Contacts of the helix formed by residues 315 - 329 (chain A) in PDB entry 4N9W
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 ASP 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A VAL* 4.2 5.9 - - - +
311A VAL* 4.2 3.2 - - + +
312A PRO* 3.4 39.9 + - + +
313A VAL 4.2 1.6 - - - +
314A ASP* 1.3 75.9 - - - +
316A ALA* 1.3 58.1 + - - +
317A ASP* 3.3 8.7 + - - +
318A GLY* 2.7 34.6 + - - -
319A MET* 2.9 27.4 + - - +
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Residues in contact with ALA 316 (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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206A VAL* 4.0 20.8 - - + +
209A ALA* 3.7 35.7 - - + +
210A ALA* 3.6 7.6 - - - +
314A ASP 3.9 1.8 + - - -
315A ASP* 1.3 72.0 + - - +
317A ASP* 1.3 64.0 + - - +
319A MET* 3.1 2.3 + - - +
320A ALA* 2.9 26.5 + - - +
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 2.6 37.2 + - - +
315A ASP* 3.3 5.7 + - - +
316A ALA* 1.3 81.3 - - - +
318A GLY* 1.3 62.3 + - - +
320A ALA* 3.4 5.1 + - - +
321A ALA* 3.0 23.7 + - - +
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Residues in contact with GLY 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ARG* 4.9 2.4 + - - -
311A VAL* 3.7 11.1 - - - +
312A PRO* 5.3 1.8 - - - -
315A ASP* 2.7 30.6 + - - -
317A ASP* 1.3 74.6 - - - +
319A MET* 1.3 56.0 + - - +
321A ALA* 3.4 6.7 + - - +
322A ALA* 3.0 28.8 + - - +
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Residues in contact with MET 319 (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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206A VAL* 4.1 19.3 - - + +
207A LEU* 5.0 3.1 - - - -
210A ALA* 4.4 7.2 - - + -
267A CYS* 3.8 17.3 - - - -
268A ALA 4.9 0.4 - - - +
269A PRO* 4.0 29.6 - - + -
291A VAL* 3.7 27.6 - - + -
292A ALA 4.8 0.2 - - - -
293A SER* 4.6 11.7 - - - +
311A VAL* 3.6 23.3 - - + +
312A PRO 5.6 1.3 - - - +
315A ASP 2.9 16.9 + - - +
316A ALA* 3.1 5.4 + - - +
318A GLY* 1.3 72.9 - - - +
320A ALA* 1.3 60.0 + - - +
322A ALA* 3.3 2.1 + - - +
323A LEU* 2.9 41.3 + - + +
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Residues in contact with ALA 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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210A ALA* 3.7 29.5 - - + +
213A LYS* 3.9 27.6 - - + -
214A LEU* 4.9 2.0 - - - +
316A ALA 2.9 15.8 + - - +
317A ASP* 3.8 4.5 - - - +
319A MET* 1.3 75.5 - - - +
321A ALA* 1.3 57.4 + - - +
323A LEU* 3.3 5.5 + - - +
324A ILE* 2.9 39.9 + - + +
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Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ARG* 4.3 8.8 + - - +
317A ASP 3.0 17.6 + - - +
318A GLY* 3.7 7.0 - - - +
320A ALA* 1.3 75.1 - - - +
322A ALA* 1.3 58.3 + - - +
324A ILE* 3.8 7.0 - - - +
325A GLY* 2.8 28.8 + - - -
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Residues in contact with ALA 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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291A VAL* 3.9 10.1 - - + -
309A ARG* 3.5 27.1 + - + +
311A VAL* 3.4 26.9 - - + -
318A GLY 3.0 19.0 + - - +
319A MET 3.6 3.8 - - - +
321A ALA* 1.3 77.9 - - - +
323A LEU* 1.3 57.2 + - - +
325A GLY* 3.4 1.0 + - - -
326A ILE* 3.0 35.7 + - - +
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Residues in contact with LEU 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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191A VAL* 4.1 9.0 - - + -
207A LEU* 3.7 30.7 - - + -
210A ALA* 5.0 3.8 - - + -
214A LEU* 4.0 26.9 - - + -
265A VAL* 4.0 28.9 - - + -
267A CYS* 4.1 17.9 - - + -
291A VAL* 4.1 11.0 - - + -
319A MET* 2.9 33.4 + - + +
320A ALA* 3.9 5.6 - - - +
322A ALA* 1.3 72.6 - - - +
324A ILE* 1.3 67.0 + - - +
326A ILE* 3.4 4.3 + - - +
327A LEU* 3.1 31.5 + - + +
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Residues in contact with ILE 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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213A LYS* 3.6 35.0 - - + +
214A LEU* 3.8 18.4 - - + +
217A ARG* 3.7 39.0 - - + +
218A PHE* 4.3 6.5 - - + -
320A ALA* 2.9 26.4 + - + +
321A ALA* 3.9 5.8 - - - +
323A LEU* 1.3 76.0 - - - +
325A GLY* 1.3 64.7 + - - +
327A LEU* 3.3 1.2 + - - +
328A GLU* 2.9 47.9 + - + +
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Residues in contact with GLY 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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309A ARG* 6.1 0.7 - - - -
321A ALA 2.8 18.4 + - - -
322A ALA* 3.8 1.6 - - - -
324A ILE* 1.3 81.6 - - - +
326A ILE* 1.3 60.1 + - - +
328A GLU* 3.5 4.9 + - - +
329A ASP* 3.1 28.9 + - - +
332A LEU* 4.5 7.2 - - - +
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Residues in contact with ILE 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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265A VAL* 4.3 18.2 - - + -
289A ALA* 4.3 12.1 - - + -
290A VAL 5.2 0.7 - - - +
291A VAL* 3.6 18.6 - - + -
309A ARG* 4.3 10.5 - - + +
322A ALA 3.0 21.1 + - - +
323A LEU* 3.8 4.5 - - - +
324A ILE 3.3 0.2 - - - -
325A GLY* 1.3 75.8 - - - +
327A LEU* 1.3 60.6 + - + +
329A ASP 3.5 10.1 - - - +
332A LEU* 4.1 12.3 - - + +
333A ARG* 2.8 43.3 + - + +
336A TYR* 3.4 41.7 - - + -
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Residues in contact with LEU 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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189A ARG* 3.1 50.0 + - + +
190A THR 5.1 0.4 - - - +
191A VAL* 4.5 13.9 - - + -
214A LEU* 4.0 22.2 - - + -
218A PHE* 3.5 28.9 - - + -
221A VAL* 4.8 2.2 - - + -
264A ASP* 3.9 23.1 - - + +
265A VAL* 4.1 18.4 - - + -
323A LEU 3.1 18.6 + - - +
326A ILE* 1.3 78.4 - - + +
328A GLU* 1.3 59.8 + - - +
330A ASP* 4.1 0.5 - - - +
333A ARG* 3.1 17.9 + - - +
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Residues in contact with GLU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG* 2.8 49.2 + - - +
218A PHE* 3.5 19.0 - - + -
324A ILE* 2.9 28.0 + - - +
325A GLY* 4.0 4.5 - - - +
327A LEU* 1.3 78.5 - - - +
329A ASP* 1.3 56.6 + - + +
330A ASP* 3.7 9.1 + - - +
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Residues in contact with ASP 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLY 3.1 16.7 + - - +
326A ILE 3.5 9.2 - - - +
327A LEU 3.4 0.8 - - - -
328A GLU* 1.3 74.7 - - + +
330A ASP* 1.3 62.3 + - - +
331A GLN* 3.1 16.3 + - - +
332A LEU* 2.9 35.9 + - + +
333A ARG* 3.0 18.2 + - - -
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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