Contacts of the helix formed by residues 545 - 558 (chain C) in PDB entry 3ZNS
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 545 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529C LEU* 3.2 46.5 - - + +
531C HIS 4.9 0.4 + - - +
532C GLN* 4.0 11.4 - - - +
538C ASN* 4.9 1.4 + - - +
544C HIS* 1.3 74.6 - - - +
546C GLY* 1.3 61.2 + - - +
547C ARG 3.0 1.8 + - - -
548C ILE* 3.3 18.0 + - - +
549C GLN* 3.3 9.0 + - - +
665C ARG* 3.4 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 546 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544C HIS* 3.0 21.3 + - - -
545C ALA* 1.3 76.6 - - - +
547C ARG* 1.3 58.6 + - - +
548C ILE 3.5 0.2 - - - -
549C GLN* 3.8 9.9 - - - -
550C SER* 2.9 32.1 + - - -
845C LEU* 3.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 547 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C PRO 3.7 9.6 - - - +
543C GLU* 2.8 34.1 + - - +
544C HIS* 3.4 41.1 + - + +
545C ALA 3.0 0.6 + - - -
546C GLY* 1.3 75.8 - - - +
548C ILE* 1.3 61.2 + - - +
550C SER* 3.2 15.9 + - - -
551C ILE* 3.4 18.2 - - - +
664C VAL 4.9 0.4 + - - -
665C ARG* 3.9 16.6 - - - +
667C PRO* 5.0 1.2 - - - +
839C LEU* 4.2 16.1 - - + +
840C GLU 2.7 31.5 + - - -
841C GLY* 3.8 7.5 + - - -
842C GLY 3.1 28.0 + - - +
843C HIS* 4.6 3.8 - - - +
845C LEU* 4.0 9.9 - - + -
848C ILE* 4.0 11.5 - - + +
1900C NU7 3.8 9.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 548 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C TYR* 3.8 13.6 - - + -
525C ASP 4.5 1.6 - - - +
528C MET* 3.8 18.4 - - + -
529C LEU* 3.5 21.5 - - + -
545C ALA 3.3 11.0 + - - +
547C ARG* 1.3 78.2 - - - +
549C GLN* 1.3 64.0 + - - +
551C ILE* 3.6 1.3 + - - -
552C TRP* 3.0 28.4 + - - +
663C VAL* 3.6 28.0 - - + +
664C VAL 3.6 28.9 - - - +
665C ARG* 3.5 29.6 - - + -
839C LEU* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 549 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C TYR* 2.7 31.8 + - - -
529C LEU* 4.2 15.9 - - + +
545C ALA 3.3 13.3 + - - +
546C GLY* 4.0 9.2 - - - +
547C ARG 3.4 0.2 - - - -
548C ILE* 1.3 82.2 - - - +
550C SER* 1.3 57.5 + - - +
552C TRP* 3.3 6.7 + - - +
553C SER* 3.1 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 550 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C GLY 2.9 22.5 + - - -
547C ARG 3.2 6.9 + - - -
549C GLN* 1.3 74.3 - - - +
551C ILE* 1.3 61.9 + - - +
553C SER* 3.2 8.3 + - - -
554C ARG* 3.0 28.1 + - - +
845C LEU* 3.6 28.6 - - - +
848C ILE* 4.8 0.2 - - - +
849C CYS* 3.3 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 551 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547C ARG 3.4 16.8 + - - +
548C ILE 3.6 6.7 + - - +
549C GLN 3.3 0.2 - - - -
550C SER* 1.3 80.4 + - - +
552C TRP* 1.3 65.7 + - - +
554C ARG* 3.1 4.3 + - + +
555C LEU* 3.1 29.8 + - + +
661C PHE* 5.1 0.7 - - + -
663C VAL* 4.1 23.6 - - + -
839C LEU* 4.1 28.9 - - + -
848C ILE* 4.0 25.8 - - + +
849C CYS* 3.8 14.6 - - - -
852C SER* 3.4 37.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 552 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C LEU* 4.0 23.8 - - + -
523C ILE 4.3 3.8 - - - -
524C TYR* 3.4 67.2 - + + -
548C ILE 3.0 18.6 + - - +
549C GLN* 3.3 11.0 + - - +
551C ILE* 1.3 79.4 - - - +
553C SER* 1.3 62.2 + - - +
555C LEU* 3.6 9.5 + - + +
556C GLN 3.6 0.5 + - - -
561C ARG* 3.2 76.9 + - - +
566C CYS* 4.0 22.2 - - + -
567C LEU 5.6 0.9 - - - -
663C VAL* 4.4 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 553 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C GLN* 3.1 30.8 + - - -
550C SER* 3.2 13.7 + - - -
552C TRP* 1.3 76.0 - - - +
554C ARG* 1.3 59.1 + - - +
556C GLN* 3.1 8.5 + - - +
557C GLU* 2.9 45.7 + - - +
561C ARG* 5.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 554 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C SER 3.0 20.9 + - - +
551C ILE* 3.1 7.8 + - + +
553C SER* 1.3 77.6 + - - +
555C LEU* 1.3 59.4 + - + +
557C GLU* 3.5 19.0 + - - +
558C ARG* 3.1 44.5 + - - +
846C THR* 4.2 11.5 + - - +
849C CYS* 3.3 47.9 + - + +
850C ASP* 2.5 36.3 + - - +
853C GLU* 3.4 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 555 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C LEU* 3.9 25.1 - - + -
551C ILE* 3.1 32.1 + - + +
552C TRP* 3.9 13.5 - - + +
553C SER 3.3 0.2 - - - -
554C ARG* 1.3 78.3 - - + +
556C GLN* 1.3 58.6 + - - +
558C ARG 3.9 0.6 - - - -
559C GLY 3.3 1.6 + - - -
560C LEU* 2.8 64.0 + - + +
561C ARG* 3.2 18.6 + - + -
661C PHE* 4.7 4.3 - - + -
663C VAL* 4.7 1.3 - - + -
852C SER* 4.3 1.3 - - - -
853C GLU* 3.8 22.0 - - + +
856C VAL* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 556 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A ARG* 6.3 0.8 - - - +
552C TRP 3.6 2.6 + - - +
553C SER* 3.1 11.5 + - - +
555C LEU* 1.3 75.8 - - - +
557C GLU* 1.3 65.3 + - + +
558C ARG 3.2 1.1 - - - -
559C GLY* 3.1 12.7 + - - -
561C ARG* 3.5 50.9 + - - +
562C SER* 4.5 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 557 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C SER* 2.9 36.3 + - - +
554C ARG* 3.5 25.5 + - - +
556C GLN* 1.3 76.5 - - + +
558C ARG* 1.3 63.1 + - + +
559C GLY 3.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 558 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554C ARG* 3.1 36.9 + - - +
555C LEU 4.4 0.2 - - - +
557C GLU* 1.3 79.4 - - + +
559C GLY* 1.3 62.4 + - - +
560C LEU* 3.3 20.8 + - + +
563C GLN* 5.4 0.2 + - - -
850C ASP* 5.3 2.0 + - - -
853C GLU* 2.8 47.5 + - + +
----------------------------------------------------------
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