Contacts of the helix formed by residues 338 - 360 (chain D) in PDB entry 6VVT
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 338 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D LEU 4.1 2.6 + - - -
325D ARG* 3.3 28.4 - - - -
326D PRO* 3.3 12.2 + - - +
337D THR* 1.3 88.6 + - - +
339D ASP* 1.3 64.6 + - - +
340D LEU* 3.3 10.5 - - - -
341D ASN* 3.3 23.7 + - - +
342D ASP* 4.3 3.1 + - - +
361F LEU* 3.8 8.0 - - - +
362F ASP* 3.8 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 339 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D THR 4.4 0.2 - - - +
338D SER* 1.3 70.0 - - - +
340D LEU* 1.3 65.7 + - - +
341D ASN 3.1 2.9 - - - -
342D ASP* 2.9 18.9 + - - +
343D LEU* 2.9 15.1 + - - +
397D ARG* 2.4 27.5 + - - -
399D LEU* 3.6 18.4 - - + +
400D LYS 3.1 32.5 + - - +
360F SER* 2.7 23.6 + - - -
362F ASP* 2.8 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D ILE* 3.9 23.3 - - + -
324D LEU 4.8 3.1 - - - +
325D ARG* 4.1 18.4 - - + -
338D SER* 3.3 4.4 - - - -
339D ASP* 1.3 76.5 - - - +
341D ASN* 1.3 52.5 + - - +
343D LEU* 3.1 7.8 + - + -
344D TYR* 2.7 53.8 + - + -
381D LEU* 4.9 2.0 - - + -
400D LYS* 3.2 24.5 - - + +
401D SER* 4.4 6.3 - - - +
402D LEU* 3.5 34.1 - - + -
405D LEU* 4.0 21.5 - - + -
362F ASP* 4.7 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 341 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D THR* 4.8 9.6 - - + -
46D LEU* 3.9 14.1 - - + +
47D PHE* 3.2 14.7 - - - -
325D ARG* 2.9 52.1 + - - +
337D THR* 2.9 27.6 + - - +
338D SER* 3.3 18.1 + - - +
339D ASP 3.1 1.0 - - - -
340D LEU* 1.3 77.9 - - - +
342D ASP* 1.3 56.9 + - - +
344D TYR* 3.9 1.7 - - - -
345D ARG* 2.9 34.5 + - - +
303F THR* 4.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D THR* 5.9 2.2 - - - +
338D SER 4.3 2.7 + - - +
339D ASP* 2.9 12.9 + - - +
341D ASN* 1.3 77.5 - - - +
343D LEU* 1.3 62.7 + - - +
345D ARG* 3.0 26.1 + - - +
346D ARG* 3.2 30.6 + - - +
399D LEU* 4.4 14.9 - - + +
303F THR* 2.9 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D ASP 2.9 15.2 + - - +
340D LEU* 3.6 6.7 - - + +
342D ASP* 1.3 74.6 - - - +
344D TYR* 1.3 65.7 + - - +
346D ARG* 3.3 11.2 + - - +
347D VAL* 3.2 25.1 + - - +
377D SER 4.8 1.3 - - - +
380D ALA* 3.6 31.4 - - + +
381D LEU* 3.6 24.5 - - + +
384D ASN* 4.9 1.8 - - + +
391D VAL* 4.4 15.5 - - + -
399D LEU* 3.4 33.0 - - + -
400D LYS 3.9 9.4 - - - +
401D SER* 3.8 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121C SER* 4.4 1.0 - - - -
46D LEU* 4.2 17.5 - - + -
95D ILE* 4.0 20.1 - - + +
317D VAL* 4.9 0.4 - - + -
318D PRO 3.2 22.8 + - - -
319D VAL* 3.6 19.3 - - + -
320D ILE* 3.0 39.8 + - + +
325D ARG* 4.4 8.1 - - - -
340D LEU* 2.7 47.6 + - + +
341D ASN* 3.9 3.8 - - - +
343D LEU* 1.3 72.2 - - - +
345D ARG* 1.3 57.6 + - - +
347D VAL* 3.1 6.0 + - + +
348D ILE* 2.8 33.7 + - + +
381D LEU* 3.7 33.5 - - + +
402D LEU* 4.3 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PRO* 3.1 38.8 + - + +
33D THR* 4.7 5.6 - - - -
46D LEU* 4.6 4.5 - - + +
341D ASN 2.9 20.7 + - - +
342D ASP* 3.0 28.5 + - - +
343D LEU 3.2 0.2 - - - -
344D TYR* 1.3 76.4 - - - +
346D ARG* 1.3 58.9 + - + +
348D ILE* 3.3 6.9 - - - +
349D ASN* 2.8 48.3 + - - +
299F ASP 5.4 0.4 + - - -
300F GLN* 2.7 33.3 + - - +
301F ALA* 3.8 9.5 + - - +
302F ARG 3.4 19.7 + - - -
303F THR* 3.8 20.6 + - - +
305F ARG* 6.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 346 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D ASP* 3.2 17.5 + - - +
343D LEU* 3.7 15.0 - - - +
344D TYR 3.3 0.2 - - - -
345D ARG* 1.3 76.6 - - + +
347D VAL* 1.3 62.7 + - - +
349D ASN* 4.5 4.3 - - - +
350D ARG* 3.0 68.9 + - - +
377D SER* 4.1 12.6 - - - +
380D ALA* 5.7 1.2 - - - +
391D VAL* 3.8 44.0 - - - +
399D LEU* 5.3 1.1 - - - -
254F ALA* 3.7 25.9 - - - +
257F ASP* 4.4 3.7 + - - +
501F SO4 5.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ILE* 4.4 18.2 - - + -
97D LEU* 4.7 9.2 - - + -
317D VAL* 5.4 2.9 - - + -
343D LEU 3.2 11.8 + - - +
344D TYR* 3.1 9.7 + - - +
346D ARG* 1.3 76.3 - - - +
348D ILE* 1.3 60.9 + - - +
351D ASN* 2.9 31.5 + - - +
374D LEU* 3.9 8.7 - - + +
377D SER* 3.2 44.4 - - - +
378D VAL* 3.7 21.8 - - + +
381D LEU* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLU* 5.8 1.6 - - - +
28D VAL* 3.9 17.3 - - + +
29D LYS* 3.5 15.7 - - - +
30D LYS 4.1 11.2 - - - +
31D PRO* 3.4 23.3 - - + -
46D LEU* 5.7 4.7 - - + -
95D ILE* 4.3 24.5 - - + -
344D TYR* 2.8 26.4 + - + +
345D ARG* 3.3 12.8 - - - +
347D VAL* 1.3 76.1 - - - +
349D ASN* 1.3 59.8 + - - +
351D ASN* 4.3 6.5 - - - +
352D ASN* 3.0 59.4 + - - +
355D LYS* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PRO* 3.2 27.8 - - - +
345D ARG* 2.8 34.2 + - - +
346D ARG* 4.0 4.6 - - - +
348D ILE* 1.3 75.7 - - - +
350D ARG* 1.3 67.0 + - + +
352D ASN* 3.2 7.4 + - - +
353D ARG* 2.9 30.8 + - - +
257F ASP* 5.6 0.9 - - - +
300F GLN* 3.5 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D ARG* 3.0 49.9 + - - +
347D VAL 4.1 1.8 - - - +
349D ASN* 1.3 75.1 - - + +
351D ASN* 1.3 63.2 + - - +
353D ARG* 3.5 8.9 + - - +
354D LEU* 3.0 15.6 + - - +
370D GLU* 2.9 26.6 - - - +
373D MET* 2.8 58.5 + - - +
374D LEU* 4.3 16.5 - - + +
376D GLU* 4.4 8.7 + - - +
377D SER* 4.0 17.2 - - - +
254F ALA* 3.9 5.1 - - - +
256F LEU* 4.7 7.3 - - - +
257F ASP* 2.9 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLU* 5.2 0.2 + - - -
95D ILE* 3.7 17.5 - - + +
96D GLU 2.9 25.2 + - - -
97D LEU* 3.6 8.5 - - + -
98D ALA* 2.8 29.4 + - - +
347D VAL 2.9 18.8 + - - +
348D ILE* 3.9 6.1 - - - +
350D ARG* 1.3 77.6 - - - +
352D ASN* 1.3 66.5 + - - +
354D LEU* 3.1 14.8 + - - +
355D LYS* 3.2 25.0 + - - +
374D LEU* 3.9 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LYS* 3.2 23.5 + - - +
31D PRO* 4.1 11.3 - - - +
348D ILE* 3.0 40.9 + - - +
349D ASN* 3.7 5.8 + - - +
351D ASN* 1.3 75.5 + - - +
353D ARG* 1.3 65.2 + - - +
355D LYS* 3.1 28.5 + - + +
356D ARG* 3.1 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349D ASN* 2.9 17.0 + - - +
350D ARG* 3.8 12.5 - - - +
352D ASN* 1.3 76.4 - - - +
354D LEU* 1.3 57.1 + - - +
356D ARG* 3.2 10.0 + - - +
357D LEU* 2.9 32.8 + - + +
370D GLU* 2.6 52.7 + - - +
373D MET* 4.0 6.1 - - - +
257F ASP* 3.4 33.6 + - - +
260F GLN* 3.7 24.0 - - - +
261F GLU* 2.9 28.6 + - - +
264F LEU* 4.1 20.0 - - + -
300F GLN* 3.6 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ALA* 3.7 22.0 - - + -
99D ALA* 3.7 25.6 - - + +
350D ARG 3.0 13.4 + - - +
351D ASN* 3.3 10.3 - - - +
352D ASN 3.1 0.4 - - - -
353D ARG* 1.3 74.3 - - - +
355D LYS* 1.3 56.7 + - - +
357D LEU* 3.1 4.1 + - + +
358D ILE* 2.7 46.1 + - + +
367D VAL* 3.8 31.6 - - + +
370D GLU* 3.7 23.5 - - + +
371D LYS* 4.1 12.8 - - + +
374D LEU* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D GLU* 4.1 18.2 + - - -
29D LYS* 5.7 4.8 - - - +
96D GLU* 4.3 8.1 + - - +
98D ALA* 3.9 17.3 - - + +
348D ILE* 5.9 0.8 - - - +
351D ASN* 3.6 30.3 - - - +
352D ASN* 3.1 23.6 + - - +
354D LEU* 1.3 77.3 - - - +
356D ARG* 1.3 62.9 + - - +
358D ILE* 3.3 7.4 + - - +
359D ASP* 2.9 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352D ASN 3.1 11.6 + - - +
353D ARG* 3.3 16.2 - - + +
355D LYS* 1.3 77.1 - - - +
357D LEU* 1.3 57.7 + - - +
359D ASP* 3.2 4.6 + - - +
360D LEU* 2.9 46.1 + - + +
261F GLU* 4.9 6.7 + - - -
264F LEU* 3.9 35.7 - - + +
268F ARG* 6.0 2.2 - - - +
24O G 5.0 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D ARG* 2.9 26.2 + - + +
354D LEU* 3.7 4.9 - - + +
356D ARG* 1.3 73.2 - - - +
358D ILE* 1.3 66.8 + - - +
360D LEU* 3.1 12.2 + - + -
361D GLY 3.2 9.0 + - - -
362D ALA* 3.3 22.5 + - + +
366D ILE* 3.4 25.6 - - + +
367D VAL* 4.3 14.0 - - + +
370D GLU* 4.0 20.9 - - + +
260F GLN* 3.4 29.4 - - - +
264F LEU* 3.8 28.5 - - + +
267F ILE* 4.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 358 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ALA* 5.4 5.8 - - + +
354D LEU* 2.7 35.7 + - + +
355D LYS* 3.7 7.4 - - - +
357D LEU* 1.3 71.4 - - - +
359D ASP* 1.3 67.9 + - - +
361D GLY* 3.2 13.0 + - - -
367D VAL* 3.4 35.0 - - + -
371D LYS* 3.9 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D LYS* 2.9 28.2 + - - +
356D ARG* 3.8 5.0 - - - +
358D ILE* 1.3 83.8 - - - +
360D LEU* 1.3 65.7 + - + +
361D GLY 3.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D ARG* 2.9 31.2 + - + +
357D LEU* 3.1 7.3 + - - +
359D ASP* 1.3 80.5 - - + +
361D GLY* 1.3 65.2 + - - +
362D ALA* 3.2 7.3 + - + +
230F LYS* 4.5 6.8 + - - -
264F LEU* 3.9 28.3 - - + +
267F ILE* 4.3 27.8 - - + +
271F GLU* 5.2 6.6 - - - +
----------------------------------------------------------
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