Contacts of the helix formed by residues 537 - 549 (chain D) in PDB entry 5U03
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 537 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D SER* 4.3 0.2 + - - -
476D GLU* 5.7 1.1 - - - -
527D PRO* 3.8 17.7 - - - +
530D LEU* 5.3 0.9 - - - -
531D SER* 3.1 27.4 + - - +
535D LYS 3.6 0.2 + - - -
536D PRO* 1.3 75.0 - - - +
538D PRO* 1.3 75.8 - - - +
539D PRO* 3.5 6.2 - - - +
540D TYR* 3.2 32.1 + - - +
541D PHE* 3.4 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 538 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D MET* 4.0 2.5 - - + -
467D LEU* 3.7 35.6 - - + +
468D TYR* 3.5 47.8 - - + +
536D PRO 4.1 3.4 - - - +
537D SER* 1.3 86.6 - - - +
539D PRO* 1.3 68.5 - - + +
540D TYR 3.2 2.2 - - - -
541D PHE* 3.8 9.0 - - + -
542D GLY* 2.7 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 539 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396D LEU* 3.7 26.7 - - + +
464D MET* 3.6 25.1 - - + -
468D TYR* 4.5 2.5 - - - +
519D PHE* 3.7 6.6 - - + -
521D VAL* 5.5 0.2 - - + -
523D VAL* 5.2 5.4 - - + -
525D TYR* 5.0 3.1 - - + +
527D PRO* 3.6 31.2 - - + -
537D SER* 3.2 11.4 - - - +
538D PRO* 1.3 104.1 - - + +
540D TYR* 1.3 60.5 + - + +
543D LEU* 3.1 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 540 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D VAL* 4.2 22.6 - - + +
320D ALA* 3.7 17.3 - - + +
321D LEU* 3.7 30.5 - - + +
324D SER* 3.6 10.8 + - - +
368D LEU* 4.4 9.3 - - + +
396D LEU* 3.6 25.8 - - + -
398D VAL* 4.3 12.4 - - + +
527D PRO* 3.9 15.8 - - + +
528D GLU* 2.7 47.8 + - + +
537D SER* 3.2 22.9 + - - +
539D PRO* 1.3 80.2 - - + +
541D PHE* 1.3 60.0 + - - +
543D LEU* 3.4 6.7 + - + +
544D LEU* 2.9 27.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
324D SER* 3.1 35.5 + - - +
327D ALA* 3.9 24.0 - - + -
328D ILE* 4.5 10.3 - - + -
467D LEU* 5.6 3.4 - - + -
536D PRO* 4.8 11.2 - - + +
537D SER 3.4 15.8 + - - +
538D PRO* 4.0 7.4 - - + +
540D TYR* 1.3 75.3 - - - +
542D GLY* 1.3 59.7 + - - +
544D LEU* 3.0 5.3 + - + +
545D LEU* 2.9 67.4 + - + +
554D TYR* 3.8 30.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 542 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D LEU* 4.3 12.6 - - - -
519D PHE* 3.6 14.7 - - - -
538D PRO 2.7 22.3 + - - -
541D PHE* 1.3 72.1 - - - +
543D LEU* 1.3 64.2 + - - +
545D LEU* 3.1 15.0 + - - +
546D ALA* 2.9 22.9 + - - +
551D LEU* 4.2 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 543 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D ILE* 3.6 30.1 - - + -
321D LEU* 5.0 1.8 - - + -
366D GLY* 5.4 0.2 - - - -
367D VAL 4.0 8.1 - - - +
368D LEU* 4.9 2.0 - - + -
394D PRO* 3.5 35.7 - - + +
395D PHE 4.1 0.4 - - - +
396D LEU* 3.8 27.6 - - + -
519D PHE* 3.5 29.1 - - + -
539D PRO 3.1 21.1 + - - +
540D TYR* 3.6 10.5 - - + +
542D GLY* 1.3 74.9 - - - +
544D LEU* 1.3 57.1 + - - +
546D ALA* 3.2 1.2 + - - +
547D SER* 2.8 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 544 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D CYS* 4.1 28.9 - - + -
321D LEU* 4.9 3.8 - - + +
324D SER* 3.4 39.7 - - - +
325D ALA* 3.7 7.2 - - + +
328D ILE* 3.5 30.5 - - + -
330D HIS* 5.6 1.3 - - + -
331D LYS 5.8 1.3 - - - +
332D LEU* 5.1 12.1 - - + -
540D TYR 2.9 15.6 + - - +
541D PHE* 3.0 11.6 + - + +
543D LEU* 1.3 75.5 - - - +
545D LEU* 1.3 54.6 + - - +
547D SER* 3.0 10.4 + - - -
548D VAL* 2.8 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 545 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D ILE* 3.8 17.3 - - + -
467D LEU* 5.1 0.9 - - + -
541D PHE* 2.9 46.8 + - + +
542D GLY* 3.4 9.4 - - - +
544D LEU* 1.3 79.7 - - - +
546D ALA* 1.3 56.5 + - - +
548D VAL* 3.8 4.5 - - - -
549D GLY 2.9 19.9 + - - -
550D ARG* 3.3 28.0 + - + +
551D LEU* 3.1 35.4 + - + +
554D TYR* 3.6 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 546 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394D PRO* 3.4 18.0 - - + +
518D PRO* 4.9 3.6 - - + +
519D PHE* 3.5 35.0 - - + -
542D GLY 2.9 12.4 + - - +
543D LEU 3.6 7.4 - - - +
545D LEU* 1.3 75.1 - - - +
547D SER* 1.3 64.8 + - - +
548D VAL 3.2 0.6 + - - -
549D GLY* 3.4 11.9 + - - +
551D LEU* 3.9 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 547 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D CYS* 5.1 2.9 - - - -
300D SER 5.1 1.3 + - - -
301D ILE* 5.7 1.9 - - - +
365D HIS* 3.7 41.6 - - - +
366D GLY* 3.4 20.8 + - - -
394D PRO* 3.6 10.0 - - - +
543D LEU* 2.8 27.9 + - - +
544D LEU* 3.2 19.3 - - - -
546D ALA* 1.3 74.5 - - - +
548D VAL* 1.3 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 548 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D GLU* 4.2 4.0 - - - +
299D CYS* 3.5 28.7 - - - -
328D ILE* 4.0 9.0 - - + -
330D HIS* 3.8 27.6 - - + +
365D HIS* 5.8 0.7 - - - -
544D LEU* 2.8 21.2 + - + +
545D LEU* 3.8 5.2 - - - +
547D SER* 1.3 76.4 - - - +
549D GLY* 1.3 57.9 + - - +
550D ARG* 3.5 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 549 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545D LEU 2.9 11.0 + - - -
546D ALA* 3.4 11.5 + - - -
548D VAL* 1.3 74.8 - - - +
550D ARG* 1.3 54.9 + - - +
551D LEU* 4.1 1.1 - - - -
552D SER* 5.5 4.2 + - - -
----------------------------------------------------------
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