Contacts of the strand formed by residues 275 - 280 (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 THR 275 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269T LEU* 3.9 4.5 - - - -
273T TRP* 4.3 2.3 - - - +
274T GLU* 1.3 82.3 - - + +
276T ALA* 1.3 62.9 + - - +
277T SER* 6.0 0.4 - - - -
319T TRP 5.3 0.2 + - - -
320T ALA* 3.2 23.8 - - - +
321T THR* 2.7 31.8 + - - +
330T LYS* 3.7 38.2 - - + +
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Residues in contact with ALA 276 (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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265T LYS* 3.7 42.9 - - + +
268T LEU* 4.1 15.9 - - + -
269T LEU* 4.0 14.8 - - + +
275T THR* 1.3 78.0 - - - +
277T SER* 1.3 66.3 + - - +
319T TRP 3.4 9.2 - - - +
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Residues in contact with SER 277 (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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265T LYS* 3.9 6.6 - - - +
275T THR* 6.0 0.5 - - - -
276T ALA* 1.3 78.5 + - - +
278T ALA* 1.3 63.2 + - - +
318T CYS* 3.2 5.0 - - - +
319T TRP* 2.9 69.9 + - - -
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Residues in contact with ALA 278 (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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261T LEU* 3.8 33.3 - - + +
264T GLN* 4.8 0.4 - - + -
265T LYS* 3.7 29.3 + - + +
277T SER* 1.3 77.4 - - - +
279T VAL* 1.3 67.3 + - - +
283T GLU* 5.2 0.3 - - - +
317T LEU 3.4 6.1 - - - -
318T CYS* 3.8 21.3 - - - -
319T TRP* 4.7 0.9 - - - -
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Residues in contact with VAL 279 (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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261T LEU* 3.6 5.8 - - - -
278T ALA* 1.3 78.8 - - - +
280T ASP* 1.3 69.2 + - - +
283T GLU* 4.2 22.2 - - + +
284T LEU* 4.2 24.0 - - + -
316T CYS* 3.3 2.1 - - - +
317T LEU* 2.9 35.1 + - + +
319T TRP* 4.5 8.7 - - + -
334T TYR* 4.0 37.2 - - + +
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Residues in contact with ASP 280 (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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231T VAL* 4.4 6.3 - - + -
232T ASN* 4.8 5.1 + - - +
261T LEU* 3.6 19.8 - - + +
279T VAL* 1.3 75.3 - - - +
281T MET* 1.3 61.9 - - - +
282T MET* 3.1 7.1 + - - +
283T GLU* 2.8 48.1 + - - +
284T LEU* 3.0 10.0 + - - +
312T MET 4.3 2.9 - - - +
313T ARG* 3.0 43.6 + - - +
315T TYR 3.3 14.6 - - - +
316T CYS* 4.1 1.3 - - - +
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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