Contacts of the helix formed by residues 285 - 299 (chain A) in PDB entry 3Q36
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 PRO 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A SER 3.7 4.9 - - - +
284A PHE* 1.3 89.0 - - + +
286A PRO* 1.3 78.4 - - + +
287A CYS* 3.1 20.4 + - - -
288A MET* 3.2 15.0 + - + -
289A ARG* 3.0 15.8 + - - +
312A PHE* 4.2 3.6 - - + -
427A TYR* 4.8 0.4 - - - -
444A PRO* 3.9 23.8 - - + +
447A PHE* 3.6 23.3 - - + -
458A SF4 3.6 25.1 - - - -
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Residues in contact with PRO 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A PRO* 1.3 86.2 - - + +
287A CYS* 1.3 61.9 + - - +
289A ARG* 3.9 7.0 - - + +
290A GLN* 3.1 25.3 + - - +
385A PRO* 3.6 17.5 - - + +
386A PHE* 3.2 37.9 - - + -
394A LEU* 6.4 0.4 - - + -
398A LEU* 5.7 2.0 - - + -
401A TYR* 4.3 19.7 + - + +
424A CYS* 3.9 5.4 - - - -
427A TYR* 3.4 32.3 - - + -
458A SF4 4.1 2.5 - - - -
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Residues in contact with CYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A PRO* 3.8 6.5 - - - -
286A PRO* 1.3 79.3 - - - +
288A MET* 1.3 97.2 + - - +
290A GLN* 3.6 5.0 + - - +
291A LEU* 3.2 27.9 + - - +
308A GLN* 3.6 7.4 - - - +
381A TYR 4.6 0.3 - - - +
383A GLY 3.3 26.0 - - - +
385A PRO* 3.5 16.1 - - + +
444A PRO* 4.5 2.0 - - - -
458A SF4 2.4 35.5 - - - -
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Residues in contact with MET 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A PHE* 3.8 14.7 - - + -
285A PRO* 3.2 7.2 + - + +
287A CYS* 1.3 86.4 - - - +
289A ARG* 1.3 61.1 + - - +
291A LEU* 3.7 10.7 - - - +
292A HIS* 2.9 30.5 + - - +
308A GLN* 3.6 36.3 - - + +
309A TYR* 4.1 5.9 - - + -
312A PHE* 3.3 69.8 - - + -
365A PHE* 5.3 3.8 - - + +
370A ILE* 4.3 2.5 - - + -
444A PRO* 3.8 20.2 - - + -
445A ASN* 5.6 0.2 - - - +
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A SER* 3.5 28.3 + - - +
281A THR* 3.9 34.6 + - - +
284A PHE* 3.8 10.4 - - + +
285A PRO 3.0 16.6 + - - +
286A PRO* 3.9 6.3 - - + +
288A MET* 1.3 76.4 - - - +
290A GLN* 1.3 56.9 + - - +
292A HIS* 3.4 3.7 + - - +
293A LYS* 3.0 27.8 + - + +
400A SER 5.1 2.0 + - - -
401A TYR* 3.1 59.0 + - + +
427A TYR* 3.3 23.9 + - - -
431A ILE* 5.7 2.0 - - - +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A PRO 3.1 11.6 + - - +
287A CYS* 3.6 4.7 + - - +
289A ARG* 1.3 78.0 - - - +
291A LEU* 1.3 61.5 + - - +
293A LYS* 3.2 6.7 + - + +
294A ALA* 2.8 31.6 + - - +
381A TYR* 3.6 29.1 + - + +
382A HIS 5.4 1.6 + - - -
383A GLY 5.4 1.4 + - - -
385A PRO* 3.5 32.4 - - - +
389A SER* 4.1 13.4 + - - -
397A LYS* 3.7 37.6 - - - +
401A TYR* 4.2 4.5 + - - +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A CYS 3.2 14.2 + - - +
288A MET* 3.3 8.0 + - - +
290A GLN* 1.3 79.1 - - - +
292A HIS* 1.3 63.1 + - - +
294A ALA* 3.4 3.1 + - - +
295A LEU* 2.9 25.7 + - - +
301A LEU* 3.9 10.9 - - + +
305A GLY* 4.2 11.9 - - - +
308A GLN* 3.6 32.8 - - + +
309A TYR* 3.7 41.1 - - + +
381A TYR* 3.0 40.8 - - + +
382A HIS* 3.5 5.4 - - + +
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Residues in contact with HIS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ILE* 3.4 20.6 - - + -
277A ASP* 2.8 24.3 + - - -
280A SER* 2.9 29.5 + - - +
284A PHE* 4.3 1.1 - - + -
288A MET 2.9 15.5 + - - +
289A ARG 3.7 5.2 - - - +
291A LEU* 1.3 76.9 - - - +
293A LYS* 1.3 64.8 + - - +
295A LEU* 3.4 3.4 + - + +
296A ARG* 3.0 58.3 + - + +
309A TYR* 2.8 35.6 + - - +
326A PHE* 4.1 6.3 - + - -
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Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ARG* 3.0 15.0 + - + +
290A GLN* 3.4 11.2 - - - +
291A LEU 3.2 0.2 - - - -
292A HIS* 1.3 76.7 - - - +
294A ALA* 1.3 66.9 + - - +
296A ARG* 2.9 16.7 + - + +
297A GLU* 3.0 49.2 + - + +
397A LYS* 4.6 19.6 - - - +
401A TYR* 6.3 1.2 - - - -
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A GLN 2.8 19.5 + - - +
291A LEU 3.8 0.7 - - - +
293A LYS* 1.3 73.6 - - - +
295A LEU* 1.3 56.2 + - - +
297A GLU* 4.8 7.0 - - - -
298A ASN* 3.0 37.4 + - - +
300A HIS 4.0 0.9 - - - +
301A LEU* 3.8 11.9 - - + -
381A TYR* 3.5 45.5 - - + -
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A LEU 2.9 18.1 + - - +
292A HIS* 3.6 5.8 - - - +
293A LYS 3.1 0.2 - - - -
294A ALA* 1.3 77.9 - - - +
296A ARG* 1.3 59.4 + - - +
299A HIS* 2.8 31.9 + - - -
300A HIS 4.0 7.6 - - - +
301A LEU* 3.7 27.1 - - + +
309A TYR* 4.3 8.1 - - + -
326A PHE* 3.6 38.8 - - + -
327A TRP* 3.9 9.9 - - + -
330A GLU* 3.6 22.1 - - + +
331A PHE* 3.8 26.9 - - + -
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Residues in contact with ARG 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LEU 4.6 6.7 + - - -
276A ILE* 4.4 7.5 - - - +
277A ASP* 2.9 32.2 + - - +
292A HIS* 3.0 47.6 + - + +
293A LYS* 2.9 8.1 + - + +
295A LEU* 1.3 77.8 - - + +
297A GLU* 1.3 61.9 + - + +
299A HIS* 3.5 20.3 + - - -
326A PHE* 3.8 22.5 - - - -
329A GLN* 4.1 13.7 + - - +
330A GLU* 2.6 43.2 + - - +
333A LYS* 4.4 6.7 - - - +
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Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A LYS* 3.0 51.0 + - + +
294A ALA* 4.2 4.2 - - - +
296A ARG* 1.3 80.4 - - + +
298A ASN* 1.3 75.8 + - - +
299A HIS* 3.4 12.6 + - - -
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Residues in contact with ASN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ALA* 3.0 19.5 + - - +
297A GLU* 1.3 91.1 + - - +
299A HIS* 1.3 74.0 + - - +
300A HIS* 2.8 20.1 + - + +
334A GLY* 5.6 0.3 - - - -
381A TYR* 3.8 29.1 + - - -
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Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 2.8 15.6 + - - -
296A ARG 3.5 16.1 + - - -
297A GLU 3.8 13.7 + - - -
298A ASN* 1.3 78.1 - - - +
300A HIS* 1.3 61.2 + - - +
330A GLU* 3.1 38.7 + - - +
331A PHE* 3.7 16.5 - - - +
333A LYS* 3.2 44.1 + - + +
334A GLY* 3.8 16.6 - - - +
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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