Contacts of the helix formed by residues 411 - 430 (chain D) in PDB entry 4U0Z
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 VAL 411 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D LEU* 3.9 26.9 - - + -
357D TYR* 4.0 24.9 - - + -
406D ALA* 3.7 28.7 - - + +
409D GLY 4.1 3.0 + - - +
410D ASP* 1.3 71.8 + - - +
412D ARG* 1.3 67.9 + - + +
413D PRO 3.5 0.7 - - - -
414D PHE* 3.3 9.0 + - + +
415D ILE* 3.1 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 412 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D ASP* 2.8 29.9 + - - -
161D TYR* 4.7 2.4 - - - +
164D THR* 3.3 27.1 + - - +
180D ARG* 3.6 12.3 - - - +
187D VAL* 3.6 17.4 - - - +
188D GLU* 5.9 2.2 - - - +
191D ASP* 4.6 7.4 - - - +
410D ASP* 3.0 31.8 + - - +
411D VAL* 1.3 80.4 - - + +
413D PRO* 1.4 66.4 - - + +
415D ILE* 3.0 24.7 + - + +
416D ARG* 3.0 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 413 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D TYR* 4.2 25.1 - - + -
401D HIS* 6.5 0.4 - - + -
402D VAL* 3.9 22.3 - - + +
405D ALA* 4.4 9.4 - - + -
410D ASP* 3.3 25.1 - - - +
411D VAL 3.7 0.2 - - - -
412D ARG* 1.4 89.8 - - + +
414D PHE* 1.4 56.0 + - - +
416D ARG* 3.3 21.3 + - + +
417D PHE* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 414 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D ALA* 3.2 31.2 - - + -
356D HIS* 3.7 27.4 - + - -
357D TYR* 3.9 23.8 - + + -
399D TYR* 3.7 24.7 - + - -
402D VAL* 3.7 38.3 + - + +
403D LEU* 3.8 15.0 - - + -
406D ALA* 5.0 5.2 - - + -
411D VAL* 3.3 10.7 + - + +
412D ARG 3.2 0.6 - - - -
413D PRO* 1.4 76.2 - - - +
415D ILE* 1.4 61.0 + - + +
417D PHE* 3.2 4.4 + + - +
418D ILE* 3.0 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 415 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D PHE* 4.0 25.6 - - + -
349D VAL* 4.4 1.5 - - - +
350D GLU* 3.7 42.8 - - + +
353D ALA* 4.0 18.4 - - + -
354D LEU* 4.3 11.4 - - + -
411D VAL* 3.1 35.1 + - + +
412D ARG* 3.0 15.9 + - + +
414D PHE* 1.4 76.1 - - + +
416D ARG* 1.3 59.8 + - + +
418D ILE* 3.6 2.1 + - - +
419D ALA* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 416 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D ILE* 3.4 43.2 + - - +
160D ASP* 5.0 0.8 + - - -
161D TYR* 5.7 4.4 - - - +
187D VAL* 3.9 12.3 - - - +
191D ASP* 3.0 39.6 + - - +
194D TYR* 4.7 5.3 - - + -
195D PHE* 6.2 0.4 - - - -
410D ASP* 5.5 0.6 + - - -
412D ARG* 3.0 41.5 + - - +
413D PRO* 3.5 39.2 - - + +
415D ILE* 1.3 74.1 - - + +
417D PHE* 1.3 54.8 + - - +
419D ALA* 3.2 8.0 + - - +
420D LYS* 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 417 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D ILE* 4.0 8.5 - - + -
395D GLN* 3.3 32.8 - - + -
398D ASP* 3.8 26.7 - - + -
399D TYR* 3.7 39.3 - + + -
402D VAL* 3.9 26.0 - - + -
413D PRO 2.9 14.9 + - - +
414D PHE* 3.2 9.4 + + - +
416D ARG* 1.3 74.2 - - - +
418D ILE* 1.4 68.7 + - + +
420D LYS* 3.1 11.0 + - + +
421D CYS* 3.0 41.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349D VAL* 4.2 14.6 - - + +
352D ALA* 5.2 1.8 - - + -
353D ALA* 3.8 26.9 - - + +
377D MET* 3.9 26.5 - - + -
381D LEU* 5.8 0.7 - - + -
389D ILE* 5.0 1.7 - - + +
391D ILE* 3.8 31.6 - - + -
414D PHE* 3.0 48.2 + - + +
415D ILE 3.9 1.6 - - - +
417D PHE* 1.4 79.5 - - + +
419D ALA* 1.3 56.2 + - - +
421D CYS* 3.3 6.5 + - + +
422D THR* 2.9 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D TYR* 3.7 19.5 - - + -
195D PHE* 3.9 12.1 - - + -
198D ILE* 3.6 13.4 - - + +
349D VAL* 3.7 14.6 - - + +
415D ILE 3.0 18.8 + - - +
416D ARG* 3.4 9.0 - - - +
418D ILE* 1.3 74.3 - - - +
420D LYS* 1.4 57.4 + - - +
422D THR* 3.1 11.8 + - - -
423D GLU* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D TYR* 3.4 16.3 + - + +
416D ARG 2.7 15.9 + - - +
417D PHE* 3.1 12.8 + - + +
419D ALA* 1.4 71.7 - - - +
421D CYS* 1.4 51.5 + - - +
423D GLU* 3.4 3.1 + - - +
424D THR* 2.8 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389D ILE* 4.1 18.4 - - + -
390D THR 4.6 6.0 - - - +
391D ILE* 4.1 15.0 - - + -
395D GLN* 3.2 32.5 - - - +
417D PHE* 3.0 33.2 + - - -
418D ILE* 3.4 11.4 - - + +
420D LYS* 1.4 74.1 - - - +
422D THR* 1.4 64.2 + - - +
424D THR* 3.3 8.6 + - - -
425D THR* 3.0 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D ILE* 3.6 20.4 - - - +
349D VAL* 3.7 25.4 - - + +
381D LEU* 4.3 13.5 - - + -
386D TYR* 5.4 3.4 - - - -
389D ILE* 3.5 31.2 - - + +
418D ILE* 2.9 27.5 + - + +
419D ALA* 3.1 13.0 + - - -
421D CYS* 1.4 74.0 - - - +
423D GLU* 1.4 55.2 + - - +
425D THR* 3.4 3.5 + - - -
426D LEU* 3.0 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 423 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D TYR* 2.9 42.7 + - + +
197D ILE* 3.9 14.6 - - + +
198D ILE* 4.3 12.3 - - + +
201D LYS* 3.5 28.4 + - + +
419D ALA 3.0 9.1 + - - +
420D LYS 3.7 2.3 - - - +
421D CYS 3.3 0.2 - - - -
422D THR* 1.4 72.9 + - - +
424D THR* 1.3 63.3 + - + +
426D LEU* 3.0 7.6 + - - -
427D ASP* 2.8 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 424 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D GLN* 5.3 5.2 + - - -
420D LYS 2.8 24.5 + - - +
421D CYS* 3.4 12.8 + - - -
423D GLU* 1.3 79.0 - - + +
425D THR* 1.3 54.6 + - - +
427D ASP* 4.0 12.9 - - + +
428D THR* 2.8 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 425 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387D PRO* 4.3 11.7 - - + -
388D PRO 3.4 25.4 - - - +
389D ILE* 3.6 17.7 - - + +
390D THR* 3.9 16.5 + - - +
421D CYS 3.0 17.5 + - - -
422D THR 3.7 4.3 - - - -
424D THR* 1.3 73.7 - - - +
426D LEU* 1.4 64.2 + - - +
428D THR* 3.6 5.8 + - - -
429D LEU* 3.3 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 426 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D ILE* 3.5 42.8 - - + +
201D LYS* 4.0 16.8 - - + -
202D VAL* 3.8 29.8 - - + +
205D VAL* 3.9 17.3 - - + +
386D TYR* 4.9 3.6 - - + -
387D PRO* 3.8 25.8 - - + -
389D ILE* 5.9 0.2 - - + -
422D THR* 3.0 23.6 + - - +
423D GLU* 3.0 7.2 + - - +
425D THR* 1.4 75.8 - - - +
427D ASP* 1.4 61.0 + - - +
429D LEU* 3.6 6.0 + - - +
430D LEU* 3.3 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 427 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D LYS* 2.5 41.1 + - - +
423D GLU* 2.8 32.0 + - - +
424D THR* 4.0 14.1 - - + +
425D THR 3.3 0.2 - - - -
426D LEU* 1.4 70.9 - - - +
428D THR* 1.3 62.2 + - - +
430D LEU* 3.3 16.1 + - - +
431D PHE* 3.5 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 428 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D VAL* 5.8 3.1 - - - +
222D THR* 5.5 11.0 - - + -
424D THR 2.8 22.1 + - - -
425D THR* 4.0 6.5 - - - -
426D LEU 3.5 0.2 - - - -
427D ASP* 1.3 76.9 - - - +
429D LEU* 1.3 63.4 + - + +
431D PHE* 3.5 21.4 - - - +
432D ALA 5.0 0.2 + - - -
123G GLU* 5.5 12.8 - - + +
124G LYS* 5.9 4.4 - - - +
127G LYS* 6.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D VAL* 3.8 30.1 - - + -
215D LEU* 5.8 2.3 - - - +
218D VAL* 5.0 17.9 - - + -
219D MET* 5.7 3.6 - - + +
222D THR* 5.5 11.0 - - + +
387D PRO* 3.8 32.3 - - + -
425D THR* 3.3 19.9 + - + +
426D LEU* 3.8 6.7 - - - +
427D ASP 3.3 0.6 - - - -
428D THR* 1.3 79.3 - - + +
430D LEU* 1.3 57.1 + - - +
431D PHE 3.2 6.3 + - - -
432D ALA* 3.6 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D LYS* 3.9 36.3 - - + +
204D LYS* 3.7 39.3 - - + +
205D VAL* 3.7 14.8 - - + -
426D LEU 3.3 19.6 + - - +
427D ASP* 3.3 11.3 + - - +
429D LEU* 1.3 72.9 - - - +
431D PHE* 1.3 60.5 + - - +
432D ALA 3.3 10.7 + - - +
----------------------------------------------------------
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