Contacts of the helix formed by residues 384 - 402 (chain A) in PDB entry 1CYY
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 GLU 384 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A MET* 3.3 35.5 - - - +
310A ARG* 3.4 38.1 + - - +
382A ASP 4.1 0.8 + - - -
383A MET* 1.3 78.0 - - + +
385A ALA* 1.3 67.7 + - - +
386A ASP* 4.6 5.9 - - + +
387A ALA* 3.1 7.0 + - + +
388A GLN* 3.1 19.2 + - - +
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Residues in contact with ALA 385 (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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383A MET 3.9 0.4 + - - -
384A GLU* 1.3 72.6 - - - +
386A ASP* 1.3 64.3 + - - +
388A GLN* 3.2 13.6 + - - +
389A LYS* 3.0 31.4 + - + +
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Residues in contact with ASP 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PHE* 3.5 36.7 - - + -
303A LYS* 3.2 25.9 + - + -
307A MET* 3.9 19.6 - - + +
384A GLU* 3.3 6.0 - - + +
385A ALA* 1.3 80.0 - - - +
387A ALA* 1.3 56.9 + - - +
389A LYS* 3.3 3.4 + - - +
390A LEU* 2.9 30.1 + - - +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A MET* 3.7 29.1 - - + +
310A ARG* 5.2 0.7 - - - -
311A LEU* 3.5 13.8 - - + +
383A MET* 3.8 33.2 - - + -
384A GLU* 3.1 14.6 + - + +
386A ASP* 1.3 78.9 - - - +
388A GLN* 1.3 57.8 + - - +
390A LEU* 3.3 0.6 + - - -
391A TYR* 2.8 29.8 + - - +
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Residues in contact with GLN 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ALA* 3.4 34.3 - - + +
378A GLU* 4.9 6.4 + - - +
380A LEU* 2.7 38.3 + - + +
381A LYS* 4.1 7.7 + - - +
383A MET* 3.2 16.2 + - + +
384A GLU 3.1 12.7 + - - +
385A ALA* 3.4 12.0 - - - +
387A ALA* 1.3 77.4 - - - +
389A LYS* 1.3 57.9 + - + +
391A TYR* 3.2 5.6 + - - +
392A GLN* 2.9 24.3 + - - +
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Residues in contact with LYS 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 3.9 26.8 - - + +
299A PHE* 4.6 4.0 - - + -
385A ALA* 3.0 17.8 + - + +
386A ASP* 3.7 11.0 - - - +
388A GLN* 1.3 78.1 - - + +
390A LEU* 1.3 61.2 + - - +
392A GLN* 3.3 22.7 + - - +
393A LEU* 3.1 21.5 + - - +
275B PRO* 3.7 22.4 - - + +
407B LYS* 5.7 1.0 - - - +
409B ASP* 3.8 11.9 - - - -
430B ARG* 3.4 41.5 - - - +
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Residues in contact with LEU 390 (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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289A LEU* 3.9 20.6 - - + -
293A ALA* 3.9 22.4 - - + -
297A LEU* 4.0 11.1 - - + +
299A PHE* 4.5 7.9 - - + -
304A THR* 3.5 30.1 - - + +
307A MET* 3.6 10.1 - - + -
308A ALA* 3.5 25.1 - - + +
311A LEU* 4.3 4.0 - - + -
386A ASP 2.9 17.4 + - - +
387A ALA* 3.7 5.4 - - - +
389A LYS* 1.3 75.8 - - - +
391A TYR* 1.3 64.3 + - - +
393A LEU* 3.2 6.0 + - + +
394A ILE* 3.0 31.4 + - + +
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Residues in contact with TYR 391 (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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311A LEU* 3.8 9.8 - - + +
316A TYR* 3.5 32.5 + - + -
317A ILE* 3.7 20.0 - - + -
370A PRO* 3.5 17.1 - - + +
372A ASP 3.5 13.5 + - - -
375A VAL* 2.6 39.8 + - + +
376A MET 3.8 2.2 - - - -
377A ALA* 3.5 28.5 - - - -
380A LEU* 3.5 20.6 - - + -
387A ALA 2.8 17.8 + - - +
388A GLN 3.5 4.3 - - - +
390A LEU* 1.3 78.7 - - - +
392A GLN* 1.3 58.5 + - - +
394A ILE* 3.2 4.8 + - + +
395A TRP* 2.8 43.4 + + + +
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Residues in contact with GLN 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ALA* 3.7 15.9 - - + +
378A GLU* 4.4 17.3 + - - +
388A GLN 2.9 13.7 + - - +
389A LYS* 3.6 17.7 - - - +
391A TYR* 1.3 76.1 - - - +
393A LEU* 1.3 58.7 + - - +
395A TRP* 3.4 8.5 + - + +
396A ARG* 2.9 74.3 + - + +
346B LYS* 6.3 1.2 - - - +
430B ARG* 3.3 30.4 + - - +
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Residues in contact with LEU 393 (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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284A PHE* 3.6 23.5 - - + -
289A LEU* 4.5 7.2 - - + -
292A ALA* 3.9 10.1 - - + +
293A ALA* 3.8 36.3 - - + +
296A ARG* 3.7 29.6 - - + +
297A LEU* 4.3 15.5 - - + -
389A LYS 3.1 12.6 + - - +
390A LEU* 3.4 11.0 - - + +
392A GLN* 1.3 75.6 - - - +
394A ILE* 1.3 64.6 + - - +
396A ARG* 3.9 4.6 - - - +
397A GLN* 3.1 18.7 + - - +
438A MET* 4.4 13.9 - - + -
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Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 4.0 10.1 - - + -
289A LEU* 3.7 32.3 - - + -
311A LEU* 4.5 4.9 - - + -
317A ILE* 4.1 21.8 - - + -
368A ILE* 3.7 42.5 - - + +
369A ARG* 3.7 20.4 - - - -
370A PRO* 4.2 2.0 - - + -
390A LEU* 3.0 31.3 + - + +
391A TYR* 3.7 4.5 - - - +
393A LEU* 1.3 75.7 - - - +
395A TRP* 1.3 65.1 + - - +
397A GLN* 3.4 2.1 + - - +
398A PHE* 3.1 22.2 + - - +
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Residues in contact with TRP 395 (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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338A TYR* 3.6 34.5 - + - -
343A PHE* 6.1 0.9 - + - -
370A PRO* 3.5 28.7 - - + -
373A VAL* 2.8 27.0 + - - +
375A VAL 3.5 20.0 + - - -
376A MET* 3.4 35.9 - - + -
377A ALA 5.6 0.7 - - - +
391A TYR* 2.8 31.4 + + + +
392A GLN* 3.5 8.5 - - + +
394A ILE* 1.3 74.1 - - - +
396A ARG* 1.3 85.6 + - + +
398A PHE* 3.4 2.3 + - - +
399A VAL* 3.0 50.7 + - + +
437A VAL* 5.0 10.8 - - + -
346B LYS* 4.9 8.7 - - - -
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Residues in contact with ARG 396 (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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296A ARG* 5.9 0.2 - - - +
392A GLN* 2.9 54.9 + - + +
393A LEU* 3.9 3.6 - - - +
394A ILE 3.3 0.2 - - - -
395A TRP* 1.3 94.7 - - + +
397A GLN* 1.3 60.1 + - - +
399A VAL* 4.8 0.9 - - - -
400A ALA* 2.9 34.1 + - - +
437A VAL* 3.3 25.7 + - - +
438A MET* 3.5 26.2 - - + +
439A PRO* 3.7 14.3 - - - +
346B LYS* 5.5 10.1 - - - +
430B ARG* 2.8 45.6 + - - +
431B PHE* 4.7 11.3 - - - +
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Residues in contact with GLN 397 (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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281A GLY* 3.7 21.9 + - - +
282A ALA 2.9 28.9 + - - +
283A PRO* 4.2 0.2 - - + -
284A PHE* 3.3 59.2 - - + +
296A ARG* 5.8 0.3 + - - -
393A LEU 3.1 4.8 + - - +
394A ILE 3.8 0.9 - - - +
396A ARG* 1.3 79.2 - - - +
398A PHE* 1.3 59.2 + - - +
400A ALA* 3.8 4.2 - - - +
401A CYS* 2.9 31.2 + - - +
434A TRP* 6.0 0.2 - - - -
438A MET* 3.9 19.5 - - - +
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Residues in contact with PHE 398 (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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283A PRO* 4.6 7.8 - - + +
327A LEU* 3.7 37.0 - - + -
331A ALA* 3.7 24.7 - - + -
334A MET* 4.2 4.7 - - + -
335A VAL* 3.7 16.9 - - + +
368A ILE 5.2 0.9 - - - +
369A ARG* 3.7 28.0 - - + -
370A PRO* 3.4 27.1 - - + -
373A VAL* 3.1 34.1 - - + -
394A ILE 3.1 17.5 + - - +
395A TRP 3.6 2.9 - - - +
397A GLN* 1.3 74.6 - - - +
399A VAL* 1.3 69.8 + - + +
401A CYS* 3.1 25.6 - - - -
402A GLN* 3.8 1.7 + - - +
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Residues in contact with VAL 399 (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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335A VAL* 3.6 17.0 - - + -
338A TYR* 4.4 16.6 - - + -
339A ILE* 3.6 20.1 - - + +
343A PHE* 4.6 0.9 - - + -
373A VAL* 4.6 5.4 - - + -
395A TRP* 3.0 49.7 + - + +
396A ARG 4.1 2.2 - - - +
398A PHE* 1.3 81.6 - - + +
400A ALA* 1.3 63.6 + - - +
402A GLN* 3.2 10.4 + - - +
403A MET* 3.4 25.5 - - - +
437A VAL* 4.3 12.3 - - + -
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Residues in contact with ALA 400 (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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280A PRO* 3.1 17.2 - - + +
396A ARG 2.9 19.9 + - - +
397A GLN* 3.9 4.9 - - - +
399A VAL* 1.3 77.4 - - - +
401A CYS* 1.3 62.3 + - - +
402A GLN 3.0 0.4 - - - -
403A MET* 3.0 17.9 + - - -
434A TRP* 3.6 20.4 - - + +
437A VAL* 3.5 20.4 - - + +
438A MET* 3.9 15.7 - - + -
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Residues in contact with CYS 401 (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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280A PRO* 3.9 1.8 - - - -
281A GLY 3.1 25.1 - - - +
283A PRO* 3.7 26.2 - - - -
327A LEU* 3.9 9.0 - - - -
353A ASN* 2.9 15.9 + - - +
355A TYR* 2.6 30.8 + - + +
397A GLN 2.9 13.1 + - - +
398A PHE* 3.1 21.3 - - - -
399A VAL 3.2 0.8 - - - -
400A ALA* 1.3 77.2 - - - +
402A GLN* 1.3 75.7 + - - +
403A MET 3.4 0.4 - - - -
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Residues in contact with GLN 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 3.6 24.3 - - + +
332A VAL* 4.6 7.7 - - + +
335A VAL* 3.5 27.1 - - + -
336A ARG* 4.6 6.6 + - + +
339A ILE* 3.3 25.6 - - + +
348A LEU* 4.6 1.7 - - - +
349A PRO* 3.2 19.5 - - - +
352A PRO* 3.5 12.3 - - - +
353A ASN* 2.9 48.5 + - - +
355A TYR* 4.0 2.0 - - - -
398A PHE 4.3 0.9 - - - +
399A VAL 3.2 4.2 + - - +
400A ALA 3.0 0.8 - - - -
401A CYS* 1.3 99.8 + - - +
403A MET* 1.3 58.1 + - - +
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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