Contacts of the helix formed by residues 417 - 432 (chain D) in PDB entry 4R0C
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 417 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D ARG* 4.3 4.7 - - - -
412D MET* 5.2 0.4 - - - -
415D GLY 3.9 3.6 + - - -
416D ILE* 1.3 78.6 - - - +
418D PRO* 1.3 74.1 - - - +
419D GLU* 3.5 14.9 + - - +
420D ALA* 3.1 24.8 + - - +
421D SER* 3.0 20.4 + - - -
490D LEU* 4.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D SER* 4.7 0.7 - - - +
191D ALA* 4.8 1.3 - - + -
198D ARG* 3.5 20.0 - - + +
200D VAL* 3.6 27.8 - - + -
408D ILE* 3.7 33.9 - - + +
412D MET* 4.0 27.4 - - + -
417D SER* 1.3 83.7 - - - +
419D GLU* 1.3 64.1 + - - +
421D SER* 3.1 4.9 + - - +
422D GLN* 2.7 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D ARG* 2.9 43.9 + - - -
199D THR 4.3 0.7 - - - +
200D VAL* 3.8 25.9 - - + +
201D ALA 4.6 2.1 + - - -
204D GLY* 3.9 25.5 - - - +
205D ASN* 3.3 21.5 + - - +
417D SER* 3.5 11.3 - - - +
418D PRO* 1.3 73.8 - - - +
420D ALA* 1.3 56.6 + - - +
422D GLN* 3.7 5.2 - - - +
423D ALA* 2.9 24.3 + - - +
490D LEU* 4.0 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D LEU* 3.4 12.3 - - + +
416D ILE* 4.0 13.7 - - + -
417D SER* 3.1 23.8 + - - +
419D GLU* 1.3 74.1 - - - +
421D SER* 1.3 64.6 + - - +
423D ALA* 3.1 5.0 + - - +
424D ALA 3.0 19.1 + - - -
480D LEU* 4.9 1.7 - - - +
484D ILE* 3.7 27.4 - - + -
490D LEU* 3.7 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D LEU* 3.7 10.1 - - - -
382D PHE* 3.5 18.2 - - - -
400D TRP* 3.9 2.0 - - - -
408D ILE* 4.1 18.6 - - - +
411D LEU* 3.4 31.0 - - - +
416D ILE* 3.4 14.9 + - - +
417D SER 3.0 14.7 + - - -
418D PRO* 3.1 6.4 + - - +
420D ALA* 1.3 77.1 - - - +
422D GLN* 1.3 60.9 + - - +
424D ALA* 3.6 2.1 + - - +
425D TYR* 3.2 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D ASP* 4.9 1.2 + - - +
183D LEU* 3.1 24.5 - - + +
184D ALA* 3.3 21.3 - - - +
187D SER* 2.5 28.7 + - - +
200D VAL* 4.4 6.6 - - - +
201D ALA 5.2 1.4 + - - -
202D ALA 5.9 1.2 + - - -
204D GLY 5.7 0.2 - - - -
205D ASN* 3.5 17.2 + - - +
400D TRP* 3.7 21.9 - - + -
418D PRO 2.7 17.7 + - - +
419D GLU* 3.7 4.2 - - - +
421D SER* 1.3 74.3 - - - +
423D ALA* 1.3 67.6 + - - +
425D TYR* 3.0 12.2 + - + +
426D ARG* 3.1 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 423 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ASN* 3.4 19.6 + - - +
208D PHE* 4.2 13.5 - - + -
419D GLU 2.9 15.0 + - - +
420D ALA* 3.1 10.7 + - - +
422D GLN* 1.3 73.1 - - - +
424D ALA* 1.3 64.6 + - - +
426D ARG* 3.0 19.2 + - - +
427D VAL* 3.3 15.7 + - - +
480D LEU* 3.8 20.6 - - + -
490D LEU* 4.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 424 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379D LEU* 3.6 43.3 - - + +
382D PHE* 4.0 7.6 - - + -
383D VAL* 3.6 16.9 - - + +
420D ALA 3.0 5.3 + - - -
421D SER 3.6 10.1 - - - +
422D GLN 3.2 0.2 - - - -
423D ALA* 1.3 76.7 - - - +
425D TYR* 1.3 61.5 + - - +
427D VAL* 3.5 1.5 + - - +
428D GLY 3.4 15.6 + - - -
480D LEU* 3.7 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 425 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D LEU* 3.6 31.2 - - + -
382D PHE* 4.2 3.3 - - + -
386D THR* 3.6 25.8 - - + +
396D ALA* 2.5 32.5 + - - -
399D LYS* 3.2 40.0 - - + +
400D TRP* 3.4 47.3 - + + -
403D LEU* 4.1 8.1 - - + -
421D SER 3.2 5.7 + - - +
422D GLN* 3.0 10.3 + - + +
424D ALA* 1.3 78.2 - - - +
426D ARG* 1.3 62.5 + - - +
428D GLY 3.4 0.9 + - - -
429D ASP* 2.9 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 426 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D SER* 3.3 48.1 + - - +
179D VAL* 4.4 6.1 - - - +
180D ASP* 2.4 43.0 + - - +
183D LEU* 3.9 24.1 - - + +
202D ALA 5.6 0.6 + - - -
205D ASN* 3.3 38.5 + - - +
208D PHE* 4.8 7.6 - - + -
209D ILE* 3.7 14.0 - - - +
422D GLN* 3.1 28.5 + - + +
423D ALA* 3.0 7.8 + - - +
425D TYR* 1.3 80.1 - - + +
427D VAL* 1.3 59.3 + - + +
429D ASP* 3.2 3.1 + - - -
430D SER* 2.9 34.5 + - - -
476D TRP* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 427 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D PHE* 3.7 24.9 - - + -
383D VAL* 3.7 19.3 - - + -
423D ALA 3.6 13.9 - - - +
424D ALA* 3.6 9.2 - - - +
425D TYR 3.2 0.2 - - - -
426D ARG* 1.3 77.4 - - - +
428D GLY* 1.3 62.5 + - - +
430D SER* 4.1 0.5 - - - -
431D SER* 2.8 34.9 + - - +
473D LEU* 4.7 2.5 - - + +
476D TRP* 3.8 45.9 - - + +
477D SER* 4.0 11.7 - - - +
480D LEU* 4.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 428 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D VAL* 3.8 28.0 - - - +
386D THR* 3.6 10.1 - - - -
387D ALA* 3.4 22.8 - - - +
390D ASN* 3.8 0.3 + - - -
424D ALA 3.4 7.3 + - - -
425D TYR 3.4 2.9 + - - -
426D ARG 3.3 0.2 - - - -
427D VAL* 1.3 83.3 - - - +
429D ASP* 1.3 58.0 + - - +
431D SER* 3.8 5.4 + - - -
432D THR* 3.5 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 429 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D PHE* 3.9 14.4 - - - -
171D SER* 4.2 6.8 + - - -
183D LEU* 5.9 0.7 - - - +
386D THR* 3.5 5.1 - - + +
390D ASN* 2.8 15.4 + - - -
396D ALA* 3.3 30.7 - - - +
399D LYS* 2.6 17.9 + - - +
425D TYR* 2.9 35.3 + - + +
426D ARG* 3.2 2.2 + - - +
428D GLY* 1.3 77.1 - - - +
430D SER* 1.3 58.6 + - - +
433D ASN* 3.0 3.1 - - - +
801D NA 2.5 44.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 430 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D SER 4.2 4.0 - - - -
168D GLY* 3.3 28.8 - - - -
170D PHE* 3.5 8.9 - - - +
171D SER* 2.9 35.9 + - - -
426D ARG 2.9 13.5 + - - -
429D ASP* 1.3 77.0 - - - +
431D SER* 1.3 66.4 + - - +
432D THR 3.3 0.2 - - - -
433D ASN* 3.1 22.2 + - - +
476D TRP* 3.7 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 431 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D GLY* 4.5 7.9 - - - -
427D VAL* 2.8 26.7 + - - +
428D GLY 4.2 3.1 - - - -
429D ASP 3.7 0.2 - - - -
430D SER* 1.3 78.3 - - - +
432D THR* 1.3 62.7 + - - +
433D ASN 3.3 2.4 + - - -
434D ILE* 4.0 8.5 - - - +
469D SER* 3.3 19.9 + - - -
472D LEU* 3.8 10.6 + - - +
473D LEU* 3.5 46.2 + - - -
476D TRP* 4.2 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 432 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387D ALA* 2.9 41.9 + - + +
390D ASN* 3.1 15.4 + - - +
391D LEU* 3.9 12.8 - - + +
428D GLY 3.5 5.7 + - - -
430D SER 3.3 0.4 - - - -
431D SER* 1.3 79.6 - - - +
433D ASN* 1.3 63.6 + - - +
434D ILE 3.1 4.2 + - - -
435D ILE* 3.3 30.9 + - + +
436D THR* 3.9 4.7 + - - +
469D SER* 3.7 16.8 - - - +
470D LEU* 6.1 0.7 - - + -
473D LEU* 4.5 12.3 - - + -
----------------------------------------------------------
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