Contacts of the strand formed by residues 198 - 208 (chain E) in PDB entry 1RFU
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 198 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188E SER 5.2 1.4 - - - +
190E LEU 5.4 0.9 - - - +
192E SER* 3.4 20.9 + - - +
194E ARG* 2.8 66.8 + - + +
195E GLY* 3.6 6.1 - - - +
196E SER* 3.1 9.8 + - - +
197E ASP* 1.3 109.1 - - - +
199E LEU* 1.3 63.6 + - - +
200E MET 3.9 0.2 + - - -
222E GLU* 4.4 16.2 - - + -
223E MET 3.1 20.0 - - - +
224E HIS* 3.3 29.5 + + + -
225E LYS* 3.9 6.5 - - - +
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Residues in contact with LEU 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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187E SER* 4.1 17.0 - - - +
188E SER 4.2 16.4 - - - +
192E SER* 4.3 0.7 - - - -
198E TYR* 1.3 73.3 - - - +
200E MET* 1.3 60.0 + - - +
221E MET 3.5 0.5 - - - +
222E GLU* 3.4 2.8 - - - -
223E MET* 2.6 65.6 + - + +
225E LYS* 4.1 30.4 - - + +
4402E ADP 3.9 42.6 - - + +
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Residues in contact with MET 200 (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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165E GLN* 4.1 5.6 - - + +
187E SER* 2.9 23.8 - - - -
188E SER* 3.0 24.7 + - - +
190E LEU* 3.5 39.3 - - + +
191E LEU 4.8 2.2 - - - +
192E SER* 3.7 17.5 - - - +
193E PRO* 3.5 22.7 - - + -
198E TYR 3.9 0.8 + - - -
199E LEU* 1.3 74.8 - - - +
201E ALA* 1.3 63.9 + - - +
202E LEU* 4.8 6.3 - - + -
220E ARG* 3.0 52.7 - - + +
221E MET 3.1 10.8 - - - +
222E GLU* 4.6 1.3 - - + +
223E MET* 4.3 0.2 - - - -
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Residues in contact with ALA 201 (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 VAL* 5.4 2.7 - - + -
185E ILE* 3.3 16.4 - - - +
186E THR* 3.4 18.2 - - - +
200E MET* 1.3 74.5 - - - +
202E LEU* 1.3 62.4 + - - +
220E ARG* 3.4 2.4 - - - -
221E MET* 2.7 55.2 + - + +
223E MET* 4.0 15.3 - - + -
237E PHE* 6.3 0.9 - - + -
260E VAL* 5.9 1.8 - - + -
4402E ADP 5.2 0.2 - - - +
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Residues in contact with LEU 202 (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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165E GLN* 4.2 11.4 - - + +
168E ALA* 3.5 32.5 - - + -
169E LEU* 4.6 3.6 - - + +
172E MET* 3.3 25.5 - - + +
184E VAL* 3.4 4.5 - - - -
185E ILE* 2.8 42.5 + - + +
188E SER* 5.9 0.7 - - - +
190E LEU* 4.2 14.8 - - + -
200E MET* 4.8 7.0 - - + -
201E ALA* 1.3 75.2 - - - +
203E GLY* 1.3 59.8 + - - +
219E ILE 3.3 2.7 - - - +
220E ARG* 3.1 43.7 - - + +
221E MET* 5.1 0.9 - - - -
312E LEU* 4.2 10.8 - - + -
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Residues in contact with GLY 203 (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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172E MET* 4.2 1.3 - - - -
183E VAL 3.3 7.0 - - - -
184E VAL* 4.1 10.3 - - - -
202E LEU* 1.3 75.0 - - - +
204E SER* 1.3 59.2 + - - -
218E ARG* 3.6 1.9 - - - -
219E ILE* 2.7 47.0 + - - +
221E MET* 4.8 1.4 - - - +
252E LEU* 3.1 20.7 - - - +
256E CYS* 5.1 0.7 - - - -
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Residues in contact with SER 204 (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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172E MET* 3.6 27.2 - - - +
173E ASP* 4.6 1.0 + - - -
176E HIS* 2.7 30.0 + - - -
182E THR* 3.4 1.9 - - - -
183E VAL 2.6 40.1 + - - +
203E GLY* 1.3 73.7 - - - -
205E GLN* 1.3 62.8 + - - +
216E THR* 5.2 2.4 - - - +
217E GLN 3.4 5.3 + - - -
218E ARG* 3.6 22.1 + - - +
252E LEU* 3.5 3.7 - - - +
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Residues in contact with GLN 205 (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 HIS* 4.2 2.2 - - - -
181E ASP 3.3 5.4 - - - +
182E THR* 3.6 24.4 + - + +
204E SER* 1.3 75.6 + - - +
206E ARG* 1.3 66.1 + - - +
207E THR* 4.4 13.8 + - - +
215E VAL 4.1 0.4 - - - +
216E THR* 3.5 5.4 - - - +
217E GLN* 2.5 71.6 + - + +
245E THR* 6.3 1.0 - - - -
249E PRO 2.8 27.4 + - - +
250E ASN* 4.8 0.4 - - - -
251E ASN 4.2 0.2 + - - -
252E LEU* 3.4 28.8 + - + +
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Residues in contact with ARG 206 (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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173E ASP* 5.6 6.1 + - - +
176E HIS* 4.2 28.5 - - + +
181E ASP* 2.8 46.3 + - - +
205E GLN* 1.3 76.0 - - - +
207E THR* 1.3 69.6 + - - +
208E ARG* 6.0 5.1 - - + +
214E VAL* 3.7 34.6 - - + +
215E VAL 3.7 4.9 - - - -
216E THR* 4.1 16.6 + - + +
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Residues in contact with THR 207 (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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205E GLN* 4.4 14.4 + - - +
206E ARG* 1.3 77.7 + - - +
208E ARG* 1.3 70.8 + - - +
209E ALA* 4.5 2.2 - - - +
214E VAL* 3.0 7.1 - - - +
215E VAL* 2.7 57.0 + - + +
217E GLN* 5.2 2.3 + - - -
250E ASN* 4.0 19.7 + - - +
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Residues in contact with ARG 208 (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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206E ARG* 6.0 5.7 - - + +
207E THR* 1.3 77.2 - - - +
209E ALA* 1.3 69.0 + - - +
210E PRO* 4.5 0.9 - - - +
212E GLY* 3.3 29.6 + - - -
213E SER 3.5 1.8 - - - -
214E VAL* 3.5 23.5 - - + +
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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