Contacts of the helix formed by residues 319 - 343 (chain W) in PDB entry 5IY8
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 VAL 319 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318W ALA* 1.3 82.6 - - - +
320W PRO* 1.4 73.4 - - + +
321W GLY* 4.3 4.0 - - - +
322W SER* 3.4 28.5 + - - +
323W ILE* 3.4 24.9 + - - +
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Residues in contact with PRO 320 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319W VAL* 1.4 85.3 - - + +
321W GLY* 1.4 57.7 - - - +
322W SER 3.1 1.8 - - - -
323W ILE* 2.9 11.4 + - + +
324W ARG* 2.8 39.6 + - - +
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Residues in contact with GLY 321 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319W VAL* 3.6 5.8 - - - +
320W PRO* 1.4 76.1 - - - +
322W SER* 1.3 56.8 + - - +
324W ARG* 3.4 28.3 + - - +
325W THR* 3.0 35.7 + - - -
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Residues in contact with SER 322 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318W ALA* 4.8 6.7 - - - -
319W VAL* 3.4 32.1 + - - +
320W PRO 3.1 0.6 - - - -
321W GLY* 1.3 74.5 - - - +
323W ILE* 1.3 57.5 + - - +
325W THR* 3.5 6.1 + - - +
326W ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 323 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285W TYR* 6.0 0.9 - - + -
312W ASP* 5.3 0.4 - - - +
316W GLN* 3.5 37.5 - - - +
318W ALA* 4.3 13.5 - - + -
319W VAL 3.5 14.1 - - - +
320W PRO* 2.9 14.5 + - + +
322W SER* 1.3 72.7 - - - +
324W ARG* 1.4 53.2 + - - +
326W ALA* 3.2 8.0 + - + +
327W GLU* 2.9 32.1 + - - +
403W PHE* 4.7 9.8 - - + -
407W VAL* 3.7 35.7 - - + -
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Residues in contact with ARG 324 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320W PRO* 2.8 22.7 + - + +
321W GLY* 3.6 32.8 + - - +
323W ILE* 1.4 66.9 - - - +
325W THR* 1.3 64.6 + - - +
327W GLU* 3.3 19.2 + - - +
328W HIS* 3.0 26.8 + - + +
407W VAL* 6.5 0.2 - - - -
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Residues in contact with THR 325 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321W GLY 3.0 18.4 + - - -
322W SER* 3.5 7.6 - - - +
324W ARG* 1.3 79.5 + - - +
326W ALA* 1.3 60.4 + - - +
328W HIS* 3.0 11.2 + - + +
329W PHE* 2.8 73.5 + - + -
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Residues in contact with ALA 326 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281W LEU* 3.5 34.3 - - + +
285W TYR* 3.4 29.3 + - + +
322W SER 2.9 20.7 + - - +
323W ILE* 3.2 12.1 + - + +
325W THR* 1.3 72.4 - - - +
327W GLU* 1.4 61.0 + - - +
329W PHE* 3.5 2.6 + - - +
330W LEU* 3.1 19.6 + - - +
403W PHE* 5.0 2.0 - - + -
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Residues in contact with GLU 327 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323W ILE 2.9 12.7 + - - +
324W ARG* 3.4 19.2 - - - +
326W ALA* 1.4 76.1 - - - +
328W HIS* 1.4 58.8 + - - +
330W LEU* 3.4 4.2 + - + +
331W GLY* 3.2 18.7 + - - -
400W LEU* 4.2 15.9 - - + +
403W PHE* 4.2 28.1 - - + -
404W ALA* 4.0 29.3 - - + +
407W VAL* 4.4 13.7 - - + +
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Residues in contact with HIS 328 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324W ARG* 3.0 13.1 + - + +
325W THR* 3.0 12.9 + - + +
327W GLU* 1.4 75.3 - - - +
329W PHE* 1.4 94.3 + + - +
331W GLY* 3.2 4.9 + - - -
332W PHE* 3.0 48.9 + + - +
335W ARG* 6.0 0.4 - - - -
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Residues in contact with PHE 329 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272W ARG* 3.4 52.0 - - - +
276W THR* 5.2 10.1 - - + -
278W GLU* 3.8 19.4 - - + +
281W LEU* 4.3 19.5 - - + -
325W THR* 2.8 46.0 + - + +
326W ALA* 3.9 4.0 - - - +
328W HIS* 1.4 102.2 - + - +
330W LEU* 1.3 54.9 + - - +
332W PHE* 3.8 9.3 - + + +
333W LEU* 3.2 26.0 + - - +
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Residues in contact with LEU 330 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263W LEU* 5.6 10.5 - - + -
278W GLU* 5.7 3.4 - - + -
281W LEU* 5.4 0.8 - - + +
282W ARG* 5.8 3.1 - - + -
285W TYR* 3.8 22.0 - - + +
326W ALA 3.1 17.0 + - - +
327W GLU 3.7 5.6 - - - +
328W HIS 3.3 0.2 - - - -
329W PHE* 1.3 71.6 - - - +
331W GLY* 1.4 64.8 + - - +
333W LEU* 3.4 8.5 + - + +
334W ARG* 3.1 24.3 + - + +
396W PRO* 5.4 4.0 - - + +
399W LEU* 4.3 24.0 - - + +
400W LEU* 4.0 28.9 - - + +
403W PHE* 3.7 33.7 - - + -
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Residues in contact with GLY 331 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327W GLU 3.2 12.2 + - - -
328W HIS* 3.6 4.7 - - - -
330W LEU* 1.4 73.4 - - - +
332W PHE* 1.3 53.9 + - - +
334W ARG* 3.3 15.0 + - - +
335W ARG* 2.8 27.5 + - - +
400W LEU* 3.7 29.6 - - - +
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Residues in contact with PHE 332 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269W THR* 4.8 16.4 - - + -
272W ARG* 5.2 12.6 - - - +
278W GLU* 5.6 0.9 - - - +
328W HIS* 3.0 36.6 + + + +
329W PHE* 3.8 11.4 - + - +
330W LEU 3.4 0.2 - - - -
331W GLY* 1.3 75.6 - - - +
333W LEU* 1.4 57.0 + - - +
335W ARG* 3.4 37.9 + - - +
336W LEU* 3.0 60.7 + - + +
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Residues in contact with LEU 333 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263W LEU* 3.7 41.7 - - + +
266W LEU* 3.7 26.0 - - + -
268W LYS* 4.3 11.2 - - - +
269W THR* 3.8 18.4 - - + -
278W GLU* 3.8 35.2 - - + +
329W PHE 3.2 15.1 + - - +
330W LEU* 3.4 8.5 + - + +
332W PHE* 1.4 73.9 - - + +
334W ARG* 1.3 56.9 + - - +
336W LEU* 3.1 4.9 + - + +
337W LEU* 2.9 38.1 + - + +
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Residues in contact with ARG 334 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330W LEU* 3.1 19.3 + - + +
331W GLY* 3.3 15.8 + - - +
333W LEU* 1.3 70.9 - - - +
335W ARG* 1.3 83.4 + - - +
337W LEU* 3.3 3.0 + - - +
338W GLU* 2.7 81.6 + - - +
396W PRO* 3.3 47.5 - - + +
397W LEU* 3.5 10.1 - - - +
400W LEU* 3.4 24.3 - - + +
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Residues in contact with ARG 335 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328W HIS* 6.0 0.4 - - - -
331W GLY 2.8 19.4 + - - +
332W PHE* 3.4 51.0 - - - +
334W ARG* 1.3 97.8 - - - +
336W LEU* 1.3 75.0 + - + +
338W GLU* 3.8 2.9 - - + +
339W TYR* 3.1 23.8 + - + +
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Residues in contact with LEU 336 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266W LEU* 4.1 26.5 - - + -
268W LYS 4.7 7.4 - - - +
269W THR* 5.0 5.4 - - + -
332W PHE* 3.0 53.5 + - + +
333W LEU* 3.1 7.2 + - + +
335W ARG* 1.3 98.0 - - - +
337W LEU* 1.3 63.1 + - - +
339W TYR* 3.3 3.9 + - - +
340W VAL* 3.0 32.1 + - + +
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Residues in contact with LEU 337 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259W CYS* 4.7 4.5 - - - +
262W ASN* 3.6 46.4 - - + +
263W LEU* 4.2 22.9 - - + +
266W LEU* 3.9 17.8 - - + +
333W LEU* 2.9 21.1 + - + +
334W ARG* 3.4 8.1 - - - +
336W LEU* 1.3 74.4 - - - +
338W GLU* 1.3 57.9 + - - +
340W VAL* 3.2 9.7 + - + +
341W LYS* 2.8 31.8 + - - +
394W PHE* 4.5 2.7 - - + -
396W PRO* 3.5 35.4 - - + -
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Residues in contact with GLU 338 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334W ARG* 2.7 60.2 + - - +
335W ARG* 3.8 7.0 - - + +
337W LEU* 1.3 72.9 - - - +
339W TYR* 1.3 61.8 + - - +
341W LYS* 3.4 3.6 + - - +
342W TRP* 3.1 24.1 + - - +
394W PHE* 3.9 26.0 - - + -
397W LEU* 4.2 19.7 - - - +
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Residues in contact with TYR 339 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335W ARG* 3.1 18.9 + - + +
336W LEU* 3.7 4.7 - - - +
338W GLU* 1.3 74.2 - - - +
340W VAL* 1.3 66.6 + - + +
342W TRP* 3.3 11.9 + + + +
343W ARG* 3.2 39.3 + - + +
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Residues in contact with VAL 340 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262W ASN* 6.2 0.2 - - - +
266W LEU* 3.7 26.5 - - + -
336W LEU* 3.1 20.0 - - + +
337W LEU* 3.4 9.6 - - + +
339W TYR* 1.3 84.1 - - + +
341W LYS* 1.3 60.1 + - - +
343W ARG* 3.5 46.6 + - - +
344W LEU* 3.8 9.2 + - + +
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Residues in contact with LYS 341 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128W LYS* 4.9 16.4 - - - +
129W ASP* 6.1 0.2 - - - -
132W GLY* 3.4 17.8 + - - -
135W HIS* 4.3 7.7 - - - +
136W SER* 2.8 35.5 + - - +
262W ASN* 6.1 0.7 - - - +
337W LEU 2.8 19.5 + - - +
338W GLU* 3.4 6.9 + - - +
340W VAL* 1.3 68.4 - - - +
342W TRP* 1.3 66.1 + - - +
344W LEU* 3.1 24.7 + - + +
345W ARG* 3.3 10.2 + - - -
346W VAL 4.8 6.0 + - - +
394W PHE* 3.7 48.0 - - + -
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Residues in contact with TRP 342 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135W HIS* 3.8 35.0 - - + -
138W THR* 4.1 21.1 - - + -
139W ALA* 3.7 38.6 + - + +
142W VAL* 4.3 25.3 - - + +
143W ARG* 3.6 16.7 - - + +
338W GLU 3.1 12.5 + - - +
339W TYR* 3.3 16.8 + + - +
341W LYS* 1.3 75.8 - - - +
343W ARG* 1.4 66.4 + - - +
344W LEU 2.9 1.9 + - - -
345W ARG 3.1 10.6 + - - -
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Residues in contact with ARG 343 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143W ARG* 2.9 46.6 + - - +
152W LEU* 4.3 4.2 - - - +
339W TYR* 3.2 25.7 + - + +
340W VAL* 3.5 44.8 + - - +
342W TRP* 1.4 77.3 - - - +
344W LEU* 1.3 57.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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