Contacts of the helix formed by residues 316 - 328 (chain A) in PDB entry 1FR8
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 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A TYR* 3.6 10.1 + - - -
315A GLY* 1.3 73.2 - - - -
317A GLU* 1.3 61.1 + - - +
318A ASP* 3.1 12.2 + - - -
319A ASP* 2.8 7.3 + - - +
320A ASP* 2.8 26.7 + - - +
360A PHE* 3.2 32.2 - - - +
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Residues in contact with GLU 317 (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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228A ARG* 3.1 43.3 + - - +
229A ALA* 4.0 24.9 - - + +
308A PRO* 4.3 2.0 - - + +
311A TYR* 3.4 37.0 - - + +
313A GLY* 5.3 4.5 + - - -
315A GLY* 3.9 11.3 + - - -
316A GLY* 1.3 87.1 + - - +
318A ASP* 1.3 64.1 + - - +
320A ASP* 3.1 6.8 + - - +
321A ILE* 2.8 36.4 + - + +
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Residues in contact with ASP 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ARG* 4.2 14.8 - - - +
286A TYR* 4.5 0.9 + - - -
289A TYR* 3.9 15.1 + - - -
290A PHE* 4.1 26.6 + - - +
291A GLY* 3.7 22.2 + - - -
316A GLY* 3.7 14.7 + - - -
317A GLU* 1.3 84.8 + - + +
319A ASP* 1.3 79.2 + - - +
321A ILE* 3.5 13.2 + - + +
322A TYR* 3.1 20.3 + - - +
360A PHE* 5.3 1.2 - - - -
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A TYR* 2.6 32.9 + - - -
288A GLN 4.1 4.9 - - - +
289A TYR* 5.0 0.5 - - - -
290A PHE 5.3 0.2 + - - -
316A GLY* 2.8 8.9 + - - +
318A ASP* 1.3 84.7 + - - +
320A ASP* 1.3 66.9 + - - +
322A TYR* 3.1 8.6 + - - +
323A ASN* 3.0 28.6 + - - +
358A GLN 4.2 0.5 - - - +
359A ARG* 3.6 18.2 + - - +
360A PHE* 2.8 49.9 + - + +
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Residues in contact with ASP 320 (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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308A PRO* 3.6 8.3 - - + +
311A TYR* 2.8 44.2 + - + +
316A GLY 2.8 8.1 + - - +
317A GLU 3.3 8.5 - - - +
319A ASP* 1.3 77.7 - - - +
321A ILE* 1.3 57.8 + - - +
323A ASN* 2.9 8.1 + - - +
324A ARG* 2.8 54.2 + - - +
362A ARG* 6.4 0.4 - - - -
365A HIS* 4.5 2.9 + - - -
366A THR* 2.8 31.0 + - - +
369A THR* 4.7 2.6 + - - -
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Residues in contact with ILE 321 (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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228A ARG* 5.0 7.2 - - - +
229A ALA* 5.1 1.6 - - + -
232A LEU* 5.5 1.6 - - + -
290A PHE* 4.1 23.8 - - + +
296A LEU* 5.6 0.2 - - + -
304A ILE* 4.4 6.5 - - + -
307A PHE* 3.4 57.7 - - + -
308A PRO* 3.8 12.6 - - + -
317A GLU* 2.8 33.1 + - + +
318A ASP* 3.7 11.0 - - + +
320A ASP* 1.3 75.2 - - - +
322A TYR* 1.3 61.9 + - - +
324A ARG* 3.3 11.0 + - - +
325A LEU* 3.1 23.8 + - + +
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Residues in contact with TYR 322 (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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287A VAL 4.5 2.5 + - - -
288A GLN* 3.3 64.5 + - + +
290A PHE* 4.4 11.4 - + + -
318A ASP 3.1 12.8 + - - +
319A ASP* 3.1 10.3 + - - +
320A ASP 3.1 0.6 - - - -
321A ILE* 1.3 76.5 - - - +
323A ASN* 1.3 73.2 + - - +
325A LEU* 3.2 12.5 + - + +
326A ALA* 3.1 22.3 + - + +
332A VAL* 3.4 25.1 - - + +
359A ARG* 4.2 4.5 - - - -
225B MET* 3.3 37.8 - - + +
313B GLY* 3.6 16.7 + - - -
314B TRP* 4.7 5.8 - - + -
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Residues in contact with ASN 323 (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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319A ASP* 3.0 15.1 + - - +
320A ASP* 2.9 9.9 + - - +
322A TYR* 1.3 78.7 - - - +
324A ARG* 1.3 66.9 + - - +
326A ALA* 3.2 6.4 + - - +
327A PHE* 3.0 35.2 + - + -
359A ARG* 2.7 30.7 + - - +
360A PHE 5.2 0.4 + - - -
362A ARG* 3.9 6.7 + - - +
363A ILE* 3.8 24.7 - - + +
366A THR* 3.3 28.4 + - - +
314B TRP* 4.2 8.0 - - - +
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Residues in contact with ARG 324 (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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304A ILE* 3.2 50.1 + - + +
305A ASN 3.2 14.1 + - - -
306A GLY 3.3 12.5 + - - -
307A PHE 3.9 1.6 - - - -
308A PRO* 3.3 32.6 - - - +
320A ASP* 2.8 31.5 + - - +
321A ILE* 3.5 9.0 - - - +
323A ASN* 1.3 77.7 - - - +
325A LEU* 1.3 61.7 + - - +
327A PHE* 3.3 3.3 + - - +
328A ARG* 3.0 20.1 + - - +
366A THR* 3.5 10.7 - - + +
369A THR* 5.3 1.6 + - - -
370A MET* 3.4 40.5 + - + +
373A ASP* 2.5 35.7 + - - +
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Residues in contact with LEU 325 (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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270A PRO* 3.7 40.4 - - + -
290A PHE* 3.9 26.5 - - + -
296A LEU* 4.5 7.0 - - + -
304A ILE* 4.1 18.8 - - + -
321A ILE* 3.1 15.6 + - + +
322A TYR* 3.3 12.8 - - - +
323A ASN 3.1 0.6 - - - -
324A ARG* 1.3 77.4 - - - +
326A ALA* 1.3 54.8 + - - +
328A ARG 3.4 2.4 + - - -
329A GLY 3.4 3.6 + - - -
330A MET* 2.7 55.0 + - + +
331A SER 4.9 1.1 - - - +
332A VAL* 4.8 11.2 - - + -
225B MET* 4.1 7.2 - - + -
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Residues in contact with ALA 326 (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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322A TYR* 3.1 11.1 + - + +
323A ASN 3.2 4.0 + - - +
325A LEU* 1.3 76.5 - - - +
327A PHE* 1.3 61.4 + - - +
329A GLY* 2.9 17.3 + - - -
330A MET 3.9 0.4 - - - -
225B MET* 3.5 33.0 + - + +
312B TRP* 4.0 2.7 - - + +
314B TRP* 3.3 32.5 - - + -
401B PRO* 3.3 20.0 - - - +
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Residues in contact with PHE 327 (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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323A ASN* 3.0 27.2 + - + +
324A ARG 3.6 4.0 - - - +
326A ALA* 1.3 78.4 - - - +
328A ARG* 1.3 66.7 + - - +
329A GLY 3.0 3.5 + - - -
363A ILE* 3.7 17.0 - - + -
366A THR* 4.2 4.9 - - - -
367A LYS* 3.3 59.2 - - + -
370A MET* 3.2 31.6 - - + -
314B TRP* 3.3 31.9 - + - -
400B THR* 4.9 0.9 + - - -
401B PRO* 4.1 22.1 - - + +
402B SER* 4.5 12.5 - - - -
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Residues in contact with ARG 328 (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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303A SER* 3.3 43.6 + - - +
304A ILE* 3.9 10.1 - - + -
324A ARG 3.0 13.3 + - - +
325A LEU 3.4 0.4 + - - +
326A ALA 3.2 0.2 - - - -
327A PHE* 1.3 92.2 + - - +
329A GLY* 1.3 63.5 + - - +
330A MET* 3.2 20.6 + - + +
370A MET* 4.3 17.9 - - - +
371A LEU* 3.8 32.5 - - - +
400B THR* 5.3 0.9 - - - -
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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