Contacts of the helix formed by residues 183 - 199 (chain E) in PDB entry 6XAV
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 GLY 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 LYS 3.8 1.0 - - - -
182E ALA* 1.3 80.2 - - - +
184E LYS* 1.3 65.6 + - - +
185E THR 3.4 3.4 - - - -
186E MET* 3.9 10.9 + - - +
187E LEU* 3.3 25.3 + - - +
345E LEU* 5.2 2.6 - - - +
355E PHE* 4.4 13.8 - - - -
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Residues in contact with LYS 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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366D ARG* 5.9 2.6 - - - +
176E ILE* 5.5 2.0 - - + -
178E ALA* 3.7 31.6 - - + +
179E PRO 3.9 10.5 + - - -
180E PRO* 4.3 6.7 - - - +
181E LYS 4.4 5.5 - - - +
182E ALA* 4.7 2.5 - - + +
183E GLY* 1.3 78.6 - - - +
185E THR* 1.3 61.1 + - - +
187E LEU* 3.8 5.5 - - - +
188E LEU* 2.9 31.5 + - - +
265E ASP* 4.6 7.0 - - + +
318E THR* 3.9 36.8 - - + +
319E ALA 4.4 1.1 - - - +
320E LEU* 3.7 32.3 - - + +
345E LEU* 4.9 4.7 - - + -
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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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367D LYS* 5.1 17.5 - - - +
183E GLY* 3.4 1.0 - - - -
184E LYS* 1.3 75.4 - - - +
186E MET* 1.3 63.4 + - - +
188E LEU* 3.2 4.6 + - - +
189E GLN* 2.9 56.7 + - + +
215E GLU* 3.3 37.7 + - + +
218E GLU* 5.2 6.1 - - - +
219E MET* 5.0 7.1 - - + +
265E ASP* 5.5 1.8 - - - -
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Residues in contact with MET 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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367D LYS* 4.3 22.9 - - - +
183E GLY* 3.9 11.0 + - - +
184E LYS 3.5 0.2 - - - -
185E THR* 1.3 77.3 - - - +
187E LEU* 1.3 62.0 + - - +
189E GLN* 3.6 20.9 + - + +
190E ASN* 3.1 24.3 + - - +
218E GLU* 5.5 3.4 - - - +
355E PHE* 6.5 1.8 - - + -
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Residues in contact with LEU 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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158E THR* 3.9 25.1 - - + +
162E LEU* 4.8 3.4 - - + -
176E ILE* 3.7 23.3 - - + -
183E GLY 3.3 16.7 + - - +
184E LYS* 3.8 5.6 - - - +
185E THR 3.2 0.8 - - - -
186E MET* 1.3 79.0 - - - +
188E LEU* 1.3 63.7 + - - +
190E ASN* 3.4 6.4 + - - +
191E ILE* 3.1 49.4 + - + +
343E LEU* 4.8 7.4 - - + -
345E LEU* 4.2 31.0 - - + -
356E PRO* 5.2 4.0 - - + -
358E ILE* 4.9 11.9 - - + -
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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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176E ILE* 5.5 1.3 - - + -
184E LYS 2.9 18.3 + - - +
185E THR* 3.7 4.9 - - - +
187E LEU* 1.3 76.1 - - - +
189E GLN* 1.3 60.6 + - + +
191E ILE* 3.2 15.3 + - + +
192E ALA* 2.9 24.2 + - + +
206E VAL* 4.2 18.2 - - + -
208E LEU* 6.2 0.9 - - + -
219E MET* 4.3 13.9 - - + -
263E LEU* 3.7 48.5 - - + +
265E ASP* 3.3 31.0 - - - +
316E ILE* 4.7 5.4 - - + +
318E THR* 5.3 5.8 - - + -
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Residues in contact with GLN 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* 2.9 40.3 + - - +
186E MET* 4.0 21.5 - - + +
188E LEU* 1.3 76.4 - - - +
190E ASN* 1.3 57.5 + - - +
192E ALA* 3.4 6.4 + - - +
193E GLN* 3.0 36.5 + - - +
215E GLU 5.8 0.2 + - - -
218E GLU* 4.1 28.1 + - - +
219E MET* 3.7 30.5 - - + +
222E LEU* 3.4 35.1 - - + +
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Residues in contact with ASN 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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149E ARG* 3.2 17.4 + - - +
155E GLU* 2.3 42.7 + - - +
158E THR* 3.4 27.9 + - + -
159E ALA* 4.4 6.2 - - - +
186E MET 3.1 18.3 + - - +
187E LEU* 3.7 8.3 - - - +
188E LEU 3.2 0.4 - - - -
189E GLN* 1.3 77.5 - - - +
191E ILE* 1.3 56.8 - - + +
193E GLN* 4.7 3.8 - - - -
194E SER* 2.8 39.8 + - - -
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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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147E MET* 3.6 25.4 - - + +
158E THR* 6.0 2.0 - - + -
159E ALA* 6.4 1.6 - - + -
162E LEU* 4.0 21.5 - - + -
168E ILE* 5.3 4.7 - - + -
176E ILE* 4.3 11.9 - - + -
187E LEU* 3.1 36.1 + - + +
188E LEU* 3.2 12.5 + - + +
190E ASN* 1.3 75.5 - - + +
192E ALA* 1.3 59.7 + - - +
194E SER 3.3 0.2 + - - -
195E ILE* 2.9 46.4 + - + +
263E LEU* 4.3 16.6 - - + -
316E ILE* 4.5 13.2 - - + -
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Residues in contact with ALA 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* 2.9 17.6 + - + +
189E GLN* 3.8 5.6 - - - +
190E ASN 3.3 0.2 - - - -
191E ILE* 1.3 78.3 - - - +
193E GLN* 1.3 61.8 + - - +
195E ILE* 3.6 0.4 + - - -
196E ALA* 3.1 20.8 + - - +
204E LEU* 3.5 32.1 - - + +
206E VAL* 4.6 4.9 - - + -
223E VAL* 3.9 21.1 - - + -
263E LEU* 4.0 15.3 - - + -
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Residues in contact with GLN 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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149E ARG* 3.4 20.8 + - - +
155E GLU* 4.8 12.8 - - - +
189E GLN* 3.0 21.8 + - - +
190E ASN* 4.8 2.6 - - - -
192E ALA* 1.3 74.7 - - - +
194E SER* 1.3 60.2 + - - +
196E ALA* 3.6 3.7 + - - +
197E TYR* 3.0 31.9 + - - +
222E LEU* 3.3 39.9 + - + +
223E VAL* 5.0 6.3 - - + -
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Residues in contact with SER 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E ARG 5.1 0.3 - - - +
147E MET* 3.3 42.2 + - - -
149E ARG* 2.9 26.9 + - - +
159E ALA* 3.8 5.6 - - - +
190E ASN* 2.8 26.0 + - - -
193E GLN* 1.3 78.8 - - - +
195E ILE* 1.3 57.0 + - - +
198E ASN* 3.0 35.9 + - - +
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Residues in contact with ILE 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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145E LEU* 5.8 4.3 - - + -
147E MET* 3.7 21.8 - - + -
168E ILE* 6.4 1.8 - - + -
191E ILE* 2.9 37.9 + - + +
192E ALA* 4.1 3.6 - - - +
194E SER* 1.3 74.8 - - - +
196E ALA* 1.3 61.7 + - - +
198E ASN* 5.1 0.9 - - - -
199E HIS* 2.8 51.7 + - + +
202E CYS* 4.5 9.2 - - + +
204E LEU* 4.8 15.7 - - + -
261E ILE* 3.7 47.8 - - + -
263E LEU* 5.1 0.9 - - + -
314E THR* 6.0 1.1 - - + -
316E ILE* 6.2 1.3 - - + -
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Residues in contact with ALA 196 (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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192E ALA 3.1 17.9 + - - +
193E GLN* 4.2 4.3 - - - +
195E ILE* 1.3 79.6 - - - +
197E TYR* 1.3 62.0 + - - +
199E HIS 4.2 4.0 - - - -
200E PRO* 3.5 24.2 - - - +
202E CYS 5.9 1.3 - - - -
204E LEU* 4.4 14.6 - - + -
224E LYS* 4.9 15.0 - - + +
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Residues in contact with TYR 197 (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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149E ARG* 3.9 33.2 - - + +
151E ASN* 4.7 16.0 + - + +
193E GLN 3.0 20.2 + - - +
194E SER 4.1 0.2 - - - +
196E ALA* 1.3 79.7 - - - +
198E ASN* 1.3 83.5 + - - +
200E PRO* 4.1 6.2 - - - +
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Residues in contact with ASN 198 (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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146E ARG* 2.7 23.4 + - - +
147E MET 3.4 4.4 + - - -
148E GLU 2.9 27.9 + - - -
149E ARG* 3.3 13.0 - - - +
194E SER 3.0 18.7 + - - +
197E TYR* 1.3 96.3 - - - +
199E HIS* 1.3 79.6 + - + +
200E PRO* 3.4 7.8 - - - +
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Residues in contact with HIS 199 (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 ARG 3.8 12.1 - - - -
145E LEU* 3.4 46.6 - - + +
146E ARG* 3.4 14.9 + - + +
147E MET* 6.2 1.1 - - - -
170E ARG* 3.8 12.2 + - - -
195E ILE* 2.8 33.5 + - + +
196E ALA* 4.2 0.7 - - - -
198E ASN* 1.3 88.0 + - + +
200E PRO* 1.3 66.4 - - - +
201E ASP* 3.2 14.1 + - - +
202E CYS* 3.4 27.1 + - + +
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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