Contacts of the helix formed by residues 298 - 304 (chain D) in PDB entry 5DO7
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 GLN 298 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296D ALA* 5.1 3.6 - - + -
297D ALA* 1.3 76.0 - - - +
299D HIS* 1.3 127.7 + - + +
301D VAL* 2.8 28.7 + - - +
302D GLN* 3.6 8.3 + - - +
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Residues in contact with HIS 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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295D GLY* 4.9 0.4 - - - -
296D ALA* 3.1 33.0 + - + +
298D GLN* 1.3 114.2 + - - +
300D MET* 1.3 52.3 + - - +
302D GLN* 2.8 32.3 + - + +
303D TYR* 2.8 19.5 + - - +
354D ARG* 2.7 57.2 + - - -
355D ASP* 3.9 21.6 + - - +
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Residues in contact with MET 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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277D PHE* 4.9 2.0 - - + -
283D VAL* 4.4 8.7 - - + +
285D LEU* 5.2 0.4 - - - -
293D TYR* 2.8 52.3 - - + +
294D LEU 3.3 7.0 - - - +
295D GLY* 3.3 20.9 - - - +
296D ALA 2.8 15.2 + - - +
297D ALA 3.8 7.2 - - - +
298D GLN 3.0 0.2 + - - -
299D HIS* 1.3 76.7 - - - +
301D VAL* 1.3 58.9 + - - +
303D TYR* 4.2 2.9 - - - -
304D PHE* 3.4 45.9 + - + -
309D TYR* 3.8 5.8 - - - -
314D TYR* 3.1 41.1 - - + -
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Residues in contact with VAL 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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294C HIS* 4.2 37.5 - - + +
277D PHE* 4.6 14.4 - - + -
297D ALA 4.0 9.9 - - - +
298D GLN* 2.8 23.1 + - - +
300D MET* 1.3 73.4 - - - +
302D GLN* 1.3 60.9 + - + +
304D PHE 4.0 0.3 + - - -
305D THR* 3.0 15.7 + - - +
309D TYR* 3.7 23.9 - - + +
314D TYR* 6.2 1.6 - - + -
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Residues in contact with GLN 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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298D GLN* 3.6 7.1 + - - +
299D HIS* 2.8 18.9 + - + +
301D VAL* 1.3 78.4 - - + +
303D TYR* 1.3 63.1 + - - +
305D THR* 2.7 34.8 + - - +
355D ASP* 5.8 1.8 + - - -
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Residues in contact with TYR 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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292D ILE 4.8 1.6 + - - -
293D TYR* 3.8 38.6 - + + -
299D HIS 2.8 11.4 + - - +
300D MET* 4.6 2.9 - - - -
301D VAL 3.4 0.4 - - - -
302D GLN* 1.3 78.5 - - - +
304D PHE* 1.3 80.1 + + - +
306D ALA* 3.1 25.6 + - + +
339D ARG 5.0 0.9 + - - -
342D ALA* 4.4 4.2 - - - +
343D GLN* 2.9 40.9 + - + +
346D ALA* 4.3 15.9 - - + +
355D ASP* 2.9 43.1 - - - +
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Residues in contact with PHE 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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285D LEU* 4.3 12.8 - - + -
292D ILE* 3.5 25.4 - - + -
293D TYR* 4.1 13.2 - - + -
300D MET* 3.4 37.7 + - + -
301D VAL 4.0 1.4 + - - -
302D GLN 3.2 0.8 - - - -
303D TYR* 1.3 90.3 - + - +
305D THR* 1.3 56.4 + - - +
306D ALA* 3.1 6.7 - - + +
307D ILE* 3.2 10.3 + - + +
308D GLY 2.8 18.9 + - - -
309D TYR* 2.8 56.1 - + + -
314D TYR* 4.9 0.2 - + - -
317D PRO* 4.8 0.7 - - + -
321D TYR* 3.2 39.9 - + - -
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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