Contacts of the strand formed by residues 214 - 224 (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 VAL 214 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206E ARG* 3.7 29.2 - - + +
207E THR 3.0 8.7 - - - +
208E ARG* 3.5 45.8 - - + +
212E GLY 3.9 2.7 - - - +
213E SER* 1.3 72.4 - - - +
215E VAL* 1.3 63.7 + - - +
216E THR* 3.5 7.8 + - - +
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Residues in contact with VAL 215 (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 4.1 0.5 - - - +
206E ARG* 3.7 1.6 - - - -
207E THR* 2.7 67.9 + - + +
209E ALA* 5.2 7.6 - - + +
213E SER* 3.9 3.6 + - - +
214E VAL* 1.3 71.7 - - - +
216E THR* 1.3 68.4 + - - +
217E GLN* 5.4 10.0 - - + +
250E ASN* 6.0 0.4 - - - +
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Residues in contact with THR 216 (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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204E SER* 5.2 2.2 - - - +
205E GLN 3.5 8.9 + - - +
206E ARG* 4.1 27.1 + - + +
214E VAL* 3.5 8.8 + - - +
215E VAL* 1.3 80.6 + - - +
217E GLN* 1.3 76.0 + - - +
218E ARG* 4.1 20.0 - - + +
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Residues in contact with GLN 217 (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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203E GLY 4.4 1.1 - - - -
204E SER* 3.4 3.8 + - - -
205E GLN* 2.5 72.7 + - + +
207E THR* 5.2 2.4 + - - -
215E VAL* 4.3 10.5 + - + +
216E THR* 1.3 75.7 - - - +
218E ARG* 1.3 64.9 + - - +
219E ILE* 5.7 3.7 - - + +
250E ASN* 3.5 23.8 + - - +
251E ASN* 3.6 4.4 + - - +
252E LEU* 3.1 31.9 - - + +
253E LYS* 4.3 4.9 - - - +
311E VAL* 6.2 2.0 - - + -
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Residues in contact with ARG 218 (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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169E LEU* 3.3 49.0 + - + +
172E MET* 5.2 0.2 - - - -
173E ASP* 2.8 37.8 + - - -
203E GLY 3.6 1.8 - - - -
204E SER* 3.6 28.9 + - - +
216E THR* 4.1 16.2 - - + +
217E GLN* 1.3 77.4 - - - +
219E ILE* 1.3 67.6 + - - +
311E VAL* 3.5 9.1 - - - +
312E LEU* 3.0 45.0 + - + +
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Residues in contact with ILE 219 (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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201E ALA 3.9 0.3 - - - +
202E LEU* 3.3 3.5 - - - +
203E GLY* 2.7 54.9 + - - +
217E GLN* 5.3 3.1 - - + +
218E ARG* 1.3 82.6 - - - +
220E ARG* 1.3 60.0 + - - +
221E MET* 4.0 8.5 - - + -
252E LEU* 3.4 20.6 - - + +
253E LYS* 3.6 28.7 - - + +
256E CYS* 3.4 38.4 - - + -
309E ALA* 4.3 8.3 - - + -
310E THR 3.2 11.4 - - - +
311E VAL* 4.4 10.8 - - + -
312E LEU* 4.3 5.1 - - - +
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Residues in contact with ARG 220 (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* 2.5 33.3 + - - +
193E PRO* 3.1 27.1 - - - +
200E MET* 3.0 34.3 - - + +
201E ALA 3.4 3.8 - - - -
202E LEU* 3.1 23.1 - - + -
219E ILE* 1.3 73.6 - - - +
221E MET* 1.3 70.0 + - - +
222E GLU* 3.7 15.7 + - - -
310E THR* 2.8 55.7 + - - +
312E LEU* 3.8 18.2 - - + +
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Residues in contact with MET 221 (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* 5.6 3.6 - - + -
199E LEU 3.5 0.7 - - - +
200E MET* 3.1 8.1 - - - +
201E ALA* 2.7 65.8 + - + +
202E LEU 5.1 0.7 - - - -
203E GLY* 4.8 3.1 - - - +
219E ILE* 4.0 16.2 - - + +
220E ARG* 1.3 81.9 - - - +
222E GLU* 1.3 67.1 + - - +
223E MET* 3.9 5.8 - - + -
237E PHE* 6.4 0.7 - - + -
256E CYS* 4.0 28.9 - - + +
257E GLU 4.8 0.4 - - - -
260E VAL* 4.0 25.6 - - + -
307E VAL* 4.9 11.0 - - + -
308E GLN 4.8 3.4 - - - +
309E ALA* 3.5 29.4 - - + +
310E THR* 4.9 0.2 - - - -
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Residues in contact with GLU 222 (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 SER* 4.2 9.8 - - - +
193E PRO* 3.6 32.8 - - + +
194E ARG* 3.0 57.2 + - - +
198E TYR* 4.4 14.4 - - + -
199E LEU 3.4 4.7 - - - +
200E MET* 4.8 1.6 - - + -
220E ARG* 3.7 16.7 + - - -
221E MET* 1.3 77.5 - - - +
223E MET* 1.3 61.7 + - - +
307E VAL* 4.2 15.8 - - - +
308E GLN 5.4 2.8 + - - -
310E THR* 5.5 5.0 - - - +
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Residues in contact with MET 223 (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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186E THR 3.5 21.5 - - - +
187E SER* 4.2 1.6 - - - -
198E TYR* 3.1 10.4 - - - -
199E LEU* 2.6 67.4 + - + +
201E ALA* 4.0 16.2 - - + -
221E MET* 4.5 9.4 - - + +
222E GLU* 1.3 76.8 - - - +
224E HIS* 1.3 63.6 + - - +
260E VAL* 3.5 26.2 - - + -
307E VAL* 4.8 7.6 - - + -
4402E ADP 3.1 37.9 - - - +
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Residues in contact with HIS 224 (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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197E ASP* 3.5 16.5 + - + +
198E TYR* 3.3 41.1 + + + -
222E GLU 4.3 0.2 + - - -
223E MET* 1.3 72.1 - - - +
225E LYS* 1.3 70.1 + - - +
226E VAL* 3.6 5.0 + - - +
264E HIS* 4.7 25.3 + - + +
268E GLN* 5.0 8.0 + - - +
4402E ADP 3.2 15.1 - - - -
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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