Contacts of the helix formed by residues 284 - 293 (chain B) in PDB entry 2P3Z
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 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A GLN* 3.7 14.0 - - - +
120B LEU* 5.2 9.0 - - + -
129B SER* 3.6 27.4 - - - -
134B MET* 3.9 18.6 - - + +
283B GLY* 1.3 82.6 + - - +
285B LEU* 1.3 67.0 + - - +
286B GLN* 3.7 12.3 + - - -
287B SER* 3.1 23.0 + - - -
288B PHE* 3.2 14.9 - - - -
306B CYS 3.1 14.8 + - - -
311B THR* 4.4 4.3 - - - -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B THR* 1.3 74.5 - - - +
286B GLN* 1.3 73.7 + - - +
288B PHE* 3.1 8.3 + - - +
289B ARG* 2.9 25.4 + - + +
311B THR* 4.0 11.5 - - + +
314B GLU* 3.5 64.4 - - + +
315B ILE* 3.8 12.8 - - + +
318B LEU* 4.1 13.2 - - + -
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Residues in contact with GLN 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A GLN* 3.8 29.5 - - + +
259A GLN* 4.1 30.6 - - + +
261A GLU* 5.1 0.9 - - - +
284B THR* 3.8 15.0 + - - +
285B LEU* 1.3 96.0 + - - +
287B SER* 1.3 61.7 + - - +
289B ARG* 3.3 10.1 + - - +
290B THR* 3.3 24.6 + - - -
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLN* 3.8 14.8 - - - +
129B SER* 4.2 6.6 + - - -
260B TYR* 3.6 21.9 + - - -
282B HIS* 4.6 8.1 - - - -
283B GLY 2.9 32.8 + - - -
284B THR* 3.1 9.5 + - - -
286B GLN* 1.3 76.7 - - - +
288B PHE* 1.3 58.9 + - - +
290B THR* 3.2 6.5 + - - -
291B LEU* 2.8 28.2 + - - +
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Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B GLY* 3.4 34.1 - - - -
282B HIS* 3.5 33.7 - - + -
283B GLY* 3.9 2.2 - - - -
284B THR 3.2 21.2 + - - -
285B LEU 3.1 8.7 + - - +
287B SER* 1.3 75.7 - - - +
289B ARG* 1.4 59.2 + - - +
291B LEU* 3.6 9.6 - - + +
292B ALA* 2.8 31.5 + - - +
299B MET* 3.6 21.5 - - + +
301B PRO* 3.6 31.0 - - + -
306B CYS* 4.0 6.5 - - + -
315B ILE* 3.3 38.4 - - + -
318B LEU* 3.6 9.6 - - + -
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Residues in contact with ARG 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLN* 6.2 0.6 - - - +
261A GLU* 3.5 49.3 + - - +
262A GLY 5.2 1.2 - - - +
285B LEU* 2.9 13.6 + - + +
286B GLN* 3.3 12.7 + - - +
288B PHE* 1.4 74.5 - - - +
290B THR* 1.3 65.2 + - - +
292B ALA* 3.3 4.0 + - - +
293B GLU* 2.9 58.7 + - + +
318B LEU* 3.5 22.3 - - + +
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLN 4.4 5.5 + - - -
260A TYR* 4.6 10.2 - - + -
261A GLU* 2.7 33.1 + - - +
290A THR* 5.5 3.1 - - + -
260B TYR* 3.7 39.3 - - + -
264B ARG* 5.1 1.6 + - - +
286B GLN 3.3 11.4 + - - -
287B SER* 3.2 9.7 + - - -
289B ARG* 1.3 75.1 - - - +
291B LEU* 1.3 67.4 + - - +
293B GLU* 3.2 14.3 + - + +
294B THR* 3.4 12.0 + - - +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B TYR* 3.8 15.4 - - + -
263B TYR* 4.6 10.8 - - + -
278B SER* 4.1 7.6 - - - +
279B GLY* 3.7 19.1 - - - +
282B HIS* 3.7 41.3 - - + +
287B SER 2.8 16.6 + - - +
288B PHE* 3.6 14.1 - - + +
289B ARG 3.2 0.2 - - - -
290B THR* 1.3 76.9 - - - +
292B ALA* 1.3 61.4 + - - +
294B THR* 2.6 33.8 + - + +
296B ILE* 3.7 24.9 - - + +
299B MET* 4.0 16.8 - - + -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B PHE 2.8 20.2 + - - +
289B ARG 3.6 4.7 - - - +
291B LEU* 1.3 72.8 - - - +
293B GLU* 1.3 62.2 + - + +
295B GLY* 3.2 11.3 + - - -
296B ILE* 4.5 5.0 + - - +
299B MET* 3.7 24.4 - - + -
318B LEU* 4.5 7.6 - - + -
322B ARG* 3.1 45.4 + - - +
324B GLN* 4.8 4.8 - - - +
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Residues in contact with GLU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A GLU* 4.4 9.6 - - - +
264B ARG* 3.1 19.4 + - - +
289B ARG* 2.9 57.0 + - + +
290B THR* 3.7 7.9 - - - +
291B LEU 3.1 0.8 - - - -
292B ALA* 1.3 75.9 - - + +
294B THR* 1.3 56.7 + - - +
295B GLY* 3.1 6.5 + - - -
322B ARG* 4.1 19.8 + - - +
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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