Contacts of the helix formed by residues 279 - 292 (chain H) in PDB entry 3Q84
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 ASP 279 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246G LYS* 5.0 1.6 - - - +
79H SER* 3.0 20.0 + - - +
80H LEU* 4.3 1.9 - - - +
277H GLY 3.5 8.9 + - - +
278H ALA* 1.3 76.0 - - - +
280H ALA* 1.3 67.6 + - - +
281H GLN* 3.3 17.4 + - - +
282H GLU* 2.9 40.8 + - + +
283H ASP* 3.4 7.4 + - - -
285H ARG* 4.5 5.7 + - - -
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Residues in contact with ALA 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239G GLU* 4.4 15.7 - - + +
242G LEU* 3.9 33.0 - - + +
243G VAL* 4.2 21.8 - - + +
246G LYS* 5.9 3.0 - - - +
80H LEU* 4.8 3.1 - - - +
278H ALA 4.4 0.2 - - - -
279H ASP* 1.3 74.7 + - - +
281H GLN* 1.3 65.0 + - + +
283H ASP* 3.2 5.6 + - - +
284H LEU* 3.1 25.7 + - - +
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Residues in contact with GLN 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239G GLU* 3.0 32.1 - - - +
279H ASP* 3.3 11.2 + - - +
280H ALA* 1.3 78.2 - - + +
282H GLU* 1.3 63.9 + - - +
284H LEU* 3.4 16.7 + - - +
285H ARG* 3.0 48.5 + - - +
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Residues in contact with GLU 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H SER* 3.7 22.5 - - - -
82H ARG* 5.0 9.3 + - - -
277H GLY 5.2 1.7 - - - +
279H ASP* 2.9 33.4 + - - +
281H GLN* 1.3 77.5 - - - +
283H ASP* 1.3 64.2 + - - +
285H ARG* 3.3 20.8 + - - +
286H TRP* 3.1 21.3 + - + +
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Residues in contact with ASP 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242G LEU* 4.2 11.9 - - + +
77H TYR* 3.8 22.4 - - + +
78H GLY* 3.7 7.4 - - - -
79H SER* 2.8 44.2 + - - -
80H LEU* 3.1 28.2 + - - +
279H ASP 3.7 2.4 - - - +
280H ALA 3.2 6.8 + - - +
282H GLU* 1.3 75.6 - - - +
284H LEU* 1.3 67.5 + - - +
286H TRP* 3.0 8.0 + - - +
287H PHE* 2.8 23.9 + - - +
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Residues in contact with LEU 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G ARG* 4.0 1.3 - - - +
235G GLN* 3.1 63.0 - - + +
238G GLU* 3.7 22.9 - - + -
239G GLU* 3.6 30.7 - - + +
242G LEU* 4.3 4.3 - - + -
77H TYR* 4.8 0.4 - - - +
280H ALA 3.1 12.9 + - - +
281H GLN* 3.7 24.7 - - - +
283H ASP* 1.3 79.8 - - - +
285H ARG* 1.3 63.6 + - + +
287H PHE* 3.4 5.1 + - - +
288H ARG* 3.1 14.7 + - - +
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Residues in contact with ARG 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279H ASP* 4.5 4.4 + - - -
281H GLN* 3.0 37.3 + - - +
282H GLU* 3.5 34.6 + - - +
283H ASP 3.1 0.2 - - - -
284H LEU* 1.3 78.7 - - + +
286H TRP* 1.3 61.2 + - - +
288H ARG* 3.3 11.8 + - - +
289H SER* 3.1 22.8 + - - -
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Residues in contact with TRP 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77H TYR* 3.3 44.4 - + + -
78H GLY* 5.5 3.4 - - - -
282H GLU* 3.1 12.8 + - + +
283H ASP* 3.0 9.3 + - - +
285H ARG* 1.3 75.8 - - - +
287H PHE* 1.3 78.7 + + - +
289H SER* 3.2 6.8 + - - -
290H THR* 2.3 64.0 + - + +
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Residues in contact with PHE 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G ARG* 4.3 9.2 - - + -
28G THR* 3.8 32.5 - - - -
31G ARG* 3.3 52.5 - - + +
231G PHE* 3.9 18.2 - + - -
77H TYR* 4.0 17.7 - + + +
283H ASP 2.8 14.0 + - - +
284H LEU 3.7 2.2 - - - +
286H TRP* 1.3 87.3 - + - +
288H ARG* 1.3 68.6 + - - +
290H THR* 3.5 4.0 - - - -
291H SER* 2.8 45.9 + - - -
292H GLY 3.3 1.9 + - - -
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Residues in contact with ARG 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228G GLU* 2.5 35.9 + - - -
231G PHE* 3.7 35.8 - - + -
232G GLU* 5.0 7.1 + - - -
235G GLN* 4.2 2.0 - - - +
284H LEU 3.1 11.2 + - - +
285H ARG* 3.6 13.5 - - - +
287H PHE* 1.3 78.0 - - - +
289H SER* 1.3 61.9 + - - +
292H GLY* 2.6 31.9 + - - +
293H PRO* 3.7 19.0 + - + +
294H GLY* 3.4 16.7 + - - +
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Residues in contact with SER 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285H ARG 3.1 13.8 + - - -
286H TRP* 3.5 7.9 - - - -
288H ARG* 1.3 84.1 - - - +
290H THR* 1.3 62.5 + - - +
294H GLY* 3.9 13.3 - - - -
295H MSE 3.4 22.7 + - - +
296H PRO* 5.3 0.3 - - - +
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Residues in contact with THR 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286H TRP* 2.3 66.7 + - + +
287H PHE* 3.4 6.2 + - - -
289H SER* 1.3 79.3 - - - +
291H SER* 1.3 64.1 + - - +
295H MSE 3.3 22.5 - - - +
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Residues in contact with SER 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G PHE* 3.7 9.9 - - - -
24G ASN 5.2 0.2 - - - +
27G ARG* 3.2 44.8 + - - +
28G THR* 4.5 6.8 + - - -
287H PHE* 2.8 37.9 + - - -
290H THR* 1.3 81.0 + - - +
292H GLY* 1.3 62.9 + - - +
295H MSE 3.7 3.6 - - - -
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Residues in contact with GLY 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G PHE* 3.0 24.5 - - - +
231G PHE* 4.2 6.7 - - - -
287H PHE 3.3 1.4 + - - -
288H ARG* 2.6 22.1 + - - -
291H SER* 1.3 73.4 - - - +
293H PRO* 1.3 72.0 - - - +
294H GLY 3.0 9.5 + - - -
295H MSE 3.2 12.1 + - - +
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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