Contacts of the helix formed by residues 344 - 360 (chain D) in PDB entry 4CKG
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 SER 344 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C ARG* 5.6 5.8 - - - -
253D GLU* 4.8 14.3 + - - -
254D GLU* 5.2 3.5 - - - +
327D PHE* 3.4 21.8 - - - +
342D ALA* 4.4 0.3 - - - +
343D ASP* 1.3 79.8 + - - +
345D GLU* 1.4 60.8 + - - +
346D ARG* 3.5 11.2 + - - +
347D LEU* 3.1 33.4 + - - +
348D LEU* 3.2 18.5 + - - +
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Residues in contact with GLU 345 (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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327D PHE* 3.5 29.6 - - + -
344D SER* 1.4 68.5 - - - +
346D ARG* 1.3 65.7 + - - +
348D LEU* 3.3 11.8 + - + +
349D GLN* 3.3 39.0 + - + +
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Residues in contact with ARG 346 (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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253D GLU* 6.6 0.2 - - - -
256D GLU* 2.8 46.9 + - + +
344D SER* 3.4 10.4 + - - +
345D GLU* 1.3 77.0 - - - +
347D LEU* 1.3 65.6 + - + +
349D GLN* 3.4 12.9 + - - +
350D LEU* 3.1 55.9 + - + +
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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
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254D GLU* 4.2 16.2 - - + +
255D PRO 4.0 8.1 - - - +
256D GLU* 4.2 12.8 - - + -
257D PRO* 3.5 33.2 - - + -
271D HIS 6.2 0.4 - - - +
342D ALA* 3.9 13.4 - - + +
343D ASP* 4.0 31.9 - - + +
344D SER* 3.1 23.3 + - - +
345D GLU 3.3 0.4 - - - -
346D ARG* 1.3 77.9 - - + +
348D LEU* 1.4 60.0 + - - +
350D LEU* 4.3 8.5 - - + -
351D TRP* 3.0 45.1 + - + +
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Residues in contact with LEU 348 (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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319D LEU* 5.2 18.6 - - + +
327D PHE* 4.0 24.0 - - + +
328D CYS 3.6 24.7 - - - +
329D PHE* 3.6 27.1 - - + -
342D ALA* 4.1 6.6 - - - +
344D SER 3.2 13.2 + - - +
345D GLU* 3.3 16.4 + - + +
347D LEU* 1.4 75.6 - - - +
349D GLN* 1.3 59.5 + - + +
351D TRP* 3.6 2.6 - - - +
352D VAL* 2.7 45.3 + - + +
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Residues in contact with GLN 349 (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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319D LEU* 6.0 4.7 - - + -
345D GLU* 3.3 26.3 + - - +
346D ARG* 3.7 13.8 + - - +
348D LEU* 1.3 87.1 - - + +
350D LEU* 1.3 53.2 + - - +
352D VAL* 4.1 5.9 - - - +
353D SER* 2.6 43.3 + - - +
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Residues in contact with LEU 350 (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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256D GLU* 4.3 11.4 - - + +
257D PRO* 3.5 33.7 - - + +
259D LEU* 4.9 14.9 - - + +
268D MET* 3.7 24.2 - - + -
346D ARG* 3.1 48.9 + - + +
347D LEU* 4.0 11.0 - - + +
349D GLN* 1.3 79.5 - - - +
351D TRP* 1.4 56.1 + - + +
353D SER* 3.5 5.2 + - - -
354D ALA* 3.0 30.0 + - - +
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Residues in contact with TRP 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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257D PRO* 4.0 15.1 - - + +
268D MET* 3.4 26.7 - - + +
269D GLU 4.2 4.0 - - - -
270D GLY* 3.9 26.5 - - - -
271D HIS 4.4 5.2 + - - -
272D LEU* 3.9 43.1 - - + +
288D PHE* 3.6 22.0 - - + -
290D ILE* 3.7 31.9 - - + -
295D LEU* 4.2 9.4 - - + -
329D PHE* 3.4 25.1 - + + -
342D ALA* 4.7 1.8 - - + -
347D LEU* 3.0 41.4 + - + +
350D LEU* 1.4 71.7 - - + +
352D VAL* 1.3 66.1 + - - +
354D ALA* 3.6 1.1 + - - +
355D VAL* 3.1 33.7 + - + +
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Residues in contact with VAL 352 (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 VAL* 3.8 28.7 - - + +
318D LYS 4.9 1.1 - - - +
319D LEU* 4.1 27.4 - - + -
329D PHE* 3.6 35.4 - - + -
348D LEU* 2.7 32.5 + - + +
349D GLN* 4.1 5.2 - - - +
351D TRP* 1.3 72.3 - - - +
353D SER* 1.4 57.3 + - - +
355D VAL* 3.4 2.4 + - - +
356D GLN* 2.9 29.0 + - + +
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Residues in contact with SER 353 (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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259D LEU* 4.8 5.8 - - - -
349D GLN* 2.6 30.0 + - - +
350D LEU* 3.9 6.7 - - - -
351D TRP 3.4 0.2 - - - -
352D VAL* 1.4 74.9 - - - +
354D ALA* 1.3 56.3 + - - +
356D GLN* 3.3 16.0 + - - +
357D SER* 2.8 33.2 + - - -
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Residues in contact with ALA 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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259D LEU* 3.5 38.7 - - + +
268D MET* 3.8 7.6 - - + -
290D ILE* 3.6 22.0 - - + +
350D LEU 3.0 19.2 + - - +
351D TRP 4.1 1.8 - - - +
353D SER* 1.3 74.5 - - - +
355D VAL* 1.4 59.9 + - - +
357D SER* 4.2 2.6 - - - +
358D SER* 2.9 27.7 + - - -
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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
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290D ILE* 4.8 12.1 - - + -
295D LEU* 5.6 6.7 - - + -
312D LEU* 4.5 22.4 - - + -
315D CYS* 4.6 3.1 - - - -
317D VAL* 4.3 7.6 - - + -
329D PHE* 4.5 7.9 - - + -
331D VAL* 3.7 33.2 - - + -
351D TRP* 3.1 23.9 + - + +
352D VAL 3.9 3.1 - - - +
354D ALA* 1.4 75.0 - - - +
356D GLN* 1.4 53.3 + - - +
358D SER* 3.0 8.5 + - - -
359D ILE* 2.8 50.2 + - + +
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Residues in contact with GLN 356 (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 VAL* 4.1 15.0 - - + +
352D VAL* 2.9 19.6 + - + +
353D SER* 3.1 22.9 + - - +
355D VAL* 1.4 74.7 - - - +
357D SER* 1.3 70.2 + - - +
359D ILE* 3.5 13.7 + - + +
360D ALA* 3.4 17.7 + - - +
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Residues in contact with SER 357 (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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259D LEU* 5.3 4.0 - - - +
266D LEU* 4.6 21.3 - - - +
353D SER* 2.8 20.2 + - - -
354D ALA* 4.2 5.4 - - - -
356D GLN* 1.3 79.9 + - - +
358D SER* 1.3 57.3 + - - +
360D ALA* 3.1 27.0 + - - +
361D SER* 3.5 6.1 + - - -
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Residues in contact with SER 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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259D LEU* 6.1 0.2 - - - +
266D LEU* 5.6 3.8 + - - +
290D ILE* 3.8 15.9 - - - +
293D ASN* 4.4 5.6 + - - +
312D LEU* 3.5 31.0 - - - +
313D ARG* 3.7 10.7 - - - +
354D ALA 2.9 16.3 + - - -
355D VAL 3.0 9.5 + - - -
357D SER* 1.3 76.3 - - - +
359D ILE* 1.3 62.3 + - - +
361D SER* 3.1 26.4 + - - -
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Residues in contact with ILE 359 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312D LEU 3.2 20.8 + - - +
313D ARG* 3.6 19.2 - - - +
315D CYS* 3.6 29.4 - - + +
316D THR* 3.8 17.9 - - - -
317D VAL* 4.0 24.7 - - + +
355D VAL* 2.8 25.4 + - + +
356D GLN* 3.8 11.0 - - + +
358D SER* 1.3 71.2 - - - +
360D ALA* 1.4 58.8 + - - +
361D SER 3.5 1.4 + - - -
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Residues in contact with ALA 360 (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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356D GLN* 3.4 10.3 + - - +
357D SER* 3.1 16.3 + - - +
359D ILE* 1.4 74.8 - - - +
361D SER* 1.4 60.4 + - - +
362D ALA 3.5 2.9 + - - -
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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