Contacts of the helix formed by residues 295 - 309 (chain D) in PDB entry 4G5O
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 295 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C GLN* 5.3 0.2 - - - +
321C THR 3.9 17.0 - - - +
322C HIS* 4.6 2.2 - - + +
323C PHE* 4.0 14.0 - - + -
402C CIT 3.4 35.4 - - - +
278D ILE* 4.3 3.1 - - - -
293D SER* 3.2 22.9 + - - +
294D ASN* 1.3 80.3 - - - +
296D TYR* 1.3 64.5 + - - +
297D GLU* 3.8 8.3 - - - -
298D GLU* 3.3 17.0 + - - +
299D ALA* 3.2 22.3 + - - +
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Residues in contact with TYR 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C TYR* 4.2 11.0 - + - -
297C GLU* 2.7 45.0 + - + +
402C CIT 2.9 18.4 + - - +
227D LEU* 5.5 1.1 - - + -
271D LYS* 3.7 35.5 - - + +
274D PHE* 3.6 28.2 - + - -
275D GLU* 3.3 41.1 - - + -
278D ILE* 3.8 15.3 - - + +
295D THR* 1.3 72.0 - - - +
297D GLU* 1.3 70.2 + - - +
299D ALA* 3.8 3.0 - - - +
300D ALA* 2.8 42.1 + - + +
323D PHE* 4.5 2.1 - - - +
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Residues in contact with GLU 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C LYS* 4.2 4.0 + - - +
296C TYR* 2.6 44.4 + - + +
297C GLU* 3.9 11.4 - - - +
300C ALA* 4.1 7.4 - - + -
301C ALA* 4.1 2.4 - - - +
323C PHE* 3.3 47.0 - - + +
402C CIT 2.9 34.4 - - - +
275D GLU* 5.9 0.2 - - - -
295D THR* 3.2 0.6 - - - -
296D TYR* 1.3 89.8 + - + +
298D GLU* 1.3 62.0 + - - +
300D ALA* 3.8 4.0 - - - +
301D ALA* 3.3 22.5 + - - +
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Residues in contact with GLU 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C ALA* 4.7 9.9 - - + -
304C GLN* 3.4 26.3 + - - +
308C GLU* 5.5 1.5 - - - +
323C PHE* 4.9 0.2 - - - -
290D TYR* 3.6 11.5 - - + +
292D GLY* 3.2 17.0 - - - -
293D SER* 2.5 43.3 + - - +
295D THR* 3.3 15.6 + - - +
297D GLU* 1.3 76.9 - - - +
299D ALA* 1.3 61.2 + - - +
301D ALA* 3.5 2.3 + - + +
302D TYR* 3.0 27.9 + - + +
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Residues in contact with ALA 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D PHE* 3.8 21.1 - - + -
278D ILE* 3.9 11.0 - - + -
283D LEU* 3.8 19.0 - - + +
290D TYR* 3.7 10.9 + - + +
293D SER 5.1 1.3 - - - +
294D ASN* 5.9 0.7 - - - +
295D THR 3.2 19.7 + - - +
296D TYR 3.8 2.0 - - - +
298D GLU* 1.3 74.8 - - - +
300D ALA* 1.3 66.0 + - - +
302D TYR* 3.1 3.5 + - - +
303D ILE* 3.1 28.3 + - - +
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Residues in contact with ALA 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C GLU* 3.9 17.9 - - + -
227D LEU* 5.6 2.0 - - + -
274D PHE* 4.0 9.5 - - + -
296D TYR* 2.8 27.8 + - + +
297D GLU 3.8 4.7 - - - +
299D ALA* 1.3 76.0 - - - +
301D ALA* 1.3 60.9 + - - +
303D ILE* 3.2 9.0 + - - +
304D GLN 3.1 18.2 + - - -
323D PHE* 3.6 32.1 - - + -
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Residues in contact with ALA 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C GLU 4.3 5.8 - - - +
298C GLU* 4.6 10.8 - - + -
301C ALA* 3.7 22.0 - - + -
297D GLU 3.3 14.9 + - - +
298D GLU* 3.8 4.0 - - + +
299D ALA 3.3 0.4 - - - -
300D ALA* 1.3 80.1 - - - +
302D TYR* 1.3 61.8 + - - +
304D GLN* 3.3 14.8 + - - +
305D CYS* 3.1 27.8 + - - -
323D PHE* 4.8 2.2 - - - -
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Residues in contact with TYR 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D LEU* 3.7 12.3 - - + -
287D TYR* 3.7 27.6 - + + -
289D GLU* 2.9 33.4 + - - +
290D TYR* 3.3 44.9 - + + -
291D THR 5.5 0.2 - - - -
298D GLU* 3.0 14.3 + - + +
299D ALA 3.1 8.0 + - - +
301D ALA* 1.3 77.2 - - - +
303D ILE* 1.3 61.3 + - - +
305D CYS* 3.2 9.7 + - + +
306D GLN* 3.0 54.6 + - + +
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Residues in contact with ILE 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D LEU* 3.7 26.9 - - + -
243D MET* 4.4 13.5 - - + -
268D LEU* 4.4 5.4 - - + -
274D PHE* 3.5 38.4 - - + -
283D LEU* 4.0 13.7 - - + -
287D TYR* 4.1 19.1 - - + +
299D ALA 3.1 10.5 + - - +
300D ALA* 3.2 6.9 + - - +
302D TYR* 1.3 75.1 - - - +
304D GLN* 1.3 63.3 + - - +
306D GLN* 3.2 10.2 + - - +
307D PHE* 3.0 44.4 + - + -
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Residues in contact with GLN 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C SER* 4.2 5.8 + - - -
295C THR* 4.5 0.4 + - - +
298C GLU* 3.3 44.8 + - - +
266D LEU* 5.5 0.4 - - - -
268D LEU* 4.0 8.8 - - + +
300D ALA 3.1 12.9 + - - +
301D ALA* 3.4 11.3 - - - +
303D ILE* 1.3 76.5 - - - +
305D CYS* 1.3 59.3 + - - +
307D PHE* 3.3 4.6 + - - +
308D GLU* 2.8 66.7 + - - +
321D THR* 3.7 25.1 - - + +
323D PHE* 3.8 18.6 - - + -
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Residues in contact with CYS 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D ALA* 3.1 21.5 + - - -
302D TYR* 3.2 10.5 + - + +
304D GLN* 1.3 76.4 - - - +
306D GLN* 1.3 62.6 + - - +
308D GLU* 4.4 7.0 - - - +
309D ASP* 2.7 51.3 + - - +
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Residues in contact with GLN 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D MET* 3.9 17.2 - - + +
287D TYR* 3.7 34.7 - - + +
289D GLU* 4.3 6.4 - - - +
302D TYR* 3.0 60.9 + - + +
303D ILE 3.2 6.5 + - - +
305D CYS* 1.3 84.5 - - - +
307D PHE* 1.3 62.2 + - + +
309D ASP* 3.8 9.4 + - - +
310D LEU* 3.2 21.0 + - - +
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Residues in contact with PHE 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D PHE* 4.1 0.2 - + - -
225D VAL* 3.6 35.2 - - + -
243D MET* 3.8 19.7 - - - -
246D SER* 3.8 14.1 - - - -
247D MET* 3.5 42.6 - - + -
250D PHE* 3.3 40.3 - + + -
266D LEU* 3.6 23.6 - - + -
268D LEU* 4.5 3.8 - - + -
287D TYR* 4.1 2.7 - - - -
303D ILE* 3.0 31.2 + - + +
304D GLN 3.9 1.1 - - - +
306D GLN* 1.3 76.4 - - - +
308D GLU* 1.3 64.5 + - - +
310D LEU* 3.1 23.4 + - + +
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Residues in contact with GLU 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D LEU* 4.8 2.0 - - + -
304D GLN* 2.8 49.8 + - - +
305D CYS* 4.0 5.3 - - - +
307D PHE* 1.3 67.3 - - - +
309D ASP* 1.3 59.9 + - - +
310D LEU 3.0 11.2 + - - -
311D ASN* 3.1 21.7 + - - +
319D ILE* 3.4 37.8 - - + +
321D THR* 2.8 28.5 + - - +
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Residues in contact with ASP 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D CYS* 2.7 38.1 + - - +
306D GLN* 4.2 8.4 + - - +
307D PHE 3.3 0.6 - - - -
308D GLU* 1.3 74.0 - - - +
310D LEU* 1.3 61.4 + - + +
311D ASN 3.3 4.5 - - - -
312D ARG* 4.6 10.0 - - - +
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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