Contacts of the strand formed by residues 315 - 322 (chain T) in PDB entry 3P71
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 315 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307C TYR* 3.6 2.0 - + - +
308C PHE* 2.9 65.3 + + + -
199T CYS* 4.8 1.3 - - - -
228T TYR* 3.6 20.4 - + + +
229T GLU 3.2 20.9 - - - -
230T GLN* 3.7 21.1 - - + -
231T VAL* 3.3 11.6 - - - +
237T PHE* 5.7 0.7 - + - -
241T MET* 3.1 26.2 - - + +
280T ASP* 3.3 2.9 - - - +
281T MET* 3.0 39.3 + - + -
311T LEU* 3.4 23.1 - - + +
312T MET* 3.2 5.8 + - - +
314T HIS* 1.3 88.5 - - + +
316T CYS* 1.3 61.3 + - - +
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Residues in contact with CYS 316 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228T TYR* 3.4 9.4 - - - -
229T GLU 2.8 43.4 + - - -
231T VAL* 3.8 12.3 - - + -
261T LEU* 3.7 18.8 - - + -
264T GLN* 3.7 24.2 - - - -
279T VAL 3.3 12.8 - - - +
280T ASP* 4.1 0.2 - - - +
281T MET* 4.1 6.7 - - - +
315T TYR* 1.3 77.3 - - - +
317T LEU* 1.3 59.5 + - - +
318T CYS* 3.5 24.7 - - - -
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Residues in contact with LEU 317 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73T ARG 5.2 0.4 - - - +
76T GLY* 3.7 17.0 - - - +
77T VAL* 3.8 27.1 - - + +
80T LEU* 3.7 25.6 - - + -
226T ILE* 4.2 12.3 - - + -
228T TYR* 3.9 20.9 - - + -
278T ALA* 3.4 1.7 - - - -
279T VAL* 2.9 32.4 + - + +
281T MET* 4.1 13.6 - - - -
284T LEU* 3.6 27.6 - - + -
316T CYS* 1.3 72.7 - - - +
318T CYS* 1.3 62.3 + - - +
319T TRP* 3.8 10.3 - - + -
334T TYR* 4.7 5.6 - - + -
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Residues in contact with CYS 318 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226T ILE* 3.5 5.4 - - - +
227T ASN* 2.8 50.2 + - + +
264T GLN* 3.9 16.2 - - + +
268T LEU* 4.0 20.2 - - + -
277T SER 3.2 11.4 - - - +
278T ALA* 3.8 14.6 - - + -
316T CYS* 3.5 30.3 - - - -
317T LEU* 1.3 76.9 - - - +
319T TRP* 1.3 65.8 + - - +
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Residues in contact with TRP 319 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80T LEU* 3.8 28.7 - - + -
224T MET* 3.8 28.0 - - + -
225T PHE 3.1 10.8 - - - +
226T ILE* 4.4 0.9 - - + -
268T LEU* 4.3 3.1 - - - -
275T THR* 4.7 0.5 + - - -
276T ALA* 3.4 1.6 - - - -
277T SER* 2.9 66.9 + - - -
278T ALA 4.6 0.7 - - - -
279T VAL* 4.5 11.4 - - + -
317T LEU* 3.8 17.9 - - + -
318T CYS* 1.3 81.0 - - - +
320T ALA* 1.3 60.6 + - - +
321T THR* 5.0 7.6 - - + -
329T LEU 5.7 0.6 + - - -
332T ILE* 3.0 31.8 + - + +
333T THR* 4.1 14.1 - - + -
334T TYR* 3.6 33.0 - + - -
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Residues in contact with ALA 320 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224T MET* 3.4 2.3 - - - +
225T PHE* 2.9 32.2 + - + +
268T LEU* 3.8 26.0 - - + +
273T TRP* 3.7 28.7 - - + -
275T THR* 3.2 15.3 - - - +
276T ALA* 4.4 0.2 - - + -
319T TRP* 1.3 74.5 - - - +
321T THR* 1.3 70.0 + - - +
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Residues in contact with THR 321 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223T ALA 3.5 8.3 - - - -
224T MET* 4.0 20.6 - - + -
273T TRP* 3.6 5.9 - - - -
274T GLU* 2.9 25.7 + - - -
275T THR* 2.7 35.5 + - - +
319T TRP* 5.0 8.5 - - + -
320T ALA* 1.3 79.1 - - - +
322T LYS* 1.3 61.8 + - - +
324T GLY 5.6 0.4 - - - -
329T LEU* 3.6 39.7 + - + +
330T LYS* 4.2 9.9 + - - +
332T ILE* 5.3 0.2 - - + -
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Residues in contact with LYS 322 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217T ALA* 3.1 21.1 - - + +
220T PHE 3.0 22.7 + - - +
221T GLU* 2.8 38.1 + - - +
222T ARG* 3.4 0.2 - - - -
223T ALA* 3.1 37.2 + - + +
272T GLY 3.4 20.6 - - - +
273T TRP* 4.2 11.7 - - + -
274T GLU* 3.8 28.8 + - + +
321T THR* 1.3 81.4 - - - +
323T GLY* 1.3 67.4 + - - +
324T GLY* 3.2 4.2 + - - +
329T LEU* 5.0 0.2 - - - +
330T LYS* 4.6 0.2 - - - +
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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