Contacts of the helix formed by residues 622 - 635 (chain O) in PDB entry 5MQF
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 PHE 622 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620O ARG 4.1 2.2 + - - -
621O GLU* 1.3 70.4 - - - +
623O ASP* 1.3 61.3 + - - +
625O CYS* 3.3 3.7 + - - +
626O ARG* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 623 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621O GLU* 4.6 0.2 - - - +
622O PHE* 1.3 79.3 - - - +
624O ARG* 1.3 58.2 + - - +
626O ARG* 4.0 4.8 - - - +
627O LYS* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 624 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616O GLU* 4.7 11.6 - - + +
621O GLU* 3.7 23.9 + - + +
622O PHE 3.3 0.4 - - - -
623O ASP* 1.3 78.7 - - - +
625O CYS* 1.3 51.6 + - - +
627O LYS* 4.5 2.4 - - - +
628O LEU* 2.7 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 625 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613O ILE* 5.3 8.3 - - + +
616O GLU* 4.7 15.4 - - + +
617O LEU* 5.3 6.3 - - + +
621O GLU 3.3 18.6 + - - +
622O PHE* 3.3 5.5 + - - +
623O ASP 3.3 0.4 - - - -
624O ARG* 1.3 77.1 - - - +
626O ARG* 1.3 59.1 + - - +
628O LEU* 4.1 3.8 - - - +
629O TYR* 2.9 30.5 + - - +
653O LEU* 6.4 2.7 - - + -
654O GLY* 6.0 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 626 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622O PHE 2.9 18.3 + - - +
623O ASP* 4.0 4.7 - - - +
625O CYS* 1.3 74.6 - - - +
627O LYS* 1.3 59.6 + - - +
629O TYR* 3.4 5.2 + - - +
630O GLU* 2.9 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 627 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623O ASP 2.9 18.4 + - - +
624O ARG* 4.5 2.0 - - - +
626O ARG* 1.3 74.4 - - - +
628O LEU* 1.3 61.5 + - - +
630O GLU* 3.2 8.1 + - - +
631O LYS* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 628 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612O TYR* 5.7 4.5 - - + +
613O ILE* 6.0 3.6 - - - -
616O GLU* 5.1 8.7 - - + -
624O ARG 2.7 24.2 + - - +
625O CYS* 4.1 4.3 - - - +
627O LYS* 1.3 77.4 - - - +
629O TYR* 1.3 56.5 + - - +
631O LYS* 3.4 5.6 + - - +
632O PHE* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 629 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625O CYS 2.9 20.7 + - - +
626O ARG* 3.8 5.4 - - - +
628O LEU* 1.3 75.3 - - - +
630O GLU* 1.3 59.6 + - - +
632O PHE* 3.8 6.5 - - - +
633O LEU* 2.9 29.3 + - - +
650O GLU* 6.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 630 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626O ARG 2.9 17.9 + - - +
627O LYS* 3.2 10.7 + - - +
629O TYR* 1.3 75.2 - - - +
631O LYS* 1.3 58.6 + - - +
633O LEU* 3.4 6.6 + - - +
634O GLU* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 631 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627O LYS 2.9 15.6 + - - +
628O LEU* 3.9 6.3 - - - +
630O GLU* 1.3 74.4 - - - +
632O PHE* 1.3 59.6 + - - +
634O GLU* 3.0 9.3 + - - +
635O PHE* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 632 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604O PRO* 5.8 9.2 - - + +
609O PHE* 5.3 12.8 - - + -
628O LEU 2.9 18.1 + - - +
629O TYR* 3.9 8.3 - - - +
631O LYS* 1.3 77.5 - - - +
633O LEU* 1.3 53.4 + - - +
635O PHE* 4.2 3.7 - - - +
636O GLY* 2.7 34.8 + - - -
637O PRO* 4.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 633 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629O TYR 2.9 19.8 + - - +
630O GLU* 3.7 7.4 - - - +
631O LYS 3.2 0.2 - - - -
632O PHE* 1.3 74.6 - - - +
634O GLU* 1.3 64.7 + - - +
636O GLY* 3.6 10.3 + - - +
637O PRO* 5.1 4.9 - - - -
662O ILE* 4.5 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 634 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630O GLU 2.9 14.4 + - - +
631O LYS* 3.0 13.4 + - - +
633O LEU* 1.3 77.7 - - - +
635O PHE* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 635 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604O PRO* 4.4 21.8 - - + -
631O LYS 2.9 14.4 + - - +
632O PHE* 4.2 3.6 - - - +
634O GLU* 1.3 77.3 - - - +
636O GLY* 1.3 63.2 + - - +
----------------------------------------------------------
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