Contacts of the helix formed by residues 183 - 195 (chain E) in PDB entry 2Y1M
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 LYS 183 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181E ILE* 3.2 9.7 - - - +
182E THR* 1.3 86.8 - - + +
184E ALA* 1.3 54.4 + - - +
185E ASP 3.7 1.1 - - - +
186E ALA* 3.3 17.9 - - + +
187E ALA 2.8 28.1 + - - -
242E ASP* 4.5 0.6 + - - -
245E THR* 4.2 20.0 - - - +
246E ARG* 4.3 13.4 - - + +
249E GLN* 2.9 45.5 + - + +
251E TRP* 6.0 2.9 - - + +
321E ASN 5.2 3.8 + - - -
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Residues in contact with ALA 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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343A ARG* 4.0 30.2 - - + +
182E THR 3.7 1.8 + - - -
183E LYS* 1.3 70.3 - - - +
185E ASP* 1.3 66.0 + - - +
186E ALA 3.1 1.1 - - - -
187E ALA* 2.9 8.6 + - - +
188E GLU* 2.8 30.0 + - - +
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Residues in contact with ASP 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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183E LYS 3.7 0.4 - - - -
184E ALA* 1.3 78.4 - - - +
186E ALA* 1.3 61.2 + - - +
188E GLU* 3.4 9.0 - - - +
189E PHE* 3.3 20.6 + - - +
251E TRP* 3.8 35.8 + - + +
252E SER* 5.0 9.2 + - - -
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Residues in contact with ALA 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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181E ILE* 3.9 4.7 - - + -
183E LYS* 3.3 18.5 + - + +
184E ALA 3.1 0.4 - - - -
185E ASP* 1.3 79.7 - - - +
187E ALA* 1.3 60.5 + - - +
189E PHE* 3.2 4.0 + - - +
190E TRP 3.2 18.9 + - - -
241E PHE* 3.4 12.0 - - + -
245E THR* 3.7 35.4 - - + +
251E TRP* 3.8 24.2 - - + +
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Residues in contact with ALA 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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343A ARG* 3.6 27.8 - - + +
181E ILE* 3.7 24.2 - - + +
183E LYS 2.8 15.9 + - - +
184E ALA* 3.3 8.7 - - - +
186E ALA* 1.3 74.1 - - - +
188E GLU* 1.3 67.4 + - - +
190E TRP* 4.2 0.5 - - - +
191E ARG* 3.3 28.1 + - + +
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Residues in contact with GLU 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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287A LYS* 5.7 0.3 + - - -
344A ASN* 2.6 34.3 + - - +
71C GLN* 4.6 12.2 + - - +
184E ALA 2.8 12.4 + - - +
185E ASP* 3.4 14.6 - - - +
187E ALA* 1.3 76.7 - - - +
189E PHE* 1.3 55.9 + - - +
191E ARG* 4.1 1.0 - - - +
192E LYS* 2.7 61.5 + - + +
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Residues in contact with PHE 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 ASP 3.3 4.4 + - - +
186E ALA 3.2 7.7 + - - +
188E GLU* 1.3 81.9 - - - +
190E TRP* 1.3 66.6 + - - +
192E LYS* 3.7 6.9 - - - +
193E ALA* 3.1 33.4 + - + +
194E PHE* 3.5 31.4 - + - -
205E PHE* 4.6 4.0 - + - -
208E ALA* 4.1 6.5 - - + -
209E LEU* 3.7 39.7 - - + -
212E VAL* 3.9 22.9 - - + -
241E PHE* 3.6 18.8 - + - -
251E TRP* 3.4 44.6 - + + +
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Residues in contact with TRP 190 (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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181E ILE* 4.3 5.8 - - + -
186E ALA 3.2 5.8 + - - +
187E ALA 4.2 3.1 - - - +
189E PHE* 1.3 86.9 - - - +
191E ARG* 1.3 87.8 + - + +
194E PHE* 2.8 55.8 + + + +
195E GLY 4.3 2.4 + - - -
197E LYS 2.9 29.4 + - - -
198E THR 3.9 5.8 - - - -
199E ILE 4.4 1.1 - - - -
200E VAL* 4.5 11.7 - - + -
205E PHE* 3.8 16.4 - + - -
236E ILE* 3.2 26.2 - - + -
238E VAL* 3.4 31.6 - - + +
241E PHE* 3.5 51.4 - + + -
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Residues in contact with ARG 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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345A GLN* 3.8 42.2 - - + +
176E GLY 3.6 16.6 + - - -
177E ASP 3.6 24.7 + - - -
178E THR* 4.3 2.4 - - - +
179E PHE 2.6 30.1 + - - +
180E ARG* 4.9 0.2 - - - +
181E ILE* 4.0 10.0 - - + +
187E ALA* 3.3 17.0 - - + +
188E GLU* 3.2 2.9 + - - +
190E TRP* 1.3 96.5 - - + +
192E LYS* 1.3 60.3 + - - +
193E ALA 2.8 10.8 + - - -
195E GLY* 2.9 45.4 + - - +
196E GLU* 4.2 6.3 + - - +
197E LYS 3.9 6.5 + - - -
238E VAL* 4.1 4.9 - - - +
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Residues in contact with LYS 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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345A GLN* 5.7 0.2 - - - +
71C GLN* 4.1 19.5 - - - -
188E GLU* 2.7 48.8 + - + +
189E PHE* 3.8 6.7 - - - +
191E ARG* 1.3 72.3 - - - +
193E ALA* 1.3 56.9 + - + +
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Residues in contact with ALA 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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189E PHE* 3.1 23.7 + - + +
190E TRP 4.3 0.4 - - - +
191E ARG 2.8 2.6 + - - -
192E LYS* 1.3 80.2 - - + +
194E PHE* 1.3 81.9 + - + +
195E GLY 3.5 1.6 - - - -
208E ALA* 4.8 8.7 - - + -
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Residues in contact with PHE 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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189E PHE* 3.5 31.6 - + - -
190E TRP* 2.8 58.2 + + - +
193E ALA* 1.3 81.3 - - + +
195E GLY* 1.3 64.7 + - - +
196E GLU 3.2 0.2 + - - -
197E LYS* 3.1 36.2 + - + +
200E VAL* 3.6 29.2 - - + -
204E SER* 3.9 11.7 - - - -
205E PHE* 4.0 21.5 - + - -
208E ALA* 3.6 33.2 - - + -
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Residues in contact with GLY 195 (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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190E TRP* 4.3 2.1 - - - +
191E ARG* 2.9 47.7 + - - +
193E ALA 3.5 2.0 - - - -
194E PHE* 1.3 76.4 - - - +
196E GLU* 1.3 59.7 + - - -
197E LYS 3.3 0.6 + - - -
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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