Contacts of the helix formed by residues 369 - 387 (chain C) in PDB entry 5TXV
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 369 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C PHE* 1.3 76.9 - - - +
370C ASP* 1.3 54.6 + - - +
371C SER* 3.7 5.3 - - - -
372C GLY* 2.6 30.3 + - - -
373C ILE* 2.7 34.9 + - - +
419C THR* 4.1 14.6 - - + -
420C ILE 2.9 17.0 + - - +
421C ASP* 3.4 21.1 - - + -
422C ALA 3.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C PHE 4.7 3.1 - - - +
369C THR* 1.3 73.7 - - - +
371C SER* 1.3 59.0 + - - +
373C ILE* 3.4 8.9 + - - +
374C LYS* 2.8 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C THR* 3.2 5.4 + - - -
370C ASP* 1.3 78.9 - - - +
372C GLY* 1.3 57.8 + - - +
374C LYS* 3.4 12.6 + - - +
375C ARG* 3.1 35.7 + - - +
422C ALA* 4.0 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C PHE* 5.6 1.1 - - - -
369C THR* 2.6 26.5 + - - -
371C SER* 1.3 72.9 - - - +
373C ILE* 1.3 62.7 + - - +
375C ARG* 3.5 0.9 + - - -
376C ILE* 3.2 31.3 + - - +
420C ILE* 4.4 4.7 - - - -
421C ASP 4.0 4.9 - - - -
422C ALA* 4.0 13.4 - - - +
425C VAL* 3.6 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C GLU* 4.0 24.4 - - + +
344C LEU* 3.7 20.2 - - + +
345C THR* 4.3 17.0 - - + -
352C THR* 4.0 23.1 - - + -
368C PHE* 3.5 36.3 - - + +
369C THR 2.7 23.4 + - - +
370C ASP* 3.7 8.7 - - - +
372C GLY* 1.3 72.1 - - - +
374C LYS* 1.3 62.9 + - - +
376C ILE* 3.3 10.4 + - + +
377C ALA* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 374 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C GLU* 3.4 29.7 - - - +
370C ASP 2.8 17.9 + - - +
371C SER* 3.6 13.2 - - - +
372C GLY 3.3 0.4 - - - -
373C ILE* 1.3 78.0 - - - +
375C ARG* 1.3 58.9 + - + +
377C ALA* 3.6 2.8 + - - +
378C GLU* 3.1 53.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C SER* 3.1 18.4 + - - +
372C GLY 3.5 1.1 + - - +
373C ILE 3.3 0.2 - - - -
374C LYS* 1.3 76.8 - - + +
376C ILE* 1.3 60.6 + - - +
378C GLU* 3.8 21.3 + - - +
379C ALA* 3.1 25.1 + - - +
422C ALA* 3.2 38.7 + - - +
423C ASP* 4.3 6.9 + - - +
425C VAL* 3.9 19.9 - - + +
426C SER* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 4.3 20.9 - - + -
352C THR* 6.0 0.2 - - + -
368C PHE* 4.5 7.0 - - + -
372C GLY 3.2 20.1 + - - +
373C ILE* 3.3 21.4 + - + +
375C ARG* 1.3 75.4 - - - +
377C ALA* 1.3 59.6 + - - +
379C ALA* 3.1 6.6 + - - +
380C ALA* 2.9 27.7 + - - +
395C LEU* 5.0 5.2 - - + +
398C VAL* 4.2 19.2 - - + +
399C LEU* 4.5 21.8 - - + +
402C LEU* 3.7 25.1 - - + -
425C VAL* 3.9 17.5 - - + -
429C LEU* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C THR* 3.7 7.9 - - - +
340C PHE* 3.5 36.6 - - + -
341C GLU* 3.6 30.1 - - + +
344C LEU* 4.3 1.7 - - + +
373C ILE 3.2 7.4 + - - +
374C LYS 3.9 2.0 - - - +
376C ILE* 1.3 79.2 - - - +
378C GLU* 1.3 57.4 + - - +
380C ALA 3.5 0.2 + - - -
381C TRP* 3.0 29.3 + - - +
395C LEU* 4.3 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C THR* 5.0 13.0 - - + -
341C GLU* 5.3 1.8 - - - +
374C LYS* 3.1 48.0 + - + +
375C ARG* 3.8 22.2 + - - +
376C ILE 3.2 0.2 - - - -
377C ALA* 1.3 74.5 - - + +
379C ALA* 1.3 62.3 + - - +
381C TRP* 3.5 7.4 + - - +
382C GLN* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C ARG 3.1 19.7 + - - +
376C ILE 3.1 5.3 + - - +
378C GLU* 1.3 74.2 - - - +
380C ALA* 1.3 65.3 + - - +
382C GLN* 3.3 6.2 + - - +
383C VAL* 3.3 28.1 + - - +
398C VAL* 4.0 18.2 - - + -
425C VAL* 5.4 0.2 - - + -
429C LEU* 4.1 14.8 - - + -
430C ASP* 5.9 1.3 - - - +
433C VAL* 4.5 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C PHE* 4.4 4.0 - - + -
376C ILE 2.9 10.4 + - - +
377C ALA 4.0 1.8 - - - +
379C ALA* 1.3 76.3 - - - +
381C TRP* 1.3 61.8 + - - +
383C VAL 3.5 0.3 + - - -
384C ASN* 3.3 23.4 + - - -
394C ARG* 3.4 35.8 - - + +
395C LEU* 3.7 31.2 - - + -
398C VAL* 4.0 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C ALA* 6.3 1.3 - - + -
335C LEU 3.1 27.6 - - - -
336C THR* 3.7 14.6 - - + -
337C THR* 3.4 31.4 - - + +
340C PHE* 4.2 15.4 - + + -
377C ALA 3.0 18.8 + - - +
378C GLU* 3.8 5.4 - - - +
380C ALA* 1.3 75.6 - - - +
382C GLN* 1.3 74.1 + - - +
384C ASN* 3.3 8.2 + - + +
385C GLU* 3.1 35.0 + - + +
389C ASN* 5.7 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C GLU 3.1 17.4 + - - +
379C ALA* 3.3 5.8 + - - +
381C TRP* 1.3 84.5 - - + +
383C VAL* 1.3 52.1 + - - +
385C GLU* 3.6 7.4 - - - +
386C SER* 2.6 62.0 + - - +
433C VAL* 3.6 25.8 + - + +
436C GLU* 5.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C ALA 3.3 18.3 + - - +
380C ALA* 4.0 1.1 - - - +
381C TRP 3.2 0.4 - - - -
382C GLN* 1.3 78.2 - - - +
384C ASN* 1.3 56.7 + - - +
386C SER* 4.3 4.9 - - - +
387C THR* 2.8 46.6 + - + +
394C ARG* 3.5 42.0 - - - +
398C VAL* 5.0 6.5 - - + -
433C VAL* 4.3 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C PHE* 4.1 14.3 - - - -
380C ALA 3.3 14.9 + - - -
381C TRP* 3.3 10.6 + - + +
383C VAL* 1.3 77.3 - - - +
385C GLU* 1.3 61.4 + - - +
387C THR 4.1 0.5 - - - -
388C GLU* 3.2 26.3 + - - +
389C ASN* 3.3 27.5 + - - +
390C ILE* 3.3 21.5 + - - +
391C GLY* 3.3 27.9 + - - +
394C ARG* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C TRP* 3.1 33.6 + - + +
382C GLN* 4.0 9.6 - - - +
384C ASN* 1.3 78.8 - - - +
386C SER* 1.3 65.3 + - - +
387C THR* 3.3 3.2 + - - +
389C ASN* 5.7 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C GLN* 2.6 55.4 + - - +
383C VAL* 4.1 3.6 - - - -
385C GLU* 1.3 74.6 - - - +
387C THR* 1.3 66.5 + - - +
433C VAL* 5.3 3.0 + - - -
436C GLU* 3.7 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C VAL* 2.8 30.0 + - + +
384C ASN 4.1 3.3 - - - +
385C GLU 3.3 2.4 - - - +
386C SER* 1.3 89.4 - - - +
388C GLU* 1.3 95.7 + - - +
394C ARG* 4.0 4.3 + - - -
436C GLU* 4.3 26.5 - - + +
316D SER* 5.6 5.7 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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