Contacts of the helix formed by residues 345 - 358 (chain A) in PDB entry 3NC0
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 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A LEU 5.8 0.2 - - - +
342A ASN 4.4 11.2 + - - +
343A LEU 2.6 7.1 + - - -
344A ARG* 1.3 76.3 - - - +
346A ALA* 1.3 75.2 + - - +
347A LEU 3.1 1.6 - - - -
348A MET* 3.4 7.4 + - - +
349A GLU* 3.0 47.8 + - - +
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Residues in contact with ALA 346 (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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287A PHE* 3.8 9.7 - - + -
288A THR* 4.0 28.9 - - + -
291A MET* 4.1 18.1 - - + +
343A LEU* 3.1 6.4 + - - +
345A GLU* 1.3 85.9 + - - +
347A LEU* 1.3 58.2 + - - +
348A MET 3.4 0.2 - - - -
349A GLU* 3.5 18.6 + - - +
350A ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 347 (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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287A PHE* 4.2 7.1 - - + -
330A LEU* 4.0 26.5 - - + -
334A GLY* 5.2 2.5 - - - +
337A LEU* 4.1 37.5 - - + +
338A GLU* 4.4 15.3 - - + -
343A LEU 3.1 17.0 + - - +
344A ARG* 4.7 9.2 - - + -
345A GLU 3.1 0.2 - - - -
346A ALA* 1.3 77.5 - - - +
348A MET* 1.3 67.0 + - - +
350A ALA* 3.4 1.2 + - - +
351A LEU* 2.9 50.9 + - + +
372A TYR* 5.5 1.3 - - - +
408A LEU* 5.4 7.0 - - + -
409A TYR* 4.7 13.0 - - + +
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Residues in contact with MET 348 (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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344A ARG* 3.6 22.4 - - + +
345A GLU* 3.4 7.9 + - - +
346A ALA 3.4 0.2 - - - -
347A LEU* 1.3 82.9 - - - +
349A GLU* 1.3 62.1 + - + +
351A LEU* 3.2 16.8 + - + +
352A HIS* 2.9 28.5 + - - +
408A LEU* 3.9 25.1 - - - +
409A TYR* 6.1 0.2 - - - -
411A THR* 5.2 5.6 - - - +
412A VAL* 3.7 30.1 - - + +
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Residues in contact with GLU 349 (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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291A MET* 4.2 19.1 - - + +
295A LYS* 4.0 26.7 + - - +
300A LEU* 4.2 23.5 - - + +
345A GLU* 3.0 35.9 + - + +
346A ALA* 3.6 20.7 - - - +
347A LEU 3.3 0.2 - - - -
348A MET* 1.3 78.4 - - + +
350A ALA* 1.3 60.2 + - - +
352A HIS* 3.1 21.2 + - - +
353A TYR* 3.1 13.9 + - - -
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Residues in contact with ALA 350 (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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287A PHE* 3.5 25.6 - - + -
291A MET* 3.8 15.6 - - + +
326A LEU* 4.2 8.8 - - + +
330A LEU* 4.6 12.3 - - + -
346A ALA 3.0 17.0 + - - +
347A LEU* 3.6 5.4 - - - +
349A GLU* 1.3 72.7 - - - +
351A LEU* 1.3 62.0 + - - +
352A HIS 3.0 5.4 + - - -
353A TYR* 3.2 15.7 + - - +
354A MET* 3.3 17.8 + - - +
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Residues in contact with LEU 351 (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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330A LEU* 3.9 17.3 - - + -
347A LEU* 2.9 32.9 + - + +
348A MET* 3.6 28.5 - - + +
350A ALA* 1.3 74.7 - - - +
352A HIS* 1.3 59.6 + - - +
354A MET* 3.9 6.7 + - + +
355A LEU* 3.2 30.4 + - - +
372A TYR* 3.7 30.5 - - + +
373A TRP* 4.1 9.4 - - + -
409A TYR* 3.7 31.0 - - + -
412A VAL* 4.2 19.7 - - + -
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Residues in contact with HIS 352 (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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300A LEU* 2.8 50.7 + - + +
348A MET 2.9 13.1 + - - +
349A GLU* 3.1 16.6 - - - +
350A ALA 3.0 0.2 - - - -
351A LEU* 1.3 77.1 - - - +
353A TYR* 1.3 63.7 + - - +
355A LEU* 3.2 16.9 + - + +
356A LEU* 3.1 45.2 + - + +
415A LYS* 6.1 4.9 - - + -
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Residues in contact with TYR 353 (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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291A MET* 3.7 27.1 - - + -
294A LEU* 3.1 38.6 + - + -
295A LYS* 3.4 7.1 + - + -
298A LEU* 2.6 37.3 + - + -
299A PRO 4.8 1.1 - - - -
300A LEU* 3.2 29.5 - - + +
304A ILE* 5.2 9.4 - - + -
322A LEU* 4.5 15.9 - - + -
326A LEU* 3.4 22.2 - - + -
349A GLU* 3.1 19.4 + - + -
350A ALA* 3.2 3.8 + - - +
352A HIS* 1.3 77.4 - - - +
354A MET* 1.3 54.3 + - - +
356A LEU* 2.9 13.5 + - + +
357A VAL* 2.7 38.5 + - + +
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Residues in contact with MET 354 (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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323A SER* 4.6 7.2 - - - +
326A LEU* 3.4 36.1 - - + -
327A CYS* 4.3 16.8 - - + +
330A LEU* 4.5 13.7 - - + -
350A ALA 3.3 12.1 + - - +
351A LEU* 4.0 5.8 - - - +
352A HIS 3.3 0.4 - - - -
353A TYR* 1.3 79.5 - - - +
355A LEU* 1.3 50.5 + - - +
357A VAL* 3.7 4.7 - - - +
358A SER* 2.7 42.9 + - - -
369A CYS* 3.6 48.4 - - + +
372A TYR* 4.6 8.3 - - + -
373A TRP* 3.5 22.2 - - + +
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Residues in contact with LEU 355 (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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351A LEU 3.2 21.5 - - - +
352A HIS* 3.2 16.1 + - + +
353A TYR 3.1 0.8 - - - -
354A MET* 1.3 77.4 - - - +
356A LEU* 1.3 66.1 + - + +
358A SER* 3.6 10.4 + - - -
359A GLU* 3.6 17.0 - - - +
373A TRP* 3.4 24.9 - - + +
412A VAL* 4.4 17.3 - - + -
415A LYS* 3.9 41.1 - - + +
416A VAL* 4.0 16.8 - - + +
419A LEU* 5.4 6.2 - - + +
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Residues in contact with LEU 356 (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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299A PRO 5.1 0.2 - - - +
300A LEU* 3.6 14.6 - - - +
302A THR 3.8 20.4 - - - +
303A ASN* 6.1 0.9 - - - -
304A ILE* 3.6 29.9 - - + +
305A ARG 5.0 0.9 + - - -
352A HIS* 3.1 46.8 + - + +
353A TYR* 2.9 14.4 + - + +
355A LEU* 1.3 76.2 - - + +
357A VAL* 1.3 67.1 + - - +
359A GLU* 2.8 25.4 + - + +
360A VAL 4.1 1.2 + - - -
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Residues in contact with VAL 357 (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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304A ILE* 4.3 15.5 - - + +
319A ILE* 4.5 8.5 - - + -
322A LEU* 3.9 29.4 - - + -
323A SER* 3.2 28.7 - - - +
326A LEU* 5.2 2.2 - - + -
353A TYR* 2.7 24.1 + - + +
354A MET* 3.7 6.5 - - + +
356A LEU* 1.3 72.8 - - - +
358A SER* 1.3 56.2 + - - +
360A VAL* 2.9 33.6 + - - +
365A ILE* 3.7 9.9 - - + +
366A PHE* 5.8 0.5 + - - -
369A CYS* 3.3 18.2 - - - -
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Residues in contact with SER 358 (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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354A MET 2.7 26.4 + - - -
355A LEU* 3.7 9.4 - - - -
356A LEU 3.1 0.2 - - - -
357A VAL* 1.3 73.1 - - - +
359A GLU* 1.3 51.9 + - - +
360A VAL 3.2 2.1 + - - -
366A PHE* 3.3 16.1 - - - +
369A CYS* 3.4 26.8 - - - +
373A TRP* 3.4 12.6 + - - -
419A LEU* 3.7 24.4 - - - +
423A ARG* 2.5 29.3 + - - -
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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