Contacts of the helix formed by residues 543 - 559 (chain A) in PDB entry 5I75
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 ALA 543 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A TRP* 5.5 2.2 - - - -
539A ILE* 3.4 11.6 + - + +
542A VAL* 1.3 88.5 - - + +
544A ILE* 1.3 72.2 + - + +
545A SER 3.4 1.8 - - - -
546A PRO* 3.5 3.9 - - - +
547A LEU* 3.3 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 3.1 42.4 - - + +
539A ILE* 3.4 24.9 - - + +
540A CYS* 3.0 20.5 + - - +
543A ALA* 1.3 82.2 - - + +
545A SER* 1.3 59.1 + - - +
547A LEU* 3.8 6.3 - - + +
548A PHE* 2.9 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE 3.9 4.9 + - - -
128A GLY* 4.1 1.1 + - - -
131A PRO* 3.4 26.2 - - - +
132A LEU* 3.8 29.6 - - - +
135A MET* 6.2 0.2 - - - -
509A ALA* 5.2 1.1 - - - -
540A CYS 2.8 21.0 + - - -
541A TRP* 4.3 5.4 - - - -
544A ILE* 1.3 70.4 - - - +
546A PRO* 1.3 71.6 - - - +
548A PHE* 2.9 18.6 + - - +
549A LEU* 3.0 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A LEU* 3.4 20.6 - - + +
509A ALA* 4.3 23.1 - - + +
510A VAL* 4.6 11.2 - - + -
513A SER* 5.1 0.2 - - - -
514A TRP* 4.7 18.2 - - + +
541A TRP 3.6 22.0 - - - +
542A VAL 3.9 9.9 - - - +
543A ALA 3.5 12.1 - - - +
545A SER* 1.3 93.9 - - - +
547A LEU* 1.3 57.2 + - + +
550A LEU* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A TRP* 6.5 1.1 - - + -
543A ALA* 3.3 28.5 + - + +
544A ILE* 4.0 6.5 - - + +
545A SER 3.2 0.2 - - - -
546A PRO* 1.3 77.6 - - + +
548A PHE* 1.3 59.7 + - - +
550A LEU* 3.7 24.1 - - + +
551A PHE* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 548 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A MET* 3.4 41.1 - - - -
127A PHE* 5.1 1.3 - - + +
128A GLY* 3.6 28.0 - - - -
129A GLY* 4.3 0.9 - - - -
132A LEU* 4.2 7.6 - - + -
330A ALA* 3.5 42.7 - - + +
333A ILE* 3.9 5.8 - - + -
334A PHE* 4.2 9.2 - + + -
544A ILE* 2.9 21.5 + - + +
545A SER* 2.9 9.6 + - - +
547A LEU* 1.3 79.5 - - - +
549A LEU* 1.3 80.3 + - + +
551A PHE* 3.7 4.4 + - - +
552A ILE* 3.4 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 3.6 22.7 - - + -
334A PHE* 3.6 32.1 - - + -
502A LEU* 3.7 17.8 - - + +
505A ALA* 3.5 39.3 - - + +
506A LEU* 3.6 21.1 - - + +
509A ALA* 4.1 11.2 - - + -
545A SER 3.0 13.8 + - - +
548A PHE* 1.3 83.8 - - + +
550A LEU* 1.3 66.6 + - - +
552A ILE* 3.1 4.8 + - + +
553A ILE* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A LEU* 4.1 23.7 - - + +
546A PRO 2.9 18.7 + - - +
547A LEU* 3.7 27.1 - - + +
548A PHE 3.4 0.2 - - - -
549A LEU* 1.3 78.0 - - - +
551A PHE* 1.3 55.9 + - - +
553A ILE* 4.0 8.1 - - + +
554A ALA* 2.9 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A MET* 5.3 11.7 - - + -
323A THR* 4.2 13.9 - - - -
326A TRP* 5.4 6.7 - - + -
327A ILE* 3.8 39.0 - - + -
330A ALA* 6.2 1.8 - - + -
547A LEU 2.9 17.4 + - - +
548A PHE* 3.9 7.0 - - - +
549A LEU 3.2 0.2 - - - -
550A LEU* 1.3 77.3 - - - +
552A ILE* 1.3 57.7 + - + +
554A ALA* 3.9 4.4 - - + -
555A SER* 2.9 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 552 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ILE* 4.3 12.8 - - + +
330A ALA* 3.6 24.5 - - + +
331A ALA* 3.5 42.2 - - + +
334A PHE* 4.5 1.8 - - + -
502A LEU* 3.6 36.1 - - + -
548A PHE* 3.4 27.1 - - + +
549A LEU 3.1 5.6 + - - +
551A PHE* 1.3 74.9 - - + +
553A ILE* 1.3 65.7 + - - +
555A SER* 3.2 6.1 + - - -
556A PHE* 2.9 23.2 + - - +
705A 69D 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A PRO* 3.4 28.7 - - + +
502A LEU* 3.5 32.3 - - + +
503A THR* 3.5 14.1 - - + +
506A LEU* 5.3 5.8 - - + -
549A LEU 3.0 17.6 + - - +
550A LEU* 4.0 10.3 - - + +
552A ILE* 1.3 76.6 - - - +
554A ALA* 1.3 59.9 + - + +
556A PHE* 3.3 1.2 + - - +
557A LEU* 2.9 52.1 + - + +
704A C14 5.9 2.9 - - + -
705A 69D 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A LEU* 2.9 23.3 + - + +
551A PHE* 3.9 7.9 - - + +
553A ILE* 1.3 78.0 - - - +
555A SER* 1.3 57.9 + - - +
557A LEU* 4.6 5.4 - - - +
558A MET* 2.9 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ILE* 3.2 42.2 - - - +
551A PHE* 2.9 22.7 + - - -
552A ILE 3.2 4.7 + - - -
554A ALA* 1.3 78.5 - - - +
556A PHE* 1.3 61.1 + - - +
558A MET* 3.6 4.5 + - - +
559A SER* 3.4 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLU* 3.6 24.2 - - + -
495A TYR* 4.1 15.5 - + - -
499A PRO* 3.7 26.2 - - + -
552A ILE 2.9 11.3 + - - +
553A ILE* 3.8 1.3 - - + +
555A SER* 1.3 74.6 - - - +
557A LEU* 1.3 74.8 + - + +
559A SER 3.0 13.3 + - - -
560A PRO* 3.0 25.6 - - + +
561A PRO* 3.6 31.9 - - + -
579A TYR* 3.8 22.0 - + - -
705A 69D 3.4 46.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A PRO* 5.1 4.0 - - + -
553A ILE* 2.9 40.5 + - + +
554A ALA* 4.1 5.6 - - - +
556A PHE* 1.3 87.0 - - + +
558A MET* 1.3 62.9 + - + +
559A SER 3.5 0.2 + - - -
560A PRO* 4.0 7.1 - - - +
579A TYR* 3.2 34.7 + - + +
704A C14 4.4 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A ALA* 2.9 28.3 + - + +
555A SER* 4.0 5.4 - - - +
557A LEU* 1.3 81.1 - - + +
559A SER* 1.3 67.3 + - - +
560A PRO* 4.1 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A SER 3.4 10.6 + - - +
556A PHE* 3.0 9.1 + - - +
558A MET* 1.3 89.4 + - - +
560A PRO* 1.3 69.8 - - - +
561A PRO* 3.4 5.2 - - - +
----------------------------------------------------------
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