Contacts of the helix formed by residues 373 - 393 (chain C) in PDB entry 3IOT
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 373 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A LEU* 5.4 2.1 - - - +
376B LYS* 3.6 40.4 - - + +
369C ALA 3.2 19.1 - - - +
370C ALA 2.6 24.1 + - - -
371C MET 2.5 8.9 + - - -
372C ALA* 1.3 76.8 - - - +
374C LEU* 1.3 60.8 + - - +
375C GLU 3.1 4.5 - - - -
376C LYS* 3.0 32.5 - - - +
377C LEU 3.6 1.7 + - - -
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Residues in contact with LEU 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LYS* 5.2 6.5 - - + +
377B LEU* 4.6 19.7 - - + -
379B LYS 6.1 0.4 - - - -
380B ALA* 4.8 13.7 - - + +
383B SER* 4.8 7.4 - - - +
370C ALA* 3.6 18.4 - - + +
371C MET* 2.9 32.2 + - + +
373C THR* 1.3 83.0 + - - +
375C GLU* 1.3 64.4 + - - +
376C LYS 3.1 1.1 - - - -
377C LEU* 3.1 39.0 + - + +
378C MET* 3.4 12.8 + - - +
408C PRO* 5.0 6.5 - - + -
410C PRO* 6.1 4.2 - - + +
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Residues in contact with GLU 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C PRO* 3.0 40.1 - - + +
335C GLN* 4.6 4.3 - - - +
337C SER* 3.8 12.0 + - - -
338C ALA* 5.2 1.8 + - + +
371C MET* 3.0 21.9 + - - +
372C ALA* 3.7 13.2 - - - -
374C LEU* 1.3 77.7 - - - +
376C LYS* 1.3 81.6 + - - +
378C MET* 3.6 20.4 + - - +
379C LYS* 3.8 15.4 + - - +
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Residues in contact with LYS 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA* 4.8 7.4 - - + +
370A ALA* 4.3 16.4 - - + +
373A THR* 4.9 9.0 - - - +
374A LEU* 3.8 23.9 - - + +
335C GLN* 5.2 8.9 - - - +
372C ALA 3.7 17.7 + - - +
373C THR* 3.0 24.0 + - - +
375C GLU* 1.3 90.3 - - - +
377C LEU* 1.3 54.3 + - - +
378C MET 2.8 1.4 + - - -
379C LYS* 2.8 34.5 + - - +
380C ALA* 2.7 33.9 + - - +
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 4.6 4.5 - - + +
377B LEU* 6.3 0.7 - - + -
373C THR 3.6 1.8 + - - -
374C LEU* 3.1 34.3 + - + +
376C LYS* 1.3 76.7 - - - +
378C MET* 1.3 57.0 + - + +
380C ALA* 3.4 11.7 - - + +
381C PHE* 2.8 42.5 + - + +
407C PRO 4.1 6.7 - - - +
408C PRO* 3.6 48.2 - - + +
409C PRO 5.3 0.7 - - - -
410C PRO* 4.3 22.2 - - + -
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Residues in contact with MET 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C LEU 3.4 12.6 + - - +
375C GLU* 3.7 16.6 - - - +
376C LYS 2.8 5.3 + - - -
377C LEU* 1.3 76.6 - - + +
379C LYS* 1.3 55.2 + - + +
381C PHE* 3.2 29.7 + - + +
382C GLU* 2.7 53.1 + - - +
385C LYS* 5.0 7.2 - - - +
410C PRO* 3.6 36.3 - - + -
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Residues in contact with LYS 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A THR* 4.0 33.3 + - - +
367A ASN* 4.4 13.2 - - - +
369A ALA* 6.0 1.8 - - - +
370A ALA* 3.6 26.9 - - + -
371A MET* 4.1 2.5 - - - +
72C GLN* 4.4 11.7 - - - +
334C PRO* 6.4 0.4 - - - +
375C GLU* 4.0 15.5 - - - +
376C LYS* 2.8 27.6 + - - +
378C MET* 1.3 72.0 - - + +
380C ALA* 1.3 53.2 + - - +
382C GLU* 3.2 14.1 - - - +
383C SER* 2.5 36.4 + - - -
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Residues in contact with ALA 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A MET* 3.3 17.3 - - + +
374A LEU* 3.5 29.2 - - + -
376C LYS 2.7 11.2 + - - +
377C LEU* 3.4 17.7 - - + +
379C LYS* 1.3 71.4 - - - +
381C PHE* 1.3 64.8 + - + +
383C SER* 3.6 2.9 - - - -
384C LEU* 3.5 28.8 + - + +
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Residues in contact with PHE 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU* 2.8 34.2 + - + +
378C MET* 3.2 24.0 + - + +
380C ALA* 1.3 80.5 - - + +
382C GLU* 1.3 50.4 + - - +
383C SER 3.2 1.1 - - - -
384C LEU* 3.3 15.5 + - + +
385C LYS* 2.8 60.4 + - - +
405C PRO 5.4 7.6 - - - -
406C PRO 5.1 8.5 - - - -
407C PRO 5.4 2.0 - - - -
408C PRO 4.5 17.5 - - - -
410C PRO* 5.7 4.3 - - + -
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Residues in contact with GLU 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ASN* 5.3 4.4 - - - +
378C MET* 2.7 42.0 + - - +
379C LYS* 3.2 12.8 + - - +
381C PHE* 1.3 69.1 - - - +
383C SER* 1.3 59.6 + - - +
385C LYS* 3.9 32.0 + - + +
386C SER* 3.2 22.3 + - - -
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Residues in contact with SER 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 3.2 36.6 + - - -
367A ASN* 5.3 4.5 - - - -
371A MET* 2.5 53.3 - - - +
379C LYS 2.5 12.4 + - - -
380C ALA 3.6 1.3 - - - -
382C GLU* 1.3 74.5 - - - +
384C LEU* 1.3 59.0 + - - +
386C SER* 3.7 3.5 + - - -
387C PHE* 3.2 16.7 + - - +
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Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A MET* 5.7 1.1 - - + -
380C ALA* 3.5 16.5 + - + +
381C PHE* 3.3 17.6 + - + +
383C SER* 1.3 83.3 - - - +
385C LYS* 1.3 61.2 + - - +
386C SER 3.5 0.2 - - - -
387C PHE* 3.8 15.0 - - + +
388C GLN* 3.2 45.3 + - + +
405C PRO* 5.9 8.3 - - + -
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Residues in contact with LYS 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C MET* 5.0 5.1 - - - +
381C PHE* 2.8 46.0 + - - +
382C GLU* 4.0 34.5 + - + -
383C SER 3.4 0.4 - - - -
384C LEU* 1.3 78.8 - - - +
386C SER* 1.3 58.0 + - - +
388C GLN* 3.7 3.1 + - - +
389C GLN* 3.1 26.1 + - - +
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Residues in contact with SER 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 4.8 3.6 + - - -
345A THR* 4.8 13.5 - - - +
349A ASN* 6.0 1.8 - - - -
382C GLU 3.2 17.7 + - - -
383C SER* 3.7 4.7 + - - -
385C LYS* 1.3 76.1 - - - +
387C PHE* 1.3 65.9 + - - +
389C GLN* 3.7 12.6 - - - +
390C GLN* 3.3 37.1 + - - +
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Residues in contact with PHE 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 2.8 46.2 + + - -
383C SER* 3.2 19.6 + - - +
384C LEU* 3.8 19.1 - - + +
385C LYS 3.3 0.4 - - - -
386C SER* 1.3 78.7 + - - +
388C GLN* 1.3 59.6 + - + +
390C GLN* 3.8 1.6 + - - +
391C GLN* 2.3 65.5 + - - +
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Residues in contact with GLN 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C LEU* 3.2 34.5 + - + +
385C LYS* 3.9 3.1 - - - +
387C PHE* 1.3 80.2 - - + +
389C GLN* 1.3 63.2 + - - +
391C GLN* 4.0 11.7 - - + +
392C GLN* 3.3 31.6 + - - +
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Residues in contact with GLN 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ARG* 3.0 25.1 + - - +
385C LYS 3.1 18.4 + - - +
386C SER* 3.7 13.0 - - - +
387C PHE 3.3 0.4 - - - -
388C GLN* 1.3 78.8 - - - +
390C GLN* 1.3 63.2 + - - +
392C GLN* 3.5 2.9 + - - +
393C GLN* 2.9 61.6 + - - +
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Residues in contact with GLN 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A THR* 4.4 17.8 - - - +
348A ILE* 3.4 31.7 - - - +
349A ASN* 4.5 8.6 + - - +
354A ARG* 4.6 4.7 - - - +
386C SER* 3.3 23.1 + - - +
387C PHE* 4.5 1.8 - - - +
389C GLN* 1.3 81.0 - - - +
391C GLN* 1.3 61.8 - - + +
392C GLN 3.1 7.6 + - - -
393C GLN* 3.4 29.9 + - + +
394C GLN* 4.0 17.2 + - - -
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Residues in contact with GLN 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C PHE* 2.3 61.9 + - - +
388C GLN* 4.1 9.9 - - + +
389C GLN 3.4 0.4 - - - -
390C GLN* 1.3 76.4 - - + +
392C GLN* 1.4 74.9 + - - +
394C GLN* 4.9 8.0 + - - +
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Residues in contact with GLN 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C GLN* 3.3 24.6 + - - +
389C GLN* 3.5 4.4 + - - +
390C GLN 3.1 0.2 - - - -
391C GLN* 1.4 86.1 + - - +
393C GLN* 1.3 58.4 - - + +
394C GLN* 3.2 12.5 + - - +
395C GLN* 5.6 1.6 - - - +
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Residues in contact with GLN 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ARG* 3.1 21.4 + - - +
389C GLN* 2.9 58.1 + - - +
390C GLN* 3.4 24.1 + - + +
392C GLN* 1.3 72.8 - - + +
394C GLN* 1.3 63.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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