Contacts of the helix formed by residues 344 - 358 (chain D) in PDB entry 3CB4
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 GLY 344 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D ASP* 3.2 17.2 + - - -
294D GLN* 3.6 13.2 - - - -
295D VAL* 3.9 14.3 - - - +
342D PHE* 3.3 4.3 - - - +
343D LEU* 1.3 80.5 - - - +
345D LEU* 1.3 66.4 + - - +
347D HIS* 3.9 0.6 - - - +
348D MET* 3.1 23.1 + - - +
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Residues in contact with LEU 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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83D ASP* 3.4 2.0 + - - -
295D VAL* 4.6 1.4 - - - +
344D GLY* 1.3 70.8 - - - -
346D LEU* 1.3 57.8 + - + +
348D MET* 3.1 25.7 + - + +
349D GLU* 2.7 60.4 + - - +
368D PRO* 4.9 1.1 - - + -
450D VAL* 3.5 26.9 - - + +
451D VAL* 3.3 36.1 - - + +
453D ASP* 5.4 7.6 - - - +
454D PHE 5.5 0.4 - - - +
455D PHE* 4.4 23.1 - - + +
470D TYR* 3.7 19.8 + - + +
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Residues in contact with LEU 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D HIS* 3.0 56.8 - - + +
83D ASP* 3.3 30.7 - - + +
84D PHE* 4.9 9.2 - - + -
345D LEU* 1.3 79.4 - - + +
347D HIS* 1.3 62.0 + - - +
349D GLU* 3.7 14.3 - - + +
350D ILE* 2.9 39.3 + - + +
455D PHE* 6.3 6.3 - - + -
470D TYR* 4.8 6.3 - - + +
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Residues in contact with HIS 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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83D ASP* 3.2 19.9 + - + +
84D PHE* 4.2 13.9 - + + -
321D ASP* 2.9 40.5 + - - -
323D SER* 3.8 6.5 + - - -
324D LEU* 4.2 6.3 + - - -
342D PHE* 3.4 19.4 - + + -
343D LEU* 3.0 45.8 - - + +
344D GLY 3.8 7.6 - - - +
346D LEU* 1.3 78.7 - - - +
348D MET* 1.3 61.3 - - - +
350D ILE* 3.3 10.4 + - + +
351D ILE* 3.1 37.1 + - + +
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Residues in contact with MET 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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295D VAL* 4.6 4.9 - - + -
297D ALA* 4.1 24.7 - - - -
299D LEU* 6.2 0.9 - - + -
342D PHE* 3.5 38.6 - - + -
344D GLY 3.1 12.8 + - - +
345D LEU* 3.2 39.7 - - + +
347D HIS* 1.3 79.9 - - - +
349D GLU* 1.3 67.8 + - + +
351D ILE* 3.2 4.9 + - - +
352D GLN* 2.8 48.3 + - + +
365D THR* 5.4 0.9 - - - -
368D PRO* 4.3 20.4 - - + -
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Residues in contact with GLU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D LEU* 2.7 51.5 + - - +
346D LEU* 4.0 12.3 - - + +
347D HIS 3.3 0.2 - - - -
348D MET* 1.3 76.1 - - + +
350D ILE* 1.3 63.8 + - - +
352D GLN* 3.9 20.1 - - - +
353D GLU* 3.2 23.6 + - - +
453D ASP* 5.4 4.0 - - - +
455D PHE* 5.1 12.7 - - - -
456D ASP* 5.6 0.9 - - - +
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Residues in contact with ILE 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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84D PHE* 4.7 20.4 - - + -
346D LEU* 2.9 31.4 + - + +
347D HIS* 3.7 8.1 - - - +
348D MET 3.3 0.2 - - - -
349D GLU* 1.3 75.3 - - - +
351D ILE* 1.3 67.2 + - + +
353D GLU* 3.4 5.6 + - - +
354D ARG* 3.0 38.8 + - - +
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Residues in contact with ILE 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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299D LEU* 5.2 1.8 - - + -
314D LEU* 5.4 2.5 - - + -
317D LEU* 4.5 19.7 - - + -
321D ASP* 3.6 10.8 - - - +
324D LEU* 3.7 20.6 - - + -
342D PHE* 3.6 33.0 - - + -
347D HIS* 3.1 39.3 + - + +
348D MET 3.5 6.5 - - - +
350D ILE* 1.3 79.9 - - + +
352D GLN* 1.3 53.1 + - + +
354D ARG* 3.1 8.0 + - + +
355D LEU* 2.8 53.9 + - + +
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Residues in contact with GLN 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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299D LEU* 4.2 16.7 - - + +
342D PHE* 6.0 0.7 - - + -
348D MET* 2.8 39.2 + - + +
349D GLU* 3.9 23.3 - - - +
351D ILE* 1.3 73.3 - - + +
353D GLU* 1.3 56.8 + - - +
355D LEU* 3.2 10.0 + - + +
356D GLU* 2.9 31.6 + - - +
363D LEU* 6.5 0.7 - - + -
365D THR* 3.3 41.8 + - - +
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Residues in contact with GLU 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 GLU 3.2 17.6 + - - +
350D ILE* 3.7 5.8 - - - +
352D GLN* 1.3 78.1 - - - +
354D ARG* 1.3 60.4 + - - +
356D GLU* 3.4 14.8 + - - +
357D ARG* 2.8 70.6 + - + +
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Residues in contact with ARG 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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317D LEU* 3.3 39.2 + - + +
320D ASN* 5.9 4.8 - - - +
350D ILE* 3.0 26.6 + - - +
351D ILE* 3.4 8.1 - - - +
353D GLU* 1.3 80.4 + - - +
355D LEU* 1.3 59.8 + - - +
356D GLU 3.2 0.2 - - - -
357D ARG* 5.4 0.2 - - - -
358D GLU* 2.7 78.4 + - - +
359D TYR* 3.3 6.7 + - + -
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Residues in contact with LEU 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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299D LEU* 3.8 25.4 - - + -
310D PHE* 4.2 9.2 - - + -
313D ALA* 4.2 12.3 - - + -
314D LEU* 4.8 6.5 - - + -
317D LEU* 3.5 31.4 - - + -
351D ILE* 2.8 37.0 + - + +
352D GLN* 3.4 9.6 - - + +
354D ARG* 1.3 73.5 - - - +
356D GLU* 1.3 57.2 + - - +
359D TYR* 3.6 17.9 - - + +
360D ASP 3.5 5.5 + - - -
361D LEU* 3.1 30.6 + - + +
363D LEU* 4.0 22.7 - - + -
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Residues in contact with GLU 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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352D GLN 2.9 16.7 + - - +
353D GLU* 3.6 15.6 - - - +
354D ARG 3.2 0.2 - - - -
355D LEU* 1.3 80.0 - - - +
357D ARG* 1.3 76.0 + - - +
360D ASP* 3.4 20.7 - - - +
361D LEU 3.8 14.2 + - - +
362D ASP* 5.5 3.0 - - - +
554E TYR* 3.9 23.9 + - + +
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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 GLU* 2.8 51.7 + - - +
354D ARG* 5.4 0.4 - - - -
356D GLU* 1.3 97.4 - - - +
358D GLU* 1.3 65.6 + - - +
359D TYR 3.3 1.1 - - - -
360D ASP* 3.8 8.1 + - - +
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Residues in contact with GLU 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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354D ARG* 2.7 66.9 + - + +
357D ARG* 1.3 78.8 - - + +
359D TYR* 1.3 81.5 + - + +
360D ASP* 3.5 0.6 - - - +
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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
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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