Contacts of the helix formed by residues 374 - 388 (chain A) in PDB entry 3RC3
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 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A CYS* 3.6 2.1 + - - +
373A PHE* 1.3 81.0 - - - +
375A LYS* 1.3 64.4 + - - +
376A ASN* 3.4 8.9 + - - +
377A ASP* 3.2 31.4 + - - +
378A ILE* 3.2 22.9 + - - +
424A THR* 5.2 2.9 - - - -
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Residues in contact with LYS 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A SER* 1.3 74.3 - - - +
376A ASN* 1.3 63.8 + - - +
378A ILE* 3.1 11.1 + - + +
379A TYR* 3.0 56.2 + - + +
396A TYR* 3.4 41.8 - - + -
397A GLY 5.5 0.2 - - - +
398A SER* 2.7 30.9 + - - +
424A THR* 5.0 4.0 - - + -
626A MSE 6.4 0.4 - - - +
629A GLU* 4.1 4.0 + - - -
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Residues in contact with ASN 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A SER* 3.1 9.0 + - - +
375A LYS* 1.3 79.4 - - - +
377A ASP* 1.3 57.0 + - - +
379A TYR* 3.3 22.1 + - - +
380A SER* 2.9 30.5 + - - -
686A LEU* 5.5 6.7 - - - +
687A ASN 4.8 4.8 + - - -
688A LEU* 3.1 35.9 + - - +
689A GLU* 5.1 5.3 + - - +
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Residues in contact with ASP 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A CYS* 3.7 20.0 - - + -
373A PHE* 4.6 2.8 + - - -
374A SER* 3.2 26.6 + - - +
376A ASN* 1.3 73.2 - - - +
378A ILE* 1.3 58.7 + - - +
380A SER* 4.5 4.8 - - - +
381A VAL* 2.7 39.5 + - - +
441A TYR* 3.5 29.8 - - + -
442A SER* 4.4 10.6 + - - -
688A LEU 5.1 2.1 - - - +
689A GLU* 5.8 3.3 - - - +
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Residues in contact with ILE 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A CYS* 3.7 11.9 - - + -
374A SER 3.2 14.8 + - - +
375A LYS* 3.1 17.6 + - + +
377A ASP* 1.3 76.4 - - - +
379A TYR* 1.3 68.3 + - + +
382A SER* 3.0 29.2 + - - +
394A VAL* 3.8 30.1 - - + -
395A ILE 4.8 1.6 - - - +
396A TYR* 4.7 7.6 - - + -
422A VAL* 3.7 19.7 - - + +
423A ALA* 3.5 38.1 - - - +
424A THR* 3.8 14.1 - - + +
673A ILE* 5.4 0.9 - - + -
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Residues in contact with TYR 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LYS* 3.0 49.5 + - + +
376A ASN* 3.7 20.0 - - - +
378A ILE* 1.3 84.9 - - + +
380A SER* 1.3 63.8 + - - +
382A SER* 3.3 2.8 + - - -
383A ARG* 3.0 26.3 + - - +
396A TYR* 4.8 10.8 + + - -
622A ILE* 3.5 43.3 - - + +
625A LEU* 5.8 1.2 - - + +
626A MSE 5.4 2.9 - - - +
673A ILE* 4.2 17.5 - - + -
677A ILE* 3.5 29.7 - - + +
686A LEU* 5.6 1.6 - - + -
688A LEU* 4.1 19.5 - - + -
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Residues in contact with SER 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASN 2.9 17.6 + - - -
377A ASP* 3.9 4.9 - - - -
379A TYR* 1.3 75.9 - - - +
381A VAL* 1.3 59.2 + - - +
383A ARG* 3.4 3.5 + - - +
384A GLN* 2.8 52.1 + - - +
441A TYR* 5.1 1.7 + - - -
688A LEU* 4.0 27.8 - - - +
689A GLU* 4.4 14.8 + - - +
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LEU* 4.6 4.7 - - + -
370A ILE* 3.7 31.2 - - + -
372A CYS* 4.3 2.5 - - - -
377A ASP* 2.7 25.0 + - - +
378A ILE 4.2 1.3 - - - +
380A SER* 1.3 70.6 - - - +
382A SER* 1.3 66.5 + - - +
384A GLN* 3.1 9.1 + - - +
385A ILE* 2.8 38.6 + - + +
422A VAL* 4.0 15.9 - - + -
441A TYR* 3.3 47.8 - - + +
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Residues in contact with SER 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ILE* 3.0 18.0 + - - +
381A VAL* 1.3 77.7 - - - +
383A ARG* 1.3 56.8 + - - +
385A ILE* 3.4 3.4 + - - +
386A GLU* 3.0 26.2 + - - +
392A SER* 4.0 21.0 + - - -
394A VAL* 4.1 21.6 - - - +
422A VAL* 4.1 8.0 - - - +
673A ILE* 4.7 0.5 - - - +
674A THR* 3.8 12.7 - - - +
677A ILE* 3.1 28.6 - - - +
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Residues in contact with ARG 383 (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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379A TYR 3.0 18.8 + - - +
380A SER* 3.8 4.5 - - - +
382A SER* 1.3 73.2 + - - +
384A GLN* 1.3 67.4 + - - +
386A GLU* 3.1 19.0 + - - +
387A ILE* 3.0 53.6 + - + +
674A THR* 4.0 22.9 - - - -
677A ILE* 4.0 9.6 - - + -
678A LYS* 3.8 40.2 - - - +
681A GLU* 2.9 35.1 + - - +
682A THR* 4.5 9.1 - - - +
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Residues in contact with GLN 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LEU* 3.8 22.5 - - + +
380A SER* 2.8 42.0 + - - +
381A VAL* 3.6 5.7 - - - +
383A ARG* 1.3 78.5 - - + +
385A ILE* 1.3 63.2 + - - +
387A ILE* 3.3 14.0 + - + +
388A ARG* 3.2 35.6 + - - +
441A TYR* 4.2 15.8 + - - -
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Residues in contact with ILE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LEU* 3.7 17.7 - - + -
364A LEU* 3.7 13.9 - - + -
370A ILE* 4.2 3.6 - - + -
381A VAL* 2.8 25.3 + - + +
382A SER 3.7 4.0 - - - +
384A GLN* 1.3 76.8 - - - +
386A GLU* 1.3 63.0 + - - +
388A ARG* 3.1 19.0 + - - +
390A LEU* 3.2 49.0 + - + +
391A GLU 4.2 1.8 - - - +
392A SER* 4.1 14.4 - - - +
420A ILE* 3.7 21.3 - - + -
422A VAL* 3.7 29.6 - - + -
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Residues in contact with GLU 386 (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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382A SER 3.0 14.4 + - - +
383A ARG* 3.1 25.0 + - - +
385A ILE* 1.3 77.1 - - - +
387A ILE* 1.3 56.7 + - + +
389A GLY* 2.7 25.3 + - - -
390A LEU 3.3 14.7 + - - +
674A THR* 2.6 44.4 + - + +
675A LYS* 5.4 4.1 - - - +
678A LYS* 5.2 4.2 - - - +
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Residues in contact with ILE 387 (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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383A ARG* 3.0 48.0 + - + +
384A GLN* 3.4 18.8 - - + +
386A GLU* 1.3 78.3 - - + +
388A ARG* 1.3 69.2 + - + +
389A GLY* 3.5 1.0 + - - -
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Residues in contact with ARG 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER* 4.6 6.3 + - - -
361A LEU* 3.7 37.5 - - - +
362A ASP* 3.1 28.7 + - - +
364A LEU* 5.7 1.6 - - - -
384A GLN* 3.2 35.6 + - - +
385A ILE* 3.1 13.1 + - - +
386A GLU 3.0 0.6 - - - -
387A ILE* 1.3 88.7 - - + +
389A GLY* 1.3 59.3 + - - +
390A LEU* 3.3 14.3 + - + +
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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