Contacts of the helix formed by residues 524 - 545 (chain D) in PDB entry 5VOT
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 GLU 524 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D TYR* 1.3 112.8 - - + +
525D ILE* 1.3 61.6 + - - +
526D TRP 2.9 2.2 - - - -
527D MET* 2.8 46.2 + - + +
528D CYS* 3.2 9.5 + - - -
176E TYR* 4.6 15.0 - - + +
180E PHE* 4.4 21.7 - - + -
181E TYR* 3.8 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 525 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A LEU* 3.6 29.9 - - + +
792A VAL* 4.1 19.5 - - + +
521D LEU* 5.0 5.2 - - + +
522D ALA* 3.5 18.3 - - + +
523D TYR 3.7 0.6 - - - -
524D GLU* 1.3 75.7 - - - +
526D TRP* 1.3 57.5 + - - +
528D CYS* 3.1 15.7 + - - +
529D ILE* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 526 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517D PHE 5.2 0.4 - - - -
518D LEU* 3.4 64.5 + - + -
520D PRO 3.6 13.1 + - - -
521D LEU* 4.8 9.6 - - + -
522D ALA* 3.6 22.2 + - + +
523D TYR 3.9 15.5 - - - +
524D GLU 2.9 0.2 - - - -
525D ILE* 1.3 77.0 - - - +
527D MET* 1.3 54.3 + - - +
529D ILE* 2.7 51.4 + - + +
530D VAL* 2.9 18.1 + - + +
584D PHE* 5.7 9.4 - + - -
616D TYR* 4.5 23.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 527 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524D GLU* 2.8 47.7 + - + +
526D TRP* 1.3 74.2 - - - +
528D CYS* 1.3 55.5 + - - +
530D VAL* 3.2 9.9 + - - +
531D PHE* 2.9 50.5 + - + -
180E PHE* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 528 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A LEU* 6.1 1.3 - - - -
792A VAL* 4.9 15.7 - - + -
796A PHE* 4.9 8.4 - - + -
524D GLU* 3.2 12.3 + - - -
525D ILE* 3.1 16.9 + - - +
527D MET* 1.3 77.5 - - - +
529D ILE* 1.3 58.7 + - + +
531D PHE* 3.1 19.7 + - - +
532D ALA* 2.9 30.7 + - - +
153E ILE* 5.8 1.1 - - - -
154E ILE* 4.8 23.8 - - + -
157E ILE* 5.1 10.8 - - - -
180E PHE* 6.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 529 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A VAL* 6.4 1.3 - - + -
521D LEU* 4.9 9.9 - - + -
525D ILE* 2.9 22.2 + - + +
526D TRP* 2.7 50.4 + - + +
528D CYS* 1.3 72.2 - - + +
530D VAL* 1.3 55.8 + - + +
532D ALA* 3.5 5.0 + - - +
533D TYR* 2.9 31.8 + - + +
584D PHE* 4.6 24.7 - - + -
605D TRP* 5.1 2.7 - - + -
608D PHE* 4.9 21.3 - - + -
612D ILE* 4.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 530 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526D TRP* 2.9 17.7 + - + +
527D MET* 3.6 10.5 - - - +
529D ILE* 1.3 76.4 - - + +
531D PHE* 1.3 71.0 + - + +
533D TYR* 3.2 8.7 - - + +
534D ILE* 2.9 37.3 + - + +
188E ILE* 6.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 531 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A PHE* 6.1 1.1 - - + -
527D MET* 2.9 35.4 + - + -
528D CYS* 3.1 22.9 + - + +
530D VAL* 1.3 83.9 - - + +
532D ALA* 1.3 64.8 + - - +
534D ILE* 3.1 3.0 + - + +
535D GLY* 2.9 19.6 + - - -
150E ILE* 4.7 14.8 - - + -
153E ILE* 5.1 17.5 - - + -
180E PHE* 5.9 9.6 - + - -
184E ALA* 3.6 34.1 - - + -
187E PHE* 3.7 36.3 - + + -
188E ILE* 5.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 532 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A PHE* 3.4 34.9 - - + -
799A LEU* 3.7 15.3 - - + -
528D CYS 2.9 14.6 + - - +
529D ILE* 4.0 5.6 - - - +
531D PHE* 1.3 72.5 - - - +
533D TYR* 1.3 64.3 + - - +
535D GLY* 4.5 1.3 - - - +
536D VAL* 2.9 31.9 + - - +
605D TRP* 4.6 7.2 - - + -
608D PHE* 5.1 4.3 - - + -
150E ILE* 5.7 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 533 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529D ILE* 2.9 21.5 + - + +
530D VAL* 3.2 11.0 - - + +
532D ALA* 1.3 78.1 - - - +
534D ILE* 1.3 81.4 + - + +
536D VAL* 3.9 2.1 - - - +
537D SER* 2.8 25.8 + - - -
577D LEU* 2.9 34.7 + - + +
580D SER* 3.4 15.9 - - - -
581D LEU* 2.8 55.1 + - + +
584D PHE* 5.1 4.7 - + + -
605D TRP* 4.1 26.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 534 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530D VAL* 2.9 31.1 + - + +
531D PHE* 3.7 3.6 - - + +
533D TYR* 1.3 92.1 - - + +
535D GLY* 1.3 65.1 + - - +
537D SER* 3.2 5.5 + - - -
538D VAL* 2.9 39.4 + - + +
577D LEU* 4.8 9.4 - - + -
187E PHE* 4.5 9.4 - - + -
188E ILE* 5.8 12.8 - - + +
191E GLU* 4.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 535 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A LEU* 5.6 3.6 - - - -
531D PHE 2.9 13.4 + - - -
532D ALA* 3.8 2.7 - - - -
534D ILE* 1.3 76.0 - - - +
536D VAL* 1.3 62.2 + - - +
538D VAL* 2.9 18.7 + - - +
539D VAL* 2.9 22.9 + - - +
143E VAL* 6.5 0.2 - - - -
147E LEU* 6.0 5.6 - - - -
187E PHE* 4.3 14.7 - - - -
191E GLU* 5.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 536 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A LEU* 4.2 14.8 - - + -
803A LEU* 3.9 28.0 - - + +
532D ALA* 2.9 25.1 + - - +
533D TYR 3.9 2.7 - - - +
535D GLY* 1.3 70.3 - - - -
537D SER* 1.3 66.1 + - - +
539D VAL* 4.7 1.1 - - - +
540D LEU* 2.9 31.3 + - + +
580D SER* 5.7 2.9 - - - +
601D VAL* 3.8 23.7 - - + +
604D VAL* 6.3 0.9 - - + -
605D TRP* 4.1 42.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 537 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533D TYR 2.8 18.1 + - - -
534D ILE* 3.3 9.2 - - - -
536D VAL* 1.3 78.2 - - - +
538D VAL* 1.3 64.3 + - - +
540D LEU* 3.5 7.8 - - - +
541D PHE* 2.9 23.9 + - - +
573D ILE* 5.1 3.8 - - - +
576D SER* 4.9 3.7 - - - -
577D LEU* 3.3 27.1 - - - +
580D SER* 2.6 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 538 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D ILE* 2.9 31.1 + - + +
535D GLY* 2.9 10.1 + - - +
537D SER* 1.3 74.4 - - - +
539D VAL* 1.3 67.7 + - - +
541D PHE* 2.8 18.9 + - + +
542D LEU* 2.9 15.1 + - + +
573D ILE* 5.2 3.6 - - + -
143E VAL* 3.6 30.1 - - + -
191E GLU* 4.4 13.9 - - + +
192E MET* 6.0 0.2 - - - -
195E VAL* 3.6 34.5 - - + +
198E VAL* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 539 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A LEU* 4.8 23.3 - - + +
806A ALA* 5.6 0.2 - - + -
807A MET* 3.6 36.1 - - + +
535D GLY* 2.9 23.8 + - - +
536D VAL* 4.3 4.0 - - - +
538D VAL* 1.3 71.1 - - - +
540D LEU* 1.3 65.0 + - - +
542D LEU* 3.2 8.3 + - - +
543D VAL* 2.9 34.5 + - + +
601D VAL* 5.1 7.6 - - + -
143E VAL* 4.3 20.0 - - + -
144E SER* 5.8 2.2 - - - +
147E LEU* 5.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 540 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536D VAL* 2.9 23.2 + - + +
537D SER* 3.5 5.4 - - - +
539D VAL* 1.3 77.7 - - - +
541D PHE* 1.3 64.1 + - - +
543D VAL* 3.1 5.1 + - + +
544D SER* 2.9 26.8 + - - -
576D SER* 4.8 16.8 - - - +
579D PHE* 4.1 28.9 - - + -
580D SER* 5.1 4.9 - - - +
593D PRO* 4.8 13.5 - - + -
598D GLY* 4.4 15.7 - - - +
601D VAL* 3.8 32.4 - - + +
602D GLY 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 541 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D SER 2.9 13.7 + - - +
538D VAL* 2.8 14.4 + - + +
540D LEU* 1.3 73.3 - - - +
542D LEU* 1.3 66.0 + - + +
544D SER* 3.2 14.0 + - - -
545D ARG* 3.3 21.0 + - + +
571D PHE* 4.7 5.8 - - + -
572D GLY* 3.5 14.4 - - - -
573D ILE* 3.1 61.5 - - + -
576D SER* 3.8 15.9 - - - +
195E VAL* 4.5 15.7 - - + -
198E VAL* 4.9 13.0 - - + -
199E HIS* 4.7 21.1 - + + -
202E ILE* 6.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 542 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A MET* 5.2 14.1 - - + -
810A ALA* 6.3 1.1 - - + -
811A LEU* 6.1 4.0 - - + -
538D VAL* 2.9 12.7 + - + +
539D VAL* 3.2 10.5 + - + +
541D PHE* 1.3 82.8 - - + +
543D VAL* 1.3 72.8 + - + +
544D SER 3.2 0.7 + - - -
545D ARG 3.3 10.2 + - - -
546D PHE* 3.3 34.2 + - + +
136E LEU 5.9 0.4 - - - +
139E GLY 4.4 16.4 - - - +
140E ILE* 4.5 9.0 - - + +
143E VAL* 4.9 11.0 - - + -
198E VAL* 3.6 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 543 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A ALA* 4.8 12.3 - - + +
807A MET* 4.7 10.3 - - - -
810A ALA* 3.9 24.2 - - + +
814A PHE* 5.4 5.5 - - - -
539D VAL* 2.9 33.8 + - + +
540D LEU* 3.7 7.0 - - - +
542D LEU* 1.3 82.5 - - + +
544D SER* 1.3 61.6 + - - +
545D ARG 3.5 0.2 + - - -
546D PHE* 4.3 5.7 + - - +
547D SER 5.6 0.5 + - - -
595D SER* 4.4 7.0 - - - +
597D SER* 3.2 28.5 - - - +
598D GLY* 4.1 15.0 - - - +
601D VAL* 5.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 544 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D LEU* 2.9 21.6 + - - +
541D PHE* 3.5 8.3 - - - -
542D LEU 3.1 0.4 - - - -
543D VAL* 1.3 79.9 - - - +
545D ARG* 1.3 58.3 + - - +
546D PHE 3.7 1.1 + - - -
547D SER* 5.2 4.9 + - - -
568D THR* 3.8 15.1 - - - +
570D GLU* 3.4 21.9 - - - +
571D PHE* 3.4 27.0 + - - -
595D SER* 5.3 9.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 545 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D PHE* 3.3 22.7 + - + +
542D LEU* 3.3 2.7 + - - -
544D SER* 1.3 79.5 - - - +
546D PHE* 1.3 56.9 + - - +
547D SER* 3.7 2.7 - - - +
548D PRO* 4.9 5.4 - - - +
566D GLU 6.0 2.7 - - - +
567D SER* 6.4 2.2 - - - +
568D THR* 6.1 0.2 - - + -
571D PHE* 4.1 22.7 - - + -
202E ILE* 3.3 26.6 - - + +
----------------------------------------------------------
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