Contacts of the helix formed by residues 287 - 300 (chain A) in PDB entry 2Y48
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 GLY 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A GLY 3.5 4.4 + - - -
286A SER* 1.3 83.3 - - - +
288A VAL* 1.3 66.1 + - - -
289A SER 3.2 2.2 + - - -
290A GLY 3.4 2.3 + - - +
291A LEU* 2.9 18.9 + - - +
314A GLY* 4.2 6.1 - - - -
624A THR* 4.8 0.6 + - - -
900A FAD 3.2 42.7 + - - -
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLY* 1.3 71.9 - - - -
289A SER* 1.3 58.6 + - - +
291A LEU* 4.3 5.8 - - + -
292A ALA* 2.8 29.8 + - - +
314A GLY 4.7 1.5 + - - +
317A VAL* 4.2 18.4 - - + -
571A TYR* 6.6 0.2 - - + -
574A VAL* 5.0 6.5 - - + -
575A PRO* 4.0 31.6 - - + -
578A LEU* 4.5 7.0 - - + -
811A VAL* 4.4 17.0 - - + +
814A ALA* 4.7 5.8 - - + -
815A LEU* 3.8 39.9 - - + +
900A FAD 3.3 10.1 + - - +
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A VAL* 1.3 77.9 - - - +
290A GLY* 1.3 68.1 + - - +
292A ALA* 3.8 0.2 - - - +
293A ALA* 3.0 16.1 + - - +
624A THR* 3.3 22.5 - - - +
799A ALA* 4.3 2.0 - - - -
800A GLY* 3.4 15.6 + - - -
814A ALA* 3.4 29.9 - - - +
815A LEU 4.4 0.2 - - - +
817A SER* 3.7 12.1 - - - -
818A GLY* 3.4 12.4 - - - -
900A FAD 2.9 19.2 + - - -
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Residues in contact with GLY 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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283A ILE* 4.0 13.8 - - - +
285A GLY 3.8 18.6 - - - -
287A GLY 3.4 5.4 + - - -
289A SER* 1.3 76.7 + - - +
291A LEU* 1.3 67.1 + - - +
293A ALA* 2.7 16.3 + - - +
294A ALA* 2.8 13.5 + - - +
306A LEU* 4.1 6.3 - - - -
624A THR* 3.9 10.0 + - - +
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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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286A SER* 3.2 35.4 - - - +
287A GLY 2.9 22.5 + - - +
288A VAL* 3.9 4.7 - - - +
290A GLY* 1.3 69.9 - - - +
292A ALA* 1.3 64.7 + - - +
294A ALA* 3.3 6.0 + - - +
295A ARG* 3.1 25.8 + - - +
306A LEU* 4.0 5.6 - - + +
313A VAL* 4.4 4.3 - - + -
314A GLY 4.4 1.3 - - - +
575A PRO* 3.8 37.2 - - + +
578A LEU* 4.1 17.7 - - + -
579A ALA* 3.9 29.2 - - + -
582A LEU* 4.2 10.5 - - + +
584A ILE* 4.4 2.7 - - + -
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Residues in contact with ALA 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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288A VAL 2.8 23.9 + - - +
289A SER 3.8 3.8 - - - +
291A LEU* 1.3 74.3 - - - +
293A ALA* 1.3 62.7 + - - +
295A ARG* 3.6 6.2 + - - +
296A GLN* 3.4 23.9 + - - +
578A LEU* 4.4 7.8 - - + +
815A LEU* 3.7 42.2 - - + +
818A GLY* 4.4 0.7 - - - -
819A LEU* 4.3 10.9 - - + +
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Residues in contact with ALA 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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283A ILE* 4.6 0.2 - - + -
289A SER 3.0 10.2 + - - +
290A GLY 2.7 13.1 + - - +
292A ALA* 1.3 68.9 - - - +
294A ALA* 1.3 66.3 + - - +
296A GLN* 2.9 14.0 + - - +
297A LEU* 3.0 18.6 + - + +
622A LEU* 3.5 30.7 - - + -
818A GLY* 3.4 26.2 - - - +
822A ALA* 3.8 8.5 - - + +
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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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283A ILE* 3.5 17.7 - - + +
290A GLY 2.8 14.3 + - - +
291A LEU 3.5 8.5 - - - +
293A ALA* 1.3 72.3 - - - +
295A ARG* 1.3 64.0 + - - +
297A LEU* 3.1 3.0 + - - +
298A GLN* 2.9 23.4 + - - +
304A VAL* 3.7 10.2 - - + +
306A LEU* 3.6 32.1 - - + -
582A LEU* 3.6 10.8 - - + -
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Residues in contact with ARG 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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265A GLY* 3.1 32.9 + - - +
266A ILE* 3.9 17.6 - - - +
267A TYR* 4.7 6.3 + - - +
291A LEU 3.1 13.1 + - - +
292A ALA* 3.7 9.2 - - - +
294A ALA* 1.3 78.3 - - - +
296A GLN* 1.3 59.7 + - - +
298A GLN* 3.5 6.5 + - - +
299A SER* 2.7 38.2 + - - +
577A ALA 4.0 6.3 + - - -
578A LEU* 3.1 34.8 + - + +
580A GLU* 2.6 43.8 + - - -
582A LEU* 4.3 15.6 - - + +
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Residues in contact with GLN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLU 4.1 2.4 + - - -
258A ARG 4.8 0.4 + - - -
260A GLY* 3.7 27.5 - - - +
263A ASN 3.8 13.3 + - - +
264A PHE* 3.8 17.3 - - - +
265A GLY 4.4 3.3 + - - -
267A TYR* 4.4 1.2 + - - -
292A ALA 3.5 13.7 - - - +
293A ALA 2.9 2.5 + - - +
295A ARG* 1.3 83.0 - - - +
297A LEU* 1.3 66.0 + - - +
299A SER* 2.9 13.2 + - - -
300A PHE* 2.8 45.0 + - + -
819A LEU* 3.7 21.0 - - + +
822A ALA* 3.3 27.1 - - + -
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Residues in contact with LEU 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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281A VAL* 3.8 24.2 - - + -
283A ILE* 4.3 11.9 - - + -
293A ALA* 3.0 16.9 + - + +
294A ALA 3.5 2.9 - - - +
296A GLN* 1.3 77.0 - - - +
298A GLN* 1.3 56.5 + - - +
300A PHE* 2.7 33.7 + - + +
301A GLY 3.1 7.4 + - - -
302A MET* 3.3 23.1 + - + +
304A VAL* 3.3 26.9 - - + -
622A LEU* 5.2 1.6 - - + -
822A ALA* 3.8 32.1 - - + +
825A ILE* 3.9 23.6 - - + -
826A ALA 4.5 0.7 - - - +
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Residues in contact with GLN 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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273A LEU* 3.9 28.1 - - + +
277A LYS* 6.0 7.9 - - - +
294A ALA 2.9 16.3 + - - +
295A ARG* 3.6 8.6 - - - +
297A LEU* 1.3 75.6 - - - +
299A SER* 1.3 57.9 + - - +
301A GLY* 2.8 21.3 + - - -
302A MET 4.0 15.7 - - - +
304A VAL* 4.0 12.4 + - + +
581A GLY* 3.2 27.6 + - - +
582A LEU* 3.8 17.9 - - + +
583A ASP 5.3 1.4 - - - +
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Residues in contact with SER 299 (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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267A TYR* 3.5 20.8 + - - -
269A ARG* 3.5 36.2 + - - +
273A LEU* 4.4 4.7 - - - +
274A PRO* 6.1 0.5 - - - +
295A ARG* 2.7 26.6 + - - +
296A GLN* 2.9 16.4 + - - -
298A GLN* 1.3 72.7 + - - +
300A PHE* 1.3 64.9 + - - +
301A GLY 3.0 3.3 + - - -
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Residues in contact with PHE 300 (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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257A GLU* 3.7 26.5 - - + -
258A ARG* 3.3 41.1 - - - +
296A GLN* 2.8 46.5 + - + -
297A LEU* 2.7 18.2 + - + +
299A SER* 1.3 77.9 - - - +
301A GLY* 1.3 63.3 - - - +
302A MET* 4.9 0.7 - - + -
822A ALA* 4.0 11.4 - - + -
826A ALA* 3.4 28.0 - - + -
830A LEU* 3.3 28.7 - - + +
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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