Contacts of the strand formed by residues 282 - 291 (chain E) in PDB entry 5TWV
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 GLU 282 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E ALA 3.8 18.5 - - - +
34E ARG* 3.9 2.9 - - - +
35E PHE* 3.8 28.9 + - + +
36E VAL 3.9 5.5 - - - +
219E VAL* 4.1 1.6 - - - +
220E VAL* 3.0 46.1 + - + +
281E LEU* 1.3 83.0 - - - +
283E ILE* 1.3 66.1 + - - +
303E SER* 2.8 31.3 + - - +
304E TYR 3.9 7.0 - - - +
305E LEU* 3.9 30.9 - - + +
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Residues in contact with ILE 283 (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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198E PHE* 5.1 22.0 - - + -
200E LEU* 5.9 3.8 - - + -
217E MET* 5.2 3.1 - - + -
218E GLN 3.5 17.3 - - - +
219E VAL* 4.1 26.5 - - + -
238E ILE* 5.1 11.7 - - + -
267E LEU* 4.7 23.3 - - + -
281E LEU* 4.5 9.9 - - + -
282E GLU* 1.3 79.5 - - - +
284E ILE* 1.3 66.9 + - - +
285E VAL* 4.1 1.3 + - + +
303E SER* 3.5 4.4 + - - -
304E TYR* 3.1 39.2 + - + +
309E ILE* 4.6 17.5 - - + -
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Residues in contact with ILE 284 (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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35E PHE* 3.9 20.0 - - + -
36E VAL* 3.9 20.2 - - + -
217E MET* 3.5 7.4 - - - +
218E GLN* 2.9 58.5 + - + +
220E VAL* 5.0 12.1 - - + -
235E GLN* 4.4 10.8 - - - +
282E GLU 4.2 0.4 - - - -
283E ILE* 1.3 72.9 - - - +
285E VAL* 1.3 62.7 + - - +
286E ILE* 3.9 16.4 - - + +
301E ARG* 6.3 2.0 - - + -
302E THR 3.5 4.9 - - - +
303E SER* 3.6 16.4 - - - +
250G PHE* 4.2 22.2 - - + -
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Residues in contact with VAL 285 (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 PHE* 4.0 25.6 - - + -
200E LEU* 4.0 17.3 - - + -
215E ILE* 4.7 8.5 - - + -
216E HIS 4.4 0.7 - - - -
217E MET* 4.3 26.0 - - + -
283E ILE* 4.5 2.9 - - + +
284E ILE* 1.3 75.7 - - - +
286E ILE* 1.3 62.1 + - - +
300E ALA 3.6 1.0 - - - +
301E ARG* 3.3 28.2 - - - +
302E THR* 2.9 29.8 + - - +
304E TYR* 3.9 22.4 - - + -
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Residues in contact with ILE 286 (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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214E THR 3.8 0.7 - - - +
215E ILE* 3.3 7.1 - - - +
216E HIS* 2.8 62.6 + - + +
218E GLN* 4.4 8.3 - - + +
284E ILE* 3.9 35.2 - - + +
285E VAL* 1.3 75.7 - - - +
287E LEU* 1.3 58.0 + - - +
288E GLU* 3.8 22.6 + - + +
299E GLN* 3.4 21.8 - - + +
301E ARG* 5.3 1.3 - - + -
250G PHE* 4.1 32.8 - - + -
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Residues in contact with LEU 287 (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 LEU* 4.0 41.7 - - + +
183E PHE* 3.7 29.4 - - + -
202E VAL* 4.2 13.9 - - + -
210E ILE* 5.1 7.0 - - + -
213E ALA* 4.9 6.7 - - + -
215E ILE* 3.7 30.7 - - + -
285E VAL* 3.9 0.8 - - + -
286E ILE* 1.3 71.1 - - - +
288E GLU* 1.3 71.2 + - - +
298E THR 3.9 0.2 - - - +
299E GLN* 3.2 10.2 + - - +
300E ALA* 2.9 40.0 + - + +
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Residues in contact with GLU 288 (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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210E ILE* 5.3 0.5 - - - +
213E ALA* 2.7 33.4 - - - +
214E THR* 3.1 36.6 + - - +
216E HIS* 3.5 21.4 + - - -
286E ILE* 3.9 16.3 - - + +
287E LEU* 1.3 82.7 - - - +
289E GLY* 1.3 53.1 + - - +
298E THR* 3.5 10.5 - - - +
299E GLN* 3.9 16.3 - - + +
211G ILE* 3.6 8.6 - - + +
212G SER* 3.1 38.5 + - - -
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Residues in contact with GLY 289 (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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210E ILE* 4.9 5.2 - - - -
211E ILE 4.1 0.7 - - - -
212E SER 4.3 2.7 - - - -
213E ALA* 3.4 20.6 - - - -
288E GLU* 1.3 79.8 - - - +
290E VAL* 1.3 59.8 + - - -
297E THR* 3.1 12.1 - - - -
298E THR* 2.8 36.0 + - - +
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Residues in contact with VAL 290 (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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297C THR* 3.9 20.0 - - - +
210E ILE* 3.1 12.1 - - - -
211E ILE* 2.9 60.9 + - + +
212E SER* 5.3 2.2 - - - -
289E GLY* 1.3 73.7 - - - -
291E VAL* 1.3 73.0 + - - +
294E THR 3.5 8.1 - - - +
295E GLY* 3.2 28.9 - - - +
296E ILE 3.4 8.3 - - - +
297E THR* 3.5 13.9 - - + +
298E THR* 4.9 1.6 - - - +
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Residues in contact with VAL 291 (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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296C ILE* 5.2 2.6 - - - +
297C THR 5.1 2.9 - - - +
174E ALA* 5.4 3.1 - - + -
177E ARG* 4.9 22.9 - - + +
209E MET 4.3 4.5 - - - -
210E ILE* 5.0 2.5 - - - -
211E ILE* 5.0 0.2 - - - +
290E VAL* 1.3 84.9 - - - +
292E GLU* 1.3 61.1 + - - +
293E THR* 3.1 8.1 - - - +
294E THR* 2.7 46.6 + - - +
295E GLY* 4.9 0.2 - - - -
296E ILE 3.5 6.1 + - - +
298E THR* 6.0 1.9 - - + +
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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