Contacts of the helix formed by residues 590 - 603 (chain G) in PDB entry 5O9Z
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 ARG 590 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585G LYS* 6.0 0.4 - - - +
588G GLY 3.7 4.0 + - - +
589G THR* 1.3 71.8 - - - +
591G GLU* 1.3 60.6 + - - +
592G SER 3.4 0.2 - - - -
593G LEU* 3.9 6.5 - - - +
594G GLU* 2.9 31.2 + - - +
617G SER 5.4 2.0 - - - +
618G LYS* 5.3 9.6 - - + -
621G ALA* 4.2 24.9 - - + -
626G ALA* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 591 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589G THR* 3.3 2.8 - - - -
590G ARG* 1.3 78.1 - - - +
592G SER* 1.3 59.2 + - - +
594G GLU* 3.9 4.4 - - - +
595G ALA* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 592 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584G GLU* 3.8 19.2 - - - +
589G THR* 3.8 17.2 + - - -
590G ARG 3.4 0.4 - - - -
591G GLU* 1.3 79.0 - - - +
593G LEU* 1.3 57.7 + - - +
595G ALA* 4.0 4.5 - - - +
596G LEU* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 593 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581G ALA* 3.5 30.5 - - + +
584G GLU* 3.8 8.4 - - + +
585G LYS* 4.1 4.9 - - + +
589G THR 3.5 14.8 + - - +
590G ARG* 4.0 5.8 - - - +
591G GLU 3.3 0.2 - - - -
592G SER* 1.3 77.8 - - - +
594G GLU* 1.3 58.3 + - - +
597G LEU* 2.9 31.9 + - - +
614G GLY* 5.1 2.3 - - - -
617G SER* 4.3 19.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 594 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590G ARG 2.9 20.3 + - - +
591G GLU* 4.0 4.9 - - - +
593G LEU* 1.3 75.7 - - - +
595G ALA* 1.3 57.8 + - - +
597G LEU* 3.8 4.3 - - - +
598G GLN* 2.9 30.7 + - - +
614G GLY* 6.1 1.6 - - - -
618G LYS* 6.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 595 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591G GLU 2.9 19.7 + - - +
592G SER* 4.0 4.3 - - - +
594G GLU* 1.3 74.8 - - - +
596G LEU* 1.3 59.8 + - - +
598G GLN* 3.3 6.0 + - - +
599G ARG* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 596 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563G TYR* 6.5 1.1 - - + -
577G TRP* 4.9 6.7 - - + +
580G ALA* 5.2 6.1 - - + -
581G ALA* 4.4 20.2 - - + +
584G GLU* 5.9 0.9 - - + -
592G SER 2.9 18.4 + - - +
593G LEU 4.3 1.8 - - - +
595G ALA* 1.3 77.8 - - - +
597G LEU* 1.3 58.7 + - - +
599G ARG* 3.9 4.9 - - - +
600G ALA* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 597 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581G ALA* 4.5 8.4 - - + +
593G LEU 2.9 23.0 + - - +
594G GLU* 4.0 4.9 - - - +
596G LEU* 1.3 75.2 - - - +
598G GLN* 1.3 59.6 + - - +
600G ALA* 3.9 5.4 - - - +
601G VAL* 2.9 29.1 + - - +
610G LEU* 4.5 14.4 - - - +
611G TRP* 6.0 0.9 - - - -
614G GLY* 4.1 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 598 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594G GLU 2.9 19.9 + - - +
595G ALA* 3.7 6.3 - - - +
596G LEU 3.3 0.2 - - - -
597G LEU* 1.3 76.9 - - - +
599G ARG* 1.3 59.2 + - - +
601G VAL* 3.2 6.6 + - - +
602G ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 599 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595G ALA 2.9 16.9 + - - +
596G LEU* 4.1 4.9 - - - +
598G GLN* 1.3 77.2 - - - +
600G ALA* 1.3 57.6 + - - +
602G ALA* 3.4 6.6 + - - +
603G HIS* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 600 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574G LYS* 5.9 6.3 - - + +
577G TRP* 3.6 29.8 - - + -
596G LEU 2.9 20.7 + - - +
597G LEU* 3.9 5.6 - - - +
599G ARG* 1.3 75.7 - - - +
601G VAL* 1.3 63.7 + - - +
603G HIS* 3.8 6.3 - - - +
604G CYS* 3.2 24.8 + - - +
610G LEU* 5.1 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 601 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597G LEU 2.9 20.7 + - - +
598G GLN* 3.2 7.6 + - - +
600G ALA* 1.3 77.4 - - - +
602G ALA* 1.3 61.3 + - - +
604G CYS 4.9 2.9 - - - -
605G PRO* 3.2 32.6 - - + +
610G LEU* 5.3 9.2 - - + +
611G TRP* 5.9 7.2 - - + +
639G PRO* 6.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 602 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598G GLN 2.9 17.0 + - - +
599G ARG* 3.9 6.7 - - - +
601G VAL* 1.3 75.4 - - - +
603G HIS* 1.3 65.8 + - - +
605G PRO* 4.0 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 603 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571G PRO* 5.5 14.7 - - + +
599G ARG 2.9 18.0 + - - +
600G ALA* 3.8 8.1 - - - +
601G VAL 3.3 0.4 - - - -
602G ALA* 1.3 80.7 - - - +
604G CYS* 1.3 60.8 + - + +
605G PRO* 3.7 2.9 - - - +
----------------------------------------------------------
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