Contacts of the helix formed by residues 289 - 301 (chain B) in PDB entry 5Y7G
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 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B PHE* 3.8 5.0 - - - -
288B PRO* 1.3 71.7 - - - +
290B ALA* 1.3 60.7 + - - +
291B ARG 3.5 1.3 - - - -
292B LEU* 3.8 17.5 + - - +
293B ARG* 3.0 31.0 + - - +
319B GLU* 2.7 17.9 + - - -
323B GLU* 4.9 1.8 - - - -
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B PHE* 3.8 13.8 - - + -
282B TYR* 3.3 27.6 - - + +
285B SER* 3.4 33.7 - - - +
287B HIS 3.3 10.2 + - - +
288B PRO 3.4 1.0 - - - -
289B GLY* 1.3 75.2 - - - +
291B ARG* 1.3 68.3 + - - +
293B ARG* 2.8 16.1 + - - +
294B ALA* 2.8 13.0 + - - +
319B GLU* 5.3 0.2 - - - +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B TYR 4.5 2.2 + - - -
283B ARG* 5.9 2.9 - - - +
285B SER 5.1 0.8 + - - -
289B GLY 3.5 0.2 - - - -
290B ALA* 1.3 76.3 - - - +
292B LEU* 1.3 61.2 + - - +
294B ALA* 3.3 8.6 + - - +
295B ILE* 3.1 24.1 + - + +
310B LEU* 4.1 15.8 - - + +
313B GLU* 3.7 34.8 + - - +
314B ALA* 3.5 28.0 - - + +
317B ALA* 3.0 29.5 + - - +
319B GLU* 3.8 22.8 + - - +
323B GLU* 2.9 35.7 + - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B GLY* 3.8 15.2 + - - +
290B ALA 3.1 0.2 - - - -
291B ARG* 1.3 77.6 - - - +
293B ARG* 1.3 70.1 + - + +
294B ALA 3.2 0.2 + - - -
295B ILE* 3.2 7.2 + - + +
296B ARG* 3.0 24.1 + - - +
322B ALA* 3.9 9.9 - - + +
323B GLU* 3.5 52.4 + - + +
326B GLY* 4.4 7.0 - - - -
327B LEU* 4.1 12.8 - - + +
330B LEU* 3.9 25.5 - - + +
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Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B PHE* 3.9 13.2 - - + -
267B GLN* 6.1 1.2 - - - +
270B GLU* 2.8 42.5 + - - +
282B TYR* 3.4 31.5 + - + -
289B GLY 3.0 19.9 + - - +
290B ALA 2.8 11.1 + - - +
292B LEU* 1.3 77.7 - - - +
294B ALA* 1.3 52.1 + - - +
296B ARG* 3.8 20.6 - - - +
297B SER* 2.8 34.7 + - - -
300B ARG* 4.2 10.3 - - - +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLN* 4.3 8.1 - - + -
282B TYR* 3.7 25.7 - - + -
283B ARG* 4.0 14.4 - - - +
290B ALA 2.8 6.8 + - - +
291B ARG* 3.5 11.4 - - - +
292B LEU 3.1 0.2 - - - -
293B ARG* 1.3 74.7 - - - +
295B ILE* 1.3 66.2 + - - +
297B SER* 3.6 2.9 - - - -
298B LEU* 2.9 29.3 + - - +
310B LEU* 3.7 17.9 - - + -
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Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG* 3.1 15.5 + - + +
292B LEU* 3.8 9.2 - - + +
294B ALA* 1.3 76.8 - - - +
296B ARG* 1.3 57.2 + - - +
298B LEU* 3.4 4.4 + - - -
299B GLU* 2.9 27.8 + - - +
307B ALA* 3.5 20.1 - - - +
310B LEU* 3.5 32.5 - - + +
311B ALA* 3.5 31.6 - - + +
314B ALA* 4.1 9.0 - - + -
327B LEU* 3.9 15.5 - - + -
330B LEU* 3.8 20.4 - - + -
334B LEU* 4.1 10.5 - - + -
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Residues in contact with ARG 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLU* 4.7 0.9 - - - +
292B LEU* 3.0 15.8 + - + +
293B ARG* 4.1 28.3 - - - +
295B ILE* 1.3 74.6 - - - +
297B SER* 1.3 65.4 + - - +
299B GLU* 3.1 41.1 + - - +
300B ARG* 3.0 62.5 + - - +
330B LEU* 4.6 10.3 - - + +
333B ARG* 3.7 12.9 - - - +
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLU* 3.6 15.5 + - - -
275B PHE* 3.7 17.8 + - - +
278B ALA* 3.5 26.9 - - - +
279B GLN* 3.6 9.7 + - - -
282B TYR* 4.1 8.7 - - - -
293B ARG 2.8 21.0 + - - -
294B ALA* 3.6 4.9 - - - -
295B ILE 3.2 0.4 - - - -
296B ARG* 1.3 74.7 - - - +
298B LEU* 1.3 59.9 + - - +
300B ARG* 2.9 22.2 + - - +
301B GLY 2.9 10.9 + - - -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B PHE* 5.7 0.7 - - - -
279B GLN* 3.7 33.4 - - + +
283B ARG* 4.5 3.4 - - - +
294B ALA 2.9 20.1 + - - +
295B ILE 3.7 3.1 - - - +
297B SER* 1.3 75.0 - - - +
299B GLU* 1.3 62.6 + - - +
301B GLY* 3.3 2.4 + - - +
302B GLU 3.2 3.8 + - - -
303B ARG* 3.0 76.8 + - + +
306B GLU* 4.1 12.6 - - + +
307B ALA* 3.8 26.7 - - + +
310B LEU* 4.2 16.2 - - + -
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE 2.9 17.3 + - - +
296B ARG* 3.1 32.5 + - - +
297B SER 3.2 0.2 - - - -
298B LEU* 1.3 76.1 - - - +
300B ARG* 1.3 56.3 + - - +
302B GLU* 3.0 16.8 + - - +
304B PHE* 3.4 29.9 - - + -
307B ALA* 3.7 5.5 - - - +
330B LEU* 3.1 26.3 - - - +
333B ARG* 3.3 26.0 + - - -
334B LEU* 3.5 26.0 - - + -
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLU* 3.1 47.2 + - - +
273B ARG* 3.4 20.5 + - - +
275B PHE* 3.0 46.4 - - + -
293B ARG* 4.2 8.3 - - - +
296B ARG* 3.0 53.6 + - - +
297B SER 2.9 8.7 + - - +
299B GLU* 1.3 77.6 - - - +
301B GLY* 1.3 55.5 + - - +
302B GLU* 3.2 10.2 + - - +
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Residues in contact with GLY 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B PHE* 3.4 17.6 - - - -
276B ASP* 5.2 3.6 - - - +
297B SER 2.9 12.1 + - - -
298B LEU* 3.5 3.8 - - - -
299B GLU 3.2 0.2 - - - -
300B ARG* 1.3 73.4 - - - +
302B GLU* 1.3 69.2 + - - +
303B ARG* 3.0 19.3 + - - +
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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