Contacts of the helix formed by residues 546 - 556 (chain G) in PDB entry 5ZRV
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 TYR 546 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545G PHE* 1.3 77.9 - - - +
547G THR* 1.3 60.0 + - - +
549G ARG* 3.6 5.3 - - - +
550G CYS* 2.9 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 547 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546G TYR* 1.3 73.7 - - - +
548G THR* 1.3 61.3 + - - +
549G ARG 3.1 0.4 - - - -
550G CYS* 3.3 1.9 + - - -
551G LEU* 2.8 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 548 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477G SER 5.2 10.6 + - - -
547G THR* 1.3 74.1 - - - +
549G ARG* 1.3 58.0 + - - +
551G LEU* 4.0 3.6 - - - +
552G ALA* 3.0 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 549 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544G GLY* 4.7 19.6 - - - -
545G PHE 4.9 3.0 - - - +
546G TYR* 3.5 13.3 + - - +
547G THR 3.1 1.0 - - - -
548G THR* 1.3 78.1 - - - +
550G CYS* 1.3 56.5 + - - +
553G PRO* 4.7 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 550 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546G TYR 2.9 14.1 + - - -
547G THR 3.6 1.8 - - - -
548G THR 3.1 0.2 - - - -
549G ARG* 1.3 75.4 - - - +
551G LEU* 1.3 63.0 + - - +
552G ALA 3.6 0.7 - - - -
553G PRO* 4.0 4.0 - - - +
554G MET* 3.7 12.1 + - - -
681G PHE* 5.5 7.6 - - - +
684G GLU* 6.1 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 551 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547G THR 2.8 16.5 + - - -
548G THR* 3.0 4.1 + - - +
550G CYS* 1.3 77.0 - - - +
552G ALA* 1.3 53.1 + - - +
554G MET* 2.9 4.7 + - - +
555G MET* 2.7 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 552 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548G THR* 3.0 14.9 + - - +
551G LEU* 1.3 76.8 - - - +
553G PRO* 1.3 55.5 - - - +
555G MET* 4.0 2.9 - - - +
556G SER* 2.9 29.3 + - - +
599G VAL 5.2 9.4 - - - -
612G GLY 4.4 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 553 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549G ARG 4.7 5.8 - - - +
550G CYS* 4.0 8.2 - - - +
551G LEU 3.4 0.6 - - - -
552G ALA* 1.3 73.2 - - - +
554G MET* 1.3 57.2 + - - -
556G SER* 4.5 1.7 - - - +
557G GLU 5.2 2.1 + - - -
611G PHE 5.5 1.1 - - - +
612G GLY* 4.3 20.9 - - - +
613G GLY* 4.9 2.9 - - - +
680G ARG* 5.3 9.1 - - - -
681G PHE* 5.3 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 554 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550G CYS 3.7 6.4 + - - -
551G LEU 2.9 9.7 + - - -
553G PRO* 1.3 76.2 - - - +
555G MET* 1.3 64.6 + - - +
556G SER 3.2 2.7 + - - -
557G GLU* 3.4 10.8 + - - -
558G VAL* 3.6 7.1 + - - -
677G LEU* 5.7 5.8 - - - +
681G PHE* 5.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 555 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551G LEU 2.7 18.8 + - - -
552G ALA* 3.1 3.7 + - - +
554G MET* 1.3 74.9 - - - +
556G SER* 1.3 56.9 + - - +
557G GLU 3.1 0.9 - - - -
558G VAL* 3.0 20.6 + - - +
559G ILE 3.9 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 556 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552G ALA 2.9 15.1 + - - -
553G PRO* 4.5 1.1 - - - -
554G MET 3.2 0.6 - - - -
555G MET* 1.3 77.1 - - - +
557G GLU* 1.3 55.6 + - - +
559G ILE* 4.4 5.7 + - - -
560G ARG* 4.6 2.4 + - - -
613G GLY* 5.3 12.5 - - - -
614G GLY 5.7 0.7 + - - -
615G ASN* 5.0 13.3 + - - -
----------------------------------------------------------
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