Contacts of the helix formed by residues 355 - 368 (chain A) in PDB entry 3RCZ
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 THR 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A ASP 3.7 1.8 + - - +
354A PHE* 1.3 77.3 - - - +
356A VAL* 1.3 64.6 + - - +
357A LYS* 3.5 6.2 + - - +
358A ASP* 2.9 36.3 + - - +
359A LEU* 3.0 21.3 + - - +
386A PRO 3.5 11.4 - - - +
387A ASN* 4.2 13.7 - - - +
388A ASP 3.2 11.0 - - - +
389A GLN* 4.0 13.2 - - + +
390A VAL* 4.3 1.7 - - - +
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A THR* 1.3 71.8 - - - +
357A LYS* 1.3 63.4 + - - +
359A LEU* 3.1 11.0 + - + +
360A ILE* 2.9 30.1 + - + +
377A LEU* 4.0 18.6 - - + +
384A LEU* 3.9 35.9 - - + +
385A ASP 3.3 23.6 - - - +
386A PRO* 3.5 10.9 + - + -
388A ASP* 2.8 21.9 + - + +
390A VAL* 4.9 8.3 - - + -
393A THR* 4.4 12.8 - - + -
395A LEU* 6.0 0.9 - - + -
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Residues in contact with LYS 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A THR* 3.7 4.7 - - - +
356A VAL* 1.3 73.9 - - - +
358A ASP* 1.3 68.2 + - - +
360A ILE* 3.1 10.6 + - + +
361A LYS* 2.8 41.4 + - + +
371A PHE* 4.0 27.6 - - + -
373A GLU* 3.4 25.5 + - - +
386A PRO* 3.0 31.7 + - + +
387A ASN* 5.4 5.4 - - - +
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Residues in contact with ASP 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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353A ASP 4.8 0.5 - - - +
354A PHE* 3.6 29.4 - - + -
355A THR* 2.9 43.7 + - - +
357A LYS* 1.3 75.5 - - - +
359A LEU* 1.3 57.9 + - - +
361A LYS* 3.1 16.9 + - - +
362A ARG* 2.9 31.0 + - - +
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LEU* 3.7 27.8 - - + -
338A LEU* 4.0 20.6 - - + -
348A LEU* 4.0 7.2 - - + -
350A ILE* 3.9 39.0 - - + -
354A PHE* 4.7 5.1 - - - -
355A THR 3.0 12.5 + - - +
356A VAL* 3.1 12.1 + - + +
358A ASP* 1.3 78.0 - - - +
360A ILE* 1.3 57.7 + - - +
362A ARG* 3.5 3.7 + - - +
363A TYR* 3.0 25.5 + - - +
377A LEU* 3.8 23.1 - - + -
384A LEU* 5.7 1.3 - - + -
390A VAL* 4.5 7.9 - - + -
395A LEU* 5.1 6.5 - - + -
401A VAL* 5.2 3.1 - - + -
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Residues in contact with ILE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A VAL* 2.9 28.3 + - + +
357A LYS* 3.1 9.4 + - - +
359A LEU* 1.3 73.9 - - - +
361A LYS* 1.3 64.9 + - - +
363A TYR* 3.1 9.2 + - + +
364A CYS* 2.9 27.6 + - - -
371A PHE* 3.7 25.4 - - + -
375A ILE* 3.6 45.8 - - + +
376A ARG* 4.4 2.9 - - - -
377A LEU* 3.5 35.0 - - + +
386A PRO* 5.4 5.6 - - + -
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Residues in contact with LYS 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LYS* 2.8 38.3 + - + +
358A ASP* 3.1 19.7 + - - +
360A ILE* 1.3 71.9 - - - +
362A ARG* 1.3 62.8 + - - +
364A CYS* 3.2 6.2 + - - +
365A THR* 3.1 27.5 + - + +
371A PHE* 3.9 47.1 - - + +
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Residues in contact with ARG 362 (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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348A LEU* 4.1 20.6 - - + -
349A SER 5.4 4.0 + - - -
350A ILE* 5.0 8.8 - - + +
351A PRO* 5.2 4.4 - - - +
354A PHE* 3.9 35.1 - - + -
358A ASP 2.9 19.4 + - - +
359A LEU* 3.9 5.8 - - - +
361A LYS* 1.3 69.0 - - - +
363A TYR* 1.3 66.9 + - - +
365A THR* 3.3 12.2 + - - -
366A GLU* 3.0 41.2 + - - +
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Residues in contact with TYR 363 (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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338A LEU* 3.6 43.7 + - + -
340A SER* 3.5 27.7 + - - -
343A SER* 3.6 14.0 + - - -
344A GLU 4.9 1.8 + - - -
346A LEU* 3.5 28.0 - - + -
348A LEU* 4.1 3.3 - - + +
359A LEU 3.0 14.7 + - - +
360A ILE* 3.4 12.8 - - + +
362A ARG* 1.3 75.3 - - - +
364A CYS* 1.3 66.6 + - - +
366A GLU* 3.1 3.3 + - - +
367A VAL* 2.9 56.4 + - + +
369A ILE* 3.8 15.4 - - + +
375A ILE* 6.1 0.2 - - + -
377A LEU* 6.2 0.2 - - + -
403A VAL* 3.8 26.7 - - + -
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Residues in contact with CYS 364 (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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360A ILE* 2.9 19.4 + - - +
361A LYS 3.5 8.3 - - - +
362A ARG 3.2 0.2 - - - -
363A TYR* 1.3 81.0 - - - +
365A THR* 1.3 59.2 + - + +
368A LYS* 2.9 23.7 + - - -
369A ILE* 3.0 48.1 + - - +
371A PHE* 3.9 25.4 - - + +
375A ILE* 3.8 25.8 - - - -
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Residues in contact with THR 365 (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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361A LYS* 3.1 13.6 + - + +
362A ARG* 3.3 21.0 + - - -
364A CYS* 1.3 76.9 - - + +
366A GLU* 1.3 65.7 + - - +
368A LYS* 3.6 22.3 + - - +
369A ILE 5.0 0.7 - - - +
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Residues in contact with GLU 366 (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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346A LEU* 3.6 32.7 - - + +
348A LEU* 3.7 13.9 - - + -
362A ARG* 3.0 34.5 + - - +
363A TYR 3.5 4.3 - - - +
365A THR* 1.3 81.4 + - - +
367A VAL* 1.3 60.2 + - - +
368A LYS* 3.6 15.1 + - - +
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A SER* 4.7 12.3 - - - +
344A GLU* 5.2 3.1 - - - +
346A LEU* 3.6 29.6 - - + -
363A TYR* 2.9 40.5 + - + +
366A GLU* 1.3 75.5 - - - +
368A LYS* 1.3 70.9 - - - +
369A ILE* 3.5 39.7 + - + +
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Residues in contact with LYS 368 (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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364A CYS 2.9 7.5 + - - -
365A THR* 3.8 13.2 + - - +
366A GLU* 3.4 18.0 + - - +
367A VAL* 1.3 81.8 - - - +
369A ILE* 1.3 62.0 + - - +
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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