Contacts of the helix formed by residues 336 - 358 (chain D) in PDB entry 4JGH
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 336 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D THR 3.7 0.8 + - - -
333D ILE 2.9 22.4 + - - +
334D THR 3.4 1.1 - - - -
335D THR* 1.3 85.5 + - - +
337D SER* 1.3 82.2 + - - +
338D GLU* 2.9 26.5 + - - +
339D LYS* 3.6 32.4 - - + +
340D TYR* 3.3 10.9 + - - +
383D PHE* 6.2 1.8 - - - -
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Residues in contact with SER 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D ASP* 1.3 80.0 + - - +
338D GLU* 1.3 68.8 + - - -
340D TYR* 3.4 9.9 - - - +
341D ARG* 3.3 40.7 + - - +
383D PHE* 6.3 2.0 - - - -
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Residues in contact with GLU 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D ASP* 2.9 18.7 + - - +
337D SER* 1.3 88.1 + - - +
339D LYS* 1.3 57.7 + - + +
340D TYR 3.0 4.9 - - - -
341D ARG* 3.2 35.7 + - - +
342D GLU* 2.9 39.4 + - + +
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Residues in contact with LYS 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D THR* 4.3 23.1 + - - +
333D ILE* 4.0 11.6 - - - +
335D THR* 5.4 0.9 - - - +
336D ASP* 3.4 33.7 + - + +
338D GLU* 1.3 77.4 - - - +
340D TYR* 1.3 63.6 + - - +
342D GLU* 3.7 32.5 + - - +
343D GLN* 3.5 18.7 + - - +
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Residues in contact with TYR 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D MET* 3.4 20.1 - - + +
333D ILE* 3.2 36.6 - - + +
336D ASP 3.3 10.2 + - - +
337D SER* 3.4 16.2 - - - +
339D LYS* 1.3 76.0 - - - +
341D ARG* 1.3 75.4 + - + +
343D GLN* 3.0 15.4 + - - +
344D LEU* 3.3 30.9 + - + +
377D VAL 4.2 7.4 + - - -
380D ALA* 3.4 36.4 - - - +
381D THR* 3.5 8.1 + - - -
382D ILE* 4.3 15.9 - - + -
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Residues in contact with ARG 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D SER* 3.3 22.3 + - - +
338D GLU* 3.2 36.8 + - - +
340D TYR* 1.3 89.7 - - + +
342D GLU* 1.3 56.6 + - - +
344D LEU* 3.0 9.6 + - + +
345D ASP* 2.7 42.6 + - - +
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Residues in contact with GLU 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D GLU* 2.9 31.4 + - + +
339D LYS* 3.7 38.9 + - - +
341D ARG* 1.3 75.3 - - - +
343D GLN* 1.3 53.4 + - - +
345D ASP* 3.3 8.8 + - - +
346D THR* 2.7 41.5 + - - +
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Residues in contact with GLN 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D ASP* 3.7 23.6 + - + +
326D MET* 3.8 16.2 - - - -
329D ALA* 3.4 26.5 - - - +
332D THR* 5.6 1.2 + - - -
333D ILE* 3.7 19.5 - - + +
339D LYS 3.5 10.3 + - - +
340D TYR 3.0 11.5 + - - +
342D GLU* 1.3 77.4 - - - +
344D LEU* 1.3 66.1 + - - +
346D THR* 3.3 15.1 + - - +
347D LEU* 3.1 28.3 + - - +
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Residues in contact with LEU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D MET* 3.3 35.9 - - + -
340D TYR* 3.3 34.9 + - + +
341D ARG* 3.0 11.0 + - + +
343D GLN* 1.3 76.6 - - - +
345D ASP* 1.3 60.2 - - - +
347D LEU* 3.3 9.3 + - + +
348D PHE* 2.9 29.8 + - - +
373D TYR* 3.6 19.7 - - + +
376D VAL* 4.7 14.6 - - + -
377D VAL* 4.3 30.3 - - + -
380D ALA* 4.7 2.9 - - + -
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Residues in contact with ASP 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D ARG* 2.7 36.6 + - - +
342D GLU* 3.5 9.4 - - - +
344D LEU* 1.3 77.2 - - - +
346D THR* 1.3 66.2 + - - +
347D LEU 3.1 1.8 - - - -
348D PHE* 4.5 4.3 - - - +
349D ASN* 2.9 37.6 + - - +
373D TYR* 4.9 2.6 + - - -
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Residues in contact with THR 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D ASP* 5.6 0.9 - - - +
342D GLU* 2.7 28.8 + - - +
343D GLN* 3.3 19.0 + - - +
345D ASP* 1.3 72.5 - - - +
347D LEU* 1.3 63.1 + - + +
349D ASN* 3.9 5.3 - - - +
350D ARG* 3.1 27.8 + - + +
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Residues in contact with LEU 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ALA 5.5 0.2 - - - +
322D GLY* 3.7 35.7 - - - +
325D ASP* 3.0 36.3 - - + +
326D MET* 4.8 7.6 - - + -
343D GLN 3.1 15.7 + - - +
344D LEU* 3.5 14.6 - - + +
345D ASP 3.1 0.6 - - - -
346D THR* 1.3 78.1 - - + +
348D PHE* 1.3 59.2 + - - +
349D ASN 3.0 1.3 - - - -
350D ARG* 2.6 45.4 + - - +
351D PHE* 2.7 33.1 + - + -
373D TYR* 5.2 3.8 - - + -
376D VAL* 5.1 2.9 - - + -
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Residues in contact with PHE 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D LEU 2.9 14.7 + - - +
345D ASP* 4.0 5.4 - - - +
347D LEU* 1.3 72.3 - - - +
349D ASN* 1.3 68.5 + - - +
351D PHE* 4.2 4.2 - - - +
352D SER* 2.8 54.1 + - - -
369D ARG* 4.0 29.6 - - - -
370D ASP* 4.9 4.0 - - - -
373D TYR* 3.3 54.8 - + + +
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Residues in contact with ASN 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D ASP* 2.9 31.1 + - - +
346D THR* 3.9 6.3 - - - +
348D PHE* 1.3 86.8 - - - +
350D ARG* 1.3 58.6 + - - +
352D SER* 4.1 3.6 - - - -
353D LYS* 3.1 27.2 + - - +
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Residues in contact with ARG 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D ASN* 5.2 4.3 + - - +
317D HIS* 4.5 6.5 + - - -
321D ALA* 4.2 23.8 + - - +
325D ASP* 3.8 21.2 + - - +
346D THR* 3.1 17.2 + - + +
347D LEU* 2.6 32.3 + - - +
349D ASN* 1.3 72.0 - - - +
351D PHE* 1.3 81.2 + - + +
353D LYS* 3.1 21.5 - - - +
354D LEU* 3.3 8.0 + - - +
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Residues in contact with PHE 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D HIS* 3.9 26.2 - + - -
318D ILE* 3.7 58.3 - - + -
321D ALA* 4.4 5.4 - - + -
322D GLY* 4.3 14.1 - - - -
347D LEU* 2.7 42.8 + - + +
348D PHE* 4.2 5.4 - - - +
350D ARG* 1.3 94.6 - - + +
352D SER* 1.3 64.6 + - - +
353D LYS 2.9 4.5 - - - -
354D LEU* 2.9 25.0 + - + +
355D VAL* 2.9 18.2 + - + +
369D ARG* 4.6 7.6 - - + -
373D TYR* 5.1 7.6 - + + -
376D VAL* 5.7 0.9 - - + -
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Residues in contact with SER 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D PHE* 2.8 39.2 + - - -
349D ASN* 4.3 4.3 - - - -
351D PHE* 1.3 77.3 - - - +
353D LYS* 1.3 59.9 - - - +
355D VAL* 3.9 4.1 - - - +
356D LYS* 3.1 24.3 + - - +
361D ASP* 4.5 1.4 - - - +
369D ARG* 2.8 37.6 + - - +
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Residues in contact with LYS 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D ASN* 5.6 2.5 - - - +
349D ASN 3.1 17.8 + - - +
350D ARG* 3.1 15.9 - - - +
352D SER* 1.3 77.0 - - - +
354D LEU* 1.3 66.0 + - - +
356D LYS* 3.7 11.2 - - - +
357D GLU* 3.1 62.6 + - + +
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Residues in contact with LEU 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D ILE* 4.0 19.5 - - + +
288D ASN* 3.4 32.7 - - - +
290D THR* 3.7 16.8 - - + -
293D LEU* 4.4 11.9 - - + -
314D LEU* 3.8 29.2 - - + -
317D HIS* 5.8 3.8 - - + -
350D ARG 3.3 7.0 + - - +
351D PHE* 2.9 20.5 + - + +
353D LYS* 1.3 79.7 - - - +
355D VAL* 1.3 65.4 + - + +
356D LYS 3.0 0.7 + - - -
357D GLU* 3.1 7.0 + - - -
358D ALA* 2.8 34.9 + - + +
359D PHE* 5.1 2.2 - - + -
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Residues in contact with VAL 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D LEU* 4.3 20.6 - - + -
318D ILE* 5.8 0.9 - - + -
351D PHE* 2.9 24.9 + - + +
352D SER* 3.9 8.3 - - - +
354D LEU* 1.3 74.9 - - + +
356D LYS* 1.3 64.9 + - - +
359D PHE* 3.1 26.0 + - + +
361D ASP* 3.2 17.1 + - - +
365D PHE* 4.3 26.5 - - + +
366D LEU* 3.4 31.4 - - + -
369D ARG* 4.4 13.5 - - + -
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Residues in contact with LYS 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352D SER 3.1 16.2 + - - +
353D LYS* 3.7 10.4 - - - +
355D VAL* 1.3 82.7 - - - +
357D GLU* 1.3 81.6 + - - +
360D GLN* 3.1 19.5 + - - +
361D ASP* 3.0 31.6 + - - +
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Residues in contact with GLU 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D ASN* 4.2 7.8 + - - +
290D THR* 3.6 32.8 - - + +
294D HIS* 4.3 10.2 - - - +
353D LYS* 3.1 55.9 + - + +
354D LEU* 4.3 1.2 - - - -
356D LYS* 1.3 92.7 - - - +
358D ALA* 1.3 61.5 + - - +
360D GLN* 4.4 1.6 + - - +
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Residues in contact with ALA 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D THR* 3.6 34.3 - - + -
293D LEU* 3.7 21.1 - - + -
294D HIS* 3.3 33.0 - - - -
297D PHE* 4.8 1.2 - - - -
354D LEU* 2.8 24.8 + - + +
357D GLU* 1.3 71.3 - - - +
359D PHE* 1.3 64.6 + - + +
360D GLN* 3.2 7.4 + - - +
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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