Contacts of the helix formed by residues 281 - 287 (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 MET 281 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308C PHE* 6.1 0.2 - - + -
69T GLY 5.0 0.9 - - - +
72T ALA* 3.6 45.1 - - + +
73T ARG* 3.6 8.1 - - + +
76T GLY* 5.6 0.9 - - - -
228T TYR* 3.6 26.2 - - + +
279T VAL 3.8 0.2 + - - -
280T ASP* 1.3 71.7 - - - +
282T MET* 1.3 58.3 + - - +
284T LEU* 3.4 17.0 + - + +
285T TYR* 2.8 26.2 + - - +
312T MET* 3.4 34.2 + - + +
315T TYR* 3.0 33.9 + - + -
317T LEU* 4.1 21.8 - - - -
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Residues in contact with MET 282 (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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280T ASP* 3.1 9.0 + - - +
281T MET* 1.3 75.1 - - - +
283T GLU* 1.3 67.5 + - - +
284T LEU 3.1 0.2 - - - -
285T TYR* 3.0 29.9 + - + +
286T ASN* 2.9 51.4 + - - +
305T MET* 5.5 6.7 - - + +
308T LEU* 4.6 6.7 - - + -
309T GLU* 3.2 46.0 - - + +
312T MET* 3.6 31.7 + - + +
313T ARG* 4.0 16.4 - - - +
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Residues in contact with GLU 283 (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* 4.4 7.8 - - - +
278T ALA 5.2 0.3 - - - +
279T VAL* 4.2 18.3 - - + +
280T ASP* 2.8 42.4 + - - +
282T MET* 1.3 72.3 - - - +
284T LEU* 1.3 61.0 + - - +
286T ASN* 3.4 6.2 + - - +
287T ARG* 2.9 53.8 + - + +
313T ARG* 3.8 8.8 - - - +
334T TYR* 4.9 1.1 - - - +
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Residues in contact with LEU 284 (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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72T ALA* 4.0 21.8 - - + +
75T HIS* 5.2 1.3 - - + -
76T GLY* 4.2 10.8 - - - +
279T VAL* 4.2 12.2 - - + +
280T ASP 3.0 11.4 + - - +
281T MET* 3.4 21.5 - - + +
282T MET 3.1 0.2 - - - -
283T GLU* 1.3 73.7 - - - +
285T TYR* 1.3 65.0 + - - +
287T ARG* 3.1 12.5 + - - +
288T LEU* 3.3 27.8 + - + +
317T LEU* 3.6 33.7 - - + -
334T TYR* 3.6 38.0 - - + -
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Residues in contact with TYR 285 (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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68T ARG* 3.4 43.9 + - + -
71T PHE* 5.7 2.9 - + - -
72T ALA* 4.4 6.7 - - + -
281T MET 2.8 15.1 + - - +
282T MET* 3.3 34.1 - - + +
284T LEU* 1.3 77.0 - - - +
286T ASN* 1.3 67.7 + - - +
288T LEU* 3.2 45.1 + - + +
293T VAL* 4.7 13.8 - - + +
296T ILE* 4.9 6.3 - - + +
297T GLU* 3.4 21.2 + - - +
305T MET* 4.5 7.0 - - + -
308T LEU* 4.0 19.5 - - + -
312T MET* 4.1 17.3 - - + -
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Residues in contact with ASN 286 (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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282T MET* 2.9 51.0 + - - +
283T GLU* 3.8 6.3 - - - +
285T TYR* 1.3 82.0 - - - +
287T ARG* 1.3 68.7 + - - +
288T LEU 3.3 4.7 + - - +
293T VAL* 6.3 0.2 - - - -
309T GLU* 5.0 0.6 + - - -
313T ARG* 4.7 8.5 - - - +
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Residues in contact with ARG 287 (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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283T GLU* 2.9 42.5 + - + +
284T LEU 3.1 8.3 + - - +
286T ASN* 1.3 83.9 - - - +
288T LEU* 1.3 64.6 + - - +
289T PRO* 3.8 2.1 - - - +
334T TYR* 3.3 33.3 - - + +
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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