Contacts of the helix formed by residues 317 - 334 (chain A) in PDB entry 3WZU
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 ILE 317 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LYS* 3.6 36.1 - - + +
255A VAL 5.1 0.2 - - - +
256A ILE* 3.6 27.5 - - + +
316A ASP* 1.3 88.9 - - - +
318A ARG* 1.3 58.0 + - - +
319A ALA 2.5 19.4 + - - -
320A ASP* 2.6 29.5 + - - +
321A VAL* 3.6 2.8 + - + -
386A LYS* 3.8 28.3 - - + -
387A TYR* 3.7 49.3 + - + +
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Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLU* 4.3 10.1 - - - +
315A TYR* 4.5 7.9 + - - -
316A ASP* 2.9 26.7 + - - +
317A ILE* 1.3 94.3 - - - +
319A ALA* 1.3 60.0 + - - +
320A ASP 3.4 0.2 - - - -
321A VAL* 3.1 24.8 - - - +
322A TRP 3.2 0.5 + - - -
381A HIS* 3.4 41.0 + - - +
382A ARG* 3.7 19.8 + - - +
384A ARG* 2.9 51.0 + - + +
385A PRO 4.4 5.4 - - - +
386A LYS* 3.9 27.2 - - - +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TYR 4.7 1.7 - - - +
301A ALA* 4.2 8.3 + - + +
303A GLU* 4.2 7.6 + - - +
304A ARG* 3.9 29.4 - - + +
314A ASP* 4.7 7.0 - - - +
315A TYR 5.9 0.2 - - - -
316A ASP 3.5 13.3 + - - +
317A ILE 2.5 6.1 + - - -
318A ARG* 1.3 73.3 - - - +
320A ASP* 1.3 66.2 + - - +
322A TRP* 3.3 6.4 - - - +
323A SER* 3.0 22.0 + - - -
384A ARG* 3.8 8.7 - - - +
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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
----------------------------------------------------------
246A LEU* 3.9 6.9 - - + +
256A ILE* 4.0 20.1 - - - +
257A HIS 2.6 30.2 + - - +
258A ARG* 3.0 17.3 - - - +
260A VAL* 3.6 17.6 - - + +
317A ILE* 2.6 13.8 + - - +
319A ALA* 1.3 71.4 - - - +
321A VAL* 1.3 66.7 + - - +
323A SER* 2.7 20.3 + - - -
324A LEU* 2.9 13.0 + - - +
387A TYR* 3.0 27.2 + - - +
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 5.6 0.2 - - - -
317A ILE* 4.2 2.7 - - + +
318A ARG* 3.1 24.7 - - - +
320A ASP* 1.3 74.8 - - - +
322A TRP* 1.3 64.4 + - - +
324A LEU* 3.0 26.4 + - - +
325A GLY 3.1 5.4 + - - -
376A CYS* 3.7 39.1 - - - +
384A ARG* 4.6 4.3 - - + +
385A PRO* 3.4 31.0 - - + +
387A TYR* 4.0 23.4 - - + -
390A LEU* 4.1 11.4 - - + -
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Residues in contact with TRP 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ALA 4.4 1.6 + - - -
299A TYR 3.2 25.5 + - - -
300A MET 3.4 15.4 + - - -
301A ALA* 3.9 4.3 - - + -
302A PRO* 3.4 19.3 - - + -
318A ARG 3.2 4.2 + - - -
319A ALA 3.3 7.4 - - - +
320A ASP 3.2 0.2 - - - -
321A VAL* 1.3 76.4 - - - +
323A SER* 1.3 57.2 + - - +
325A GLY* 2.9 18.5 + - - -
326A ILE* 3.1 41.7 + - + +
338A TYR* 4.7 7.6 - - - -
351A VAL* 3.9 22.0 - - + -
354A GLU 5.9 0.4 - - - -
356A PRO* 4.8 11.4 - - + -
357A PRO* 5.0 1.3 - - + -
376A CYS 4.5 6.3 - - - -
377A LEU* 3.8 26.7 - - + +
378A THR 3.9 9.9 - - - -
379A LYS* 4.3 12.6 - - + -
384A ARG* 2.7 52.9 - - - +
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG 4.6 3.6 + - - -
260A VAL* 3.0 31.9 + - - +
299A TYR* 3.6 27.6 + - - +
319A ALA 3.0 14.6 + - - -
320A ASP* 2.7 18.0 + - - -
322A TRP* 1.3 72.8 - - - +
324A LEU* 1.3 55.1 + - - -
326A ILE* 3.9 4.9 - - - +
327A SER* 2.5 38.9 + - - -
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Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A MET* 5.7 3.4 - - + -
239A THR* 4.8 5.8 - - + -
242A ILE* 4.3 28.9 - - + -
243A VAL* 3.6 31.0 - - + -
246A LEU* 5.1 6.1 - - + -
260A VAL* 4.2 9.8 - - + +
265A ILE* 6.2 1.8 - - + -
320A ASP 2.9 9.5 + - - +
321A VAL* 3.0 15.3 - - - +
323A SER* 1.3 74.2 - - - +
325A GLY* 1.3 67.2 + - - +
327A SER* 3.1 7.2 + - - -
328A LEU* 2.8 45.4 + - + +
372A PHE* 4.3 16.4 - - + -
376A CYS* 4.5 7.2 - - - -
387A TYR* 6.2 1.3 - - + -
390A LEU* 5.2 4.0 - - + -
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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
----------------------------------------------------------
321A VAL 3.1 3.8 + - - -
322A TRP 2.9 9.2 + - - -
324A LEU* 1.3 78.4 - - - +
326A ILE* 1.3 52.7 + - - -
328A LEU* 2.6 31.5 + - - +
329A VAL* 2.8 16.8 + - - +
373A VAL* 4.9 3.8 - - - -
376A CYS* 4.1 13.3 - - - +
377A LEU* 3.6 19.3 - - - -
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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
----------------------------------------------------------
298A ALA 5.1 3.1 - - - +
299A TYR* 3.7 32.1 - - + -
322A TRP* 3.1 48.2 + - + +
323A SER* 4.1 2.2 - - - +
325A GLY* 1.3 73.6 - - - +
327A SER* 1.3 54.6 + - - +
329A VAL* 4.5 5.2 - - - +
330A GLU* 2.6 34.3 + - - +
336A PHE* 4.1 13.2 - - + -
337A PRO* 3.8 18.8 - - + -
338A TYR* 4.7 9.0 - - + +
357A PRO* 4.2 19.7 - - + -
377A LEU* 3.6 14.7 - - + +
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Residues in contact with SER 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A MET* 5.9 1.3 - - - -
260A VAL* 3.4 12.5 + - - -
261A LYS* 3.5 2.4 - - - -
262A PRO* 3.3 31.4 - - - +
265A ILE* 4.9 7.4 - - - -
299A TYR* 4.0 4.7 - - - -
323A SER 2.5 23.6 + - - -
324A LEU* 3.3 9.4 - - - -
326A ILE* 1.3 78.1 - - - +
328A LEU* 1.3 50.6 + - - +
330A GLU* 3.7 3.4 - - - +
331A LEU* 2.7 49.3 + - - +
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Residues in contact with LEU 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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235A LEU* 4.1 24.3 - - + +
238A MET* 4.5 15.0 - - + -
239A THR* 3.4 20.6 - - - +
324A LEU* 2.8 39.9 + - + +
325A GLY* 2.6 15.4 + - - +
327A SER* 1.3 67.8 - - - +
329A VAL* 1.3 55.5 + - - +
331A LEU* 2.8 5.4 + - - +
332A ALA* 2.4 40.3 + - - +
369A PHE* 4.5 6.1 - - + -
372A PHE* 3.9 24.9 - - + -
373A VAL* 3.6 25.4 - - + -
376A CYS* 5.3 0.4 - - - -
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLY 2.8 20.5 + - - +
326A ILE* 3.9 6.1 - - - +
328A LEU* 1.3 67.7 - - - +
330A GLU* 1.3 61.3 + - - +
331A LEU 2.9 1.0 + - - -
332A ALA* 4.3 4.7 - - - +
333A THR* 2.6 50.1 + - + +
337A PRO* 4.6 15.9 - - + -
357A PRO* 3.6 27.6 - - + +
358A LEU 5.1 1.1 - - - +
359A LEU* 4.4 11.0 - - + +
360A PRO* 5.1 1.3 - - + -
373A VAL* 3.8 25.1 - - + +
377A LEU* 3.8 10.5 - - + -
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Residues in contact with GLU 330 (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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220A GLU* 2.9 23.4 - - - +
223A LYS* 4.9 15.1 - - + +
262A PRO* 4.0 10.3 - - - +
299A TYR* 2.4 31.9 + - - -
326A ILE 2.6 24.1 + - - +
327A SER 3.7 4.0 - - - +
329A VAL* 1.3 71.5 - - - +
331A LEU* 1.3 62.3 + - + +
334A GLY* 2.9 26.2 + - - -
335A GLN* 3.2 18.9 + - - +
336A PHE* 3.4 27.7 - - + +
337A PRO* 4.1 11.7 - - + +
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ALA* 4.4 15.7 - - + -
223A LYS* 4.5 19.6 - - + +
229A PRO* 3.7 1.0 - - - +
230A ILE* 3.2 45.8 + - + +
235A LEU* 3.9 15.5 - - + -
238A MET* 4.2 24.7 - - + -
262A PRO* 3.7 30.1 - - + -
265A ILE* 4.9 0.7 - - + -
327A SER* 2.7 30.0 + - - +
328A LEU* 2.8 4.5 + - - +
330A GLU* 1.3 78.6 - - + +
332A ALA* 1.3 64.3 + - - +
334A GLY* 3.7 5.1 + - - -
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Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PRO* 2.5 31.0 - - - +
230A ILE 4.1 4.2 - - - +
235A LEU* 3.5 20.8 - - + +
328A LEU 2.4 24.2 + - - +
329A VAL 4.1 1.8 - - - +
331A LEU* 1.3 72.4 - - - +
333A THR* 1.3 54.2 + - - +
359A LEU* 4.3 12.6 - - + -
363A MET* 4.8 0.5 - - - +
365A PHE* 3.8 33.0 - - + -
369A PHE* 4.1 9.9 - - + -
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Residues in contact with THR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PRO* 3.7 14.2 - - - +
329A VAL* 2.6 30.5 + - + +
332A ALA* 1.3 76.6 - - - +
334A GLY* 1.3 60.6 + - - +
335A GLN* 3.0 42.4 + - - +
339A LYS* 4.9 3.9 + - - +
359A LEU* 3.9 25.6 - - + -
360A PRO* 4.0 17.0 - - + -
363A MET* 4.3 17.0 - - - +
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Residues in contact with GLY 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LYS* 3.0 39.6 - - - -
228A GLY* 5.3 0.9 - - - -
229A PRO* 3.9 21.6 - - - +
330A GLU* 2.9 13.1 + - - -
331A LEU 3.7 1.3 + - - -
332A ALA 3.3 2.6 - - - -
333A THR* 1.3 76.7 - - - +
335A GLN* 1.3 66.6 + - - +
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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) + - + + + + + -
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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