEU* 1.3 75.6 - - - +
194E GLU* 1.3 59.2 + - - +
196E GLY* 3.0 16.5 + - - -
197E TYR 3.3 16.8 - - - +
198E SER* 4.4 16.3 + - - +
199E PHE 5.1 2.0 - - - +
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Residues in contact with GLU 194 (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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109A LEU 4.9 0.9 - - - -
110A ASN 4.2 6.1 - - - +
111A PRO* 3.2 11.1 - - - +
112A LYS* 2.8 61.5 + - + +
113A ALA 4.6 0.3 + - - -
190E LYS 5.3 0.4 - - - +
191E ILE* 3.0 37.9 + - - +
192E LEU 3.0 1.0 - - - -
193E THR* 1.3 81.1 + - - +
195E ARG* 1.3 58.8 + - + +
251E ASN* 5.2 0.3 - - - +
252E GLU* 4.8 5.5 - - - +
255E ARG* 2.4 34.9 + - - -
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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