Contacts of the helix formed by residues 289 - 301 (chain F) in PDB entry 4R8A
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263F PHE* 3.9 6.5 - - - -
287F HIS 3.1 0.2 + - - -
288F PRO* 1.3 72.5 - - - +
290F ALA* 1.3 63.8 + - - +
291F ARG 3.4 2.5 - - - -
292F LEU* 3.5 12.2 + - - +
293F ARG* 3.1 27.2 + - - +
319F GLU* 3.0 20.1 + - - -
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Residues in contact with ALA 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F PHE* 3.6 20.9 - - + -
282F TYR* 3.4 29.2 - - + +
285F SER* 3.5 23.1 - - - +
287F HIS 2.9 17.8 + - - +
288F PRO 3.4 0.6 - - - -
289F GLY* 1.3 76.6 - - - +
291F ARG* 1.3 61.3 + - - +
293F ARG* 3.0 4.7 + - - +
294F ALA 2.9 24.3 + - - -
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Residues in contact with ARG 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F TYR 4.5 2.9 + - - -
283F ARG* 6.0 1.3 - - - +
285F SER 5.2 1.3 + - - +
287F HIS 4.7 0.4 + - - -
289F GLY* 3.4 0.6 - - - -
290F ALA* 1.3 77.9 - - - +
292F LEU* 1.3 60.4 + - - +
294F ALA* 3.2 17.0 + - - +
295F ILE* 3.2 16.4 + - + +
310F LEU* 4.5 22.6 - - + +
313F GLU* 4.5 12.3 + - - +
314F ALA* 3.5 34.2 + - + +
317F ALA* 3.3 26.9 + - - +
318F PRO* 3.9 0.4 - - - +
319F GLU* 3.9 13.7 + - - +
323F GLU* 2.6 45.2 + - - +
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Residues in contact with LEU 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289F GLY* 3.5 13.6 + - - +
290F ALA 3.2 0.2 - - - -
291F ARG* 1.3 77.3 - - - +
293F ARG* 1.3 68.5 + - + +
295F ILE* 3.4 9.0 + - + +
296F ARG* 3.3 33.3 + - - +
322F ALA 4.7 2.2 - - - +
323F GLU* 3.9 29.9 + - + +
326F GLY* 4.0 19.1 - - - -
327F LEU* 4.0 32.1 - - + +
330F LEU* 3.7 25.1 - - + +
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Residues in contact with ARG 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F PHE* 4.1 11.7 - - + -
267F GLN* 6.0 0.2 - - + -
270F GLU* 2.4 38.8 + - - -
282F TYR* 3.4 33.3 + - + +
289F GLY 3.1 16.0 + - - +
290F ALA 3.0 7.5 + - - +
292F LEU* 1.3 79.9 - - - +
294F ALA* 1.3 61.5 + - - +
296F ARG* 3.5 42.6 + - - +
297F SER* 3.0 34.3 + - - -
300F ARG* 4.7 6.5 - - - +
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Residues in contact with ALA 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F GLN* 4.1 5.6 - - + +
282F TYR* 3.7 14.8 - - + -
283F ARG* 3.7 30.5 - - + +
290F ALA 2.9 11.7 + - - +
291F ARG* 3.3 14.4 - - - +
292F LEU 3.2 0.2 - - - -
293F ARG* 1.3 77.0 - - - +
295F ILE* 1.3 56.1 + - - +
297F SER* 3.5 3.6 + - - -
298F LEU* 3.0 32.2 + - - +
310F LEU* 4.0 10.8 - - + -
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Residues in contact with ILE 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F ARG* 3.2 17.2 + - + +
292F LEU* 3.7 15.7 - - + +
293F ARG 3.3 0.4 - - - -
294F ALA* 1.3 73.3 - - - +
296F ARG* 1.3 59.7 + - - +
298F LEU* 3.1 9.9 + - - +
299F GLU* 2.9 25.1 + - - +
307F ALA* 3.5 20.2 - - + +
310F LEU* 3.7 24.9 - - + +
311F ALA* 3.7 25.4 - - + +
314F ALA* 4.3 6.1 - - + -
327F LEU* 3.9 17.5 - - + -
330F LEU* 3.8 14.1 - - + -
334F LEU* 3.8 18.4 - - + -
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Residues in contact with ARG 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F GLU* 4.8 0.7 - - - -
292F LEU* 3.3 21.5 + - - +
293F ARG* 3.5 41.9 - - - +
295F ILE* 1.3 79.1 - - - +
297F SER* 1.3 58.3 + - - +
299F GLU* 3.4 21.6 + - - +
300F ARG* 3.1 40.5 + - - +
326F GLY* 4.0 18.6 + - - -
329F ARG* 3.8 26.5 - - - +
330F LEU* 3.9 23.1 - - + +
333F ARG* 4.2 9.9 - - - +
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Residues in contact with SER 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F GLU* 3.3 27.9 - - - +
275F PHE* 3.5 35.0 - - - +
278F ALA* 4.1 1.4 - - - +
279F GLN* 4.1 11.7 - - - -
282F TYR* 3.5 8.3 - - - -
293F ARG 3.0 22.2 + - - -
294F ALA 3.7 3.8 - - - -
296F ARG* 1.3 75.8 - - - +
298F LEU* 1.3 60.3 + - - +
299F GLU 3.1 0.2 - - - -
300F ARG* 3.3 2.7 + - - -
301F GLY* 3.0 23.6 + - - -
303F ARG* 5.9 0.2 - - - -
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Residues in contact with LEU 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F GLN* 3.5 31.4 - - + +
283F ARG* 4.9 4.7 - - - +
294F ALA 3.0 18.5 + - - +
295F ILE* 3.4 8.3 - - - +
297F SER* 1.3 75.6 - - - +
299F GLU* 1.3 58.9 + - - +
301F GLY 3.5 0.7 + - - -
302F GLU 3.4 1.9 + - - -
303F ARG* 2.8 73.0 + - + +
306F GLU* 3.8 17.0 - - + +
307F ALA* 3.5 31.2 - - + +
310F LEU* 4.4 17.0 - - + -
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Residues in contact with GLU 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F ILE 2.9 13.0 + - - +
296F ARG* 3.5 16.8 - - - +
297F SER 3.1 0.2 - - - -
298F LEU* 1.3 73.2 - - - +
300F ARG* 1.3 60.6 + - + +
301F GLY 3.1 4.3 - - - -
302F GLU* 2.9 22.5 + - - +
304F PHE* 3.8 27.1 - - + -
307F ALA* 4.1 4.0 - - - +
330F LEU* 3.7 12.0 - - + +
333F ARG* 2.6 56.1 + - - +
334F LEU* 4.5 13.8 - - + +
337F LYS* 6.0 1.2 - - - +
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Residues in contact with ARG 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F GLU* 3.8 27.9 + - - +
271F LYS* 6.2 0.4 - - - +
273F ARG* 3.2 30.1 - - - +
275F PHE* 3.5 47.9 - - + -
293F ARG* 4.7 4.4 - - - +
296F ARG* 3.1 23.8 + - + +
297F SER 3.3 3.8 + - - +
299F GLU* 1.3 79.0 - - + +
301F GLY* 1.3 58.2 + - - +
302F GLU* 3.1 10.2 + - - +
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Residues in contact with GLY 301 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F PHE* 4.2 12.5 - - - -
276F ASP* 4.7 8.0 - - - +
297F SER 3.0 15.6 + - - -
298F LEU 3.9 2.0 - - - -
299F GLU 3.1 0.6 - - - -
300F ARG* 1.3 76.4 - - - +
302F GLU* 1.3 69.9 + - - +
303F ARG* 3.1 17.3 + - - +
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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