Contacts of the helix formed by residues 363 - 376 (chain A) in PDB entry 3RC0
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 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A MET* 5.7 1.6 - - + -
353A ALA 4.0 9.0 - - - +
354A PHE* 3.3 14.0 - - - +
355A VAL* 2.9 44.2 + - + +
361A VAL* 3.7 3.9 - - - +
362A LEU* 1.3 72.4 - - + +
364A GLU* 1.3 63.0 + - - +
366A GLU* 3.2 28.0 - - + +
367A LEU* 3.3 20.8 + - - +
482A EDO 4.0 3.1 - - - +
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Residues in contact with GLU 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 GLU* 2.5 30.2 - - - +
361A VAL* 3.5 20.5 - - - +
362A LEU 2.7 7.0 + - - +
363A THR* 1.3 69.7 - - - +
365A GLU* 1.3 62.4 + - - +
367A LEU* 3.4 1.7 + - - +
368A THR* 3.0 33.9 + - - +
398A GLY 3.8 13.7 - - - +
399A SER* 3.3 9.8 - - - -
400A LEU* 3.0 26.9 + - + +
482A EDO 3.3 12.7 - - - -
204B SER* 3.4 5.9 - - - -
205B LEU* 2.8 32.5 + - + +
206B ARG 4.5 1.2 + - - -
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Residues in contact with GLU 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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347A MET* 3.7 18.3 - - + +
364A GLU* 1.3 76.8 - - - +
366A GLU* 1.3 74.1 + - - +
368A THR* 3.3 7.6 - - - +
369A THR* 2.8 32.5 + - - +
395A ARG* 5.0 7.4 - - + +
396A GLU 4.6 9.0 - - - +
398A GLY 5.9 0.7 - - - -
482A EDO 3.1 31.3 + - - -
206B ARG* 4.0 39.9 + - + +
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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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315A MET* 4.8 7.4 - - + -
346A GLU 4.9 2.0 - - - +
347A MET* 3.4 44.7 - - + +
354A PHE* 3.7 12.6 - - + -
363A THR* 3.2 23.6 - - + +
365A GLU* 1.3 78.9 - - - +
367A LEU* 1.3 58.0 + - - +
369A THR* 3.9 1.4 - - - -
370A THR* 2.8 31.5 + - - -
482A EDO 2.9 32.3 + - - -
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ILE* 6.0 0.4 - - + -
318A VAL* 5.3 4.3 - - + -
354A PHE* 3.6 34.8 - - + -
356A ILE* 4.3 13.0 - - + -
361A VAL* 3.9 19.5 - - + -
363A THR 3.3 14.3 + - - +
364A GLU 4.0 2.0 - - - +
365A GLU 3.3 0.2 - - - -
366A GLU* 1.3 76.2 - - - +
368A THR* 1.3 65.9 + - - +
369A THR 3.1 1.3 - - - -
370A THR* 3.0 3.6 + - + -
371A LEU* 2.8 45.9 + - + +
400A LEU* 3.7 22.4 - - + -
416A LEU* 4.4 23.8 - - + -
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Residues in contact with THR 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 GLU 3.0 21.7 + - - +
365A GLU* 3.0 9.5 + - - -
367A LEU* 1.3 74.3 - - - +
369A THR* 1.3 60.1 + - - +
371A LEU* 3.5 7.7 + - - +
372A LYS* 3.1 27.0 + - - +
396A GLU* 3.2 24.4 + - - +
398A GLY 4.0 16.3 + - - +
400A LEU* 3.4 35.2 - - + -
412A TRP* 4.0 7.5 - - - -
477A EDO 4.0 15.3 - - - -
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Residues in contact with THR 369 (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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342A LEU* 4.0 4.7 - - + -
345A LEU* 4.0 19.1 - - + -
347A MET* 3.8 25.4 - - + -
365A GLU* 2.8 21.2 + - - -
366A GLU 3.9 0.7 - - - -
368A THR* 1.3 77.8 + - - +
370A THR* 1.3 65.3 + - - +
372A LYS* 3.4 8.2 + - + +
373A VAL* 3.1 28.3 + - + +
395A ARG* 3.6 14.4 - - + +
396A GLU* 3.4 24.4 + - + +
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Residues in contact with THR 370 (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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318A VAL* 4.2 11.9 - - + -
339A TRP* 5.2 2.5 - - + -
342A LEU* 3.8 17.5 - - + +
347A MET* 4.4 0.3 + - - +
348A VAL* 3.2 26.2 - - + +
354A PHE* 3.4 19.8 - - + -
366A GLU 2.8 21.1 + - - -
367A LEU* 3.0 7.4 + - + -
369A THR* 1.3 74.7 - - - +
371A LEU* 1.3 65.5 + - - +
374A LEU* 3.1 46.8 + - + +
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Residues in contact with LEU 371 (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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318A VAL* 5.1 4.7 - - + -
367A LEU* 2.8 43.4 + - + +
368A THR* 3.9 5.2 - - - +
370A THR* 1.3 73.2 - - - +
372A LYS* 1.3 68.4 + - - +
375A CYS* 3.1 28.2 + - - +
400A LEU* 5.0 4.3 - - + -
408A LEU* 4.5 6.7 - - + -
412A TRP* 3.8 51.1 - - + +
415A LEU* 3.8 27.4 - - + -
416A LEU* 4.2 24.9 - - + +
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Residues in contact with LYS 372 (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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368A THR 3.1 18.9 + - - +
369A THR* 3.6 9.0 - - + +
370A THR 3.3 0.2 - - - -
371A LEU* 1.3 77.3 - - - +
373A VAL* 1.3 65.3 + - + +
375A CYS* 3.8 0.5 - - - +
376A MET* 2.9 53.9 + - + +
395A ARG 5.9 1.8 - - - -
396A GLU* 3.4 32.4 - - + +
412A TRP* 3.5 25.0 + - + -
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Residues in contact with VAL 373 (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 ARG* 2.6 64.9 + - + +
341A PHE* 4.2 19.7 - - + -
342A LEU* 3.7 21.8 - - + -
345A LEU* 5.1 0.7 - - + -
369A THR* 3.1 22.6 + - + +
372A LYS* 1.3 84.2 - - + +
374A LEU* 1.3 55.7 + - - +
375A CYS 3.2 0.2 + - - -
376A MET* 3.5 17.9 - - - +
381A PHE* 4.1 13.9 - - + -
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Residues in contact with LEU 374 (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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318A VAL* 4.0 13.0 - - + +
319A ARG* 5.0 1.8 - - - +
322A ALA* 4.4 20.8 - - + +
335A VAL* 4.5 7.4 - - + +
338A ARG* 3.5 44.3 + - + +
339A TRP* 4.3 12.6 - - + +
342A LEU* 4.0 13.7 - - + -
370A THR* 3.1 40.6 + - + +
371A LEU 4.3 0.2 - - - +
373A VAL* 1.3 76.1 - - - +
375A CYS* 1.3 59.6 + - - +
415A LEU* 3.8 26.5 - - + -
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Residues in contact with CYS 375 (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 ARG* 5.0 0.2 - - - -
371A LEU 3.1 20.3 + - - +
373A VAL 3.1 0.4 - - - -
374A LEU* 1.3 82.1 - - - +
376A MET* 1.3 65.8 + - - +
377A PRO* 3.7 2.6 - - - +
409A LYS* 6.1 0.4 - - + -
411A SER* 3.5 45.3 + - - +
412A TRP* 3.6 20.4 - - + +
415A LEU* 4.0 20.4 - - - -
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Residues in contact with MET 376 (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 ARG* 2.7 39.3 + - - +
372A LYS* 2.9 34.8 + - + +
373A VAL* 3.5 25.4 - - - +
375A CYS* 1.3 78.7 - - - +
377A PRO* 1.3 81.0 - - + +
380A GLU* 3.4 28.5 - - + +
381A PHE* 3.9 21.8 - - + -
384A LEU* 4.6 11.4 - - + -
409A LYS* 6.0 2.7 - - - +
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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