Contacts of the helix formed by residues 345 - 360 (chain D) in PDB entry 4GQS
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 MET 345 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326D GLU* 3.1 17.9 - - - +
327D ILE* 3.9 34.3 - - + +
330D VAL* 3.4 27.4 - - + -
331D VAL* 4.2 11.2 - - + -
337D PRO* 6.1 0.9 - - - -
341D ASP* 3.2 18.2 - - - +
342D ARG* 2.8 12.7 + - - +
343D GLY 3.3 1.2 - - - -
344D HIS* 1.3 79.7 - - - +
346D PRO* 1.3 64.6 - - - +
348D THR* 3.0 38.6 - - + +
349D ASP* 3.2 23.6 + - - +
446D PHE* 3.9 15.5 - - - -
450D THR* 4.4 5.8 - - + -
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Residues in contact with PRO 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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326D GLU* 3.1 12.8 - - - +
329D ARG* 5.8 1.8 - - - +
343D GLY 5.1 1.8 - - - +
344D HIS 3.5 8.7 - - - +
345D MET* 1.3 83.7 - - - +
347D TYR* 1.3 59.8 + - + +
349D ASP* 3.1 4.5 + - + +
350D ALA* 2.6 39.4 + - - +
413D LEU* 4.2 1.8 - - + -
417D GLY 3.6 24.7 - - - +
418D ASN* 4.2 3.6 - - - +
419D PHE* 3.9 27.0 - - + +
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Residues in contact with TYR 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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319D VAL* 3.5 46.6 - - - +
322D LYS* 3.8 37.7 + - + +
323D VAL* 3.8 12.1 - - + -
326D GLU* 3.5 13.8 + - + +
346D PRO* 1.3 81.7 - - + +
348D THR* 1.3 55.3 + - - +
350D ALA* 2.8 6.1 + - - +
351D VAL* 2.6 58.8 + - + +
409D PRO* 3.5 20.4 - - + +
410D ARG* 5.4 3.4 - - + -
413D LEU* 3.6 24.1 - - + +
417D GLY 5.0 0.2 + - - -
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Residues in contact with THR 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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323D VAL* 3.9 25.6 + - + +
326D GLU* 2.7 23.0 + - - +
345D MET* 3.0 19.6 - - + +
347D TYR* 1.3 82.5 - - - +
349D ASP* 1.3 59.9 + - - +
351D VAL* 3.3 6.8 + - - +
352D VAL* 3.0 30.6 + - + +
446D PHE* 3.3 31.9 - - + -
450D THR* 3.8 16.6 - - + -
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Residues in contact with ASP 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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342D ARG* 3.5 28.0 - - + +
345D MET 3.2 16.4 + - - +
346D PRO* 3.1 5.0 + - + +
348D THR* 1.3 81.4 - - - +
350D ALA* 1.3 61.5 + - - +
352D VAL* 3.7 9.0 + - - +
353D HIS* 3.6 26.3 + - - -
419D PHE* 3.1 40.3 - - + -
442D ARG* 3.3 23.7 + - - -
446D PHE* 5.2 2.4 - - - -
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Residues in contact with ALA 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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346D PRO 2.6 20.9 + - - +
347D TYR* 2.8 9.5 + - + +
349D ASP* 1.3 72.4 - - - +
351D VAL* 1.3 61.2 + - - +
353D HIS* 3.5 4.7 + - - +
354D GLU* 3.2 21.1 + - - +
409D PRO 4.0 8.3 - - - +
412D PHE* 3.5 28.3 - - - +
413D LEU* 3.5 19.3 - - + -
419D PHE* 4.1 12.3 - - + -
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Residues in contact with VAL 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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313D LEU* 4.6 9.0 - - + -
319D VAL* 3.9 17.5 - - + -
323D VAL* 4.2 8.3 - - + -
347D TYR* 2.6 51.7 + - + +
348D THR* 3.7 4.9 - - - +
350D ALA* 1.3 70.0 - - - +
352D VAL* 1.3 68.9 + - + +
353D HIS 3.0 3.2 + - - -
354D GLU* 3.1 4.2 + - - +
355D VAL* 3.0 33.8 + - + +
407D PHE* 4.5 6.3 - - + -
409D PRO* 3.7 20.6 - - + -
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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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348D THR* 3.0 27.1 - - + +
349D ASP* 3.8 10.5 - - - +
350D ALA 3.4 0.2 - - - -
351D VAL* 1.3 78.8 - - + +
353D HIS* 1.3 68.2 + - + +
355D VAL* 3.4 9.3 - - + +
356D GLN* 3.4 25.7 + - + +
442D ARG* 5.4 7.0 - - - +
445D LEU* 4.1 33.2 - - + +
446D PHE* 4.8 11.4 - - + +
449D LEU* 4.7 19.5 - - + -
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Residues in contact with HIS 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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349D ASP* 3.6 11.7 + - - -
350D ALA 3.5 5.3 + - - +
351D VAL 3.0 0.6 - - - -
352D VAL* 1.3 81.3 - - + +
354D GLU* 1.3 52.8 + - - +
355D VAL 2.8 4.7 - - - -
356D GLN* 2.7 24.9 + - - +
357D ARG* 2.7 18.2 + - - +
412D PHE* 3.4 32.0 - - + -
419D PHE* 3.2 36.4 - + - -
421D LYS* 3.8 18.4 + - - -
425D PHE* 3.4 25.0 - + + -
442D ARG* 2.7 40.6 + - - -
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Residues in contact with GLU 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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350D ALA 3.2 6.8 + - - +
351D VAL* 3.1 8.0 + - - +
353D HIS* 1.3 77.8 - - - +
355D VAL* 1.3 56.5 + - - +
357D ARG* 2.9 30.2 + - - -
358D TYR* 3.0 30.7 + - - +
406D MET 3.3 2.4 - - - +
407D PHE* 3.4 21.0 - - + -
408D ASP 2.8 43.0 + - - +
409D PRO* 3.6 16.4 - - + -
411D HIS* 2.7 28.3 + - - +
412D PHE* 3.8 8.7 - - + -
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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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305D THR* 4.4 13.9 - - + +
309D ALA* 4.1 29.2 - - + +
312D LEU* 3.6 17.5 - - + -
313D LEU* 6.0 1.6 - - + -
351D VAL* 3.0 25.5 + - + +
352D VAL* 3.4 12.1 - - - +
353D HIS 2.8 1.2 + - - -
354D GLU* 1.3 77.3 - - - +
356D GLN* 1.3 59.0 + - - +
358D TYR* 3.2 1.0 + - - +
359D ILE* 2.9 42.0 + - + +
407D PHE* 3.4 28.7 - - + -
449D LEU* 6.3 0.7 - - + -
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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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305D THR* 3.9 21.3 - - + +
352D VAL* 3.4 17.4 + - + +
353D HIS* 2.7 12.1 + - - +
355D VAL* 1.3 72.5 - - - +
357D ARG* 1.3 60.3 + - - +
358D TYR 3.1 5.3 + - - -
359D ILE* 3.8 8.2 - - + +
360D ASP* 3.2 21.3 + - - -
361D LEU 4.8 0.3 + - - -
395D LEU* 4.1 5.7 - - - +
425D PHE* 3.8 13.3 - - + -
427D PRO* 4.1 21.1 - - + +
428D PHE* 3.7 26.1 - - - -
442D ARG* 4.9 5.7 + - - +
445D LEU* 5.3 5.0 - - - +
501D HEM 3.4 41.9 - - - +
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Residues in contact with ARG 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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353D HIS 2.7 18.5 + - - +
354D GLU* 2.9 33.5 + - - +
356D GLN* 1.3 72.5 - - - +
358D TYR* 1.3 65.3 + - - +
360D ASP 4.5 0.9 - - - -
395D LEU* 2.9 54.5 + - + +
396D HIS* 2.8 26.8 + - - -
401D PHE* 3.5 39.3 - - + +
404D PRO* 2.9 44.3 + - - +
406D MET 3.4 8.9 + - - -
411D HIS* 3.6 9.3 + - - -
412D PHE* 3.8 14.8 - - + -
425D PHE* 4.6 4.8 - - + -
427D PRO* 4.9 0.7 - - - -
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Residues in contact with TYR 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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308D TYR* 4.5 5.2 - + - -
312D LEU* 3.9 22.0 - - + -
354D GLU 3.0 19.3 + - - +
355D VAL 3.6 2.0 - - - +
356D GLN 3.1 0.4 - - - -
357D ARG* 1.3 86.1 - - - +
359D ILE* 1.3 74.8 + - + +
360D ASP* 3.2 1.8 - - - +
396D HIS* 3.3 22.3 + + - -
404D PRO 4.6 1.3 - - - -
405D GLU* 2.9 29.4 + - - -
406D MET 4.0 3.6 - - - -
407D PHE* 3.8 33.9 - + + -
469D THR* 3.1 40.6 + - - -
470D THR* 4.9 0.9 - - - -
471D PRO* 4.8 12.8 - - + +
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Residues in contact with ILE 359 (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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304D THR 4.9 0.4 - - - +
305D THR* 4.0 38.4 - - + +
308D TYR* 3.4 53.5 - - + -
312D LEU* 4.0 11.0 - - + -
355D VAL* 2.9 21.2 + - + +
356D GLN* 3.8 8.5 - - + +
358D TYR* 1.3 80.3 - - + +
360D ASP* 1.3 73.9 + - - +
361D LEU* 3.6 25.4 - - + +
471D PRO* 4.6 8.8 - - - +
478D SER* 3.1 14.3 + - - +
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Residues in contact with ASP 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 3.2 11.6 + - - -
358D TYR 3.2 7.4 - - - +
359D ILE* 1.3 81.2 - - - +
361D LEU* 1.3 67.4 + - - +
362D ILE 2.9 16.9 + - - +
363D PRO* 3.2 20.1 - - - +
391D LEU* 4.5 0.5 - - - +
392D THR* 2.9 40.3 + - + +
395D LEU* 3.7 22.2 - - + +
396D HIS* 4.3 12.3 - - + +
478D SER* 2.8 10.4 + - - -
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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
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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