Contacts of the helix formed by residues 605 - 613 (chain C) in PDB entry 5DO7
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 GLY 605 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580C PHE* 3.5 40.7 - - - -
582C GLY* 4.5 1.0 - - - -
583C LEU* 3.4 25.1 + - - +
585C PHE* 4.5 1.8 - - - -
604C GLN* 1.3 75.2 - - - +
606C ILE* 1.3 62.1 + - - +
608C PHE 3.6 1.9 + - - -
609C ILE* 3.4 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 606 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG 4.8 11.9 - - - +
106A ALA* 5.0 1.3 - - - -
107A GLY 5.7 1.8 - - - +
581C TYR 3.7 22.7 - - - +
582C GLY* 4.9 2.5 - - - -
604C GLN* 4.3 5.8 - - + +
605C GLY* 1.3 73.0 - - - +
607C GLN* 1.3 73.0 + - + +
608C PHE 3.0 4.9 - - - -
609C ILE* 2.8 32.1 + - + +
610C GLU* 2.8 39.0 + - + +
617C THR* 5.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 607 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA* 5.0 8.0 - - + +
107A GLY* 3.7 34.2 + - - +
108A THR* 6.1 0.2 - - - -
601C ALA* 4.0 14.6 - - - +
602C PHE* 3.7 15.0 - - - +
603C THR* 3.6 14.0 + - - -
604C GLN* 3.1 39.2 + - + +
605C GLY 3.4 0.6 - - - -
606C ILE* 1.3 88.8 - - + +
608C PHE* 1.3 58.8 + - - +
610C GLU* 4.4 5.9 - - - +
611C LYS* 4.1 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 608 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C ILE* 4.5 23.1 - - + -
420C VAL* 3.9 27.8 - - + -
423C LEU* 6.6 0.4 - - + -
548C PHE* 4.5 6.3 - + - -
576C VAL* 3.9 21.1 - - + -
580C PHE* 3.2 37.7 - + + -
601C ALA* 4.6 12.3 - - + -
602C PHE 5.2 1.7 + - - +
604C GLN 4.0 6.0 + - - +
605C GLY 3.6 7.9 + - - +
606C ILE 3.0 0.6 - - - -
607C GLN* 1.3 77.2 - - - +
609C ILE* 1.3 68.4 + - - +
610C GLU 3.1 1.8 - - - -
611C LYS* 2.8 28.4 + - + +
612C THR* 3.3 40.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 609 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C VAL* 4.2 16.6 - - + +
577C VAL* 4.1 21.1 - - + -
580C PHE* 3.7 32.5 - - + +
581C TYR* 4.4 5.8 - - - +
605C GLY 3.4 18.1 + - - +
606C ILE* 2.8 28.1 + - + +
608C PHE* 1.3 77.8 - - - +
610C GLU* 1.3 64.7 + - - +
612C THR* 3.6 1.3 + - - -
613C CYS* 2.9 40.8 + - - +
617C THR* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 610 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 5.3 3.3 - - - +
106A ALA* 4.0 30.6 + - + +
647A HIS* 5.9 0.2 + - - -
606C ILE* 2.8 35.8 + - + +
607C GLN 4.7 1.3 - - - +
609C ILE* 1.3 78.5 - - - +
611C LYS* 1.3 63.6 + - - +
612C THR 3.2 1.2 + - - -
613C CYS 3.8 0.2 + - - -
614C PRO* 3.6 45.2 - - + +
617C THR* 3.6 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 611 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C ASN* 3.9 25.3 + - - +
553C GLN* 5.6 3.8 - - - +
599C MET* 6.3 0.2 - - - +
600C CYS* 3.7 28.0 - - - +
601C ALA* 4.1 15.1 - - + +
607C GLN 4.1 12.4 + - - +
608C PHE* 2.8 28.0 + - + +
610C GLU* 1.3 76.2 - - - +
612C THR* 1.3 60.9 + - + +
614C PRO* 5.7 0.2 - - - +
446D MET* 3.1 45.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 612 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C SER 5.7 0.2 - - - -
547C GLY* 5.0 12.8 - - - -
548C PHE* 4.9 13.9 - - - +
551C ASN* 4.1 20.1 - - - +
552C ILE* 3.4 26.4 + - - +
553C GLN* 4.5 4.0 + - - +
576C VAL* 4.6 1.4 - - - +
608C PHE* 3.3 46.8 + - + -
609C ILE* 3.6 3.8 + - - -
610C GLU 3.2 1.7 - - - -
611C LYS* 1.3 83.6 - - + +
613C CYS* 1.3 84.0 + - - +
614C PRO* 4.0 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 613 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C SER 5.0 6.1 - - - +
548C PHE* 5.9 0.2 - - - -
552C ILE* 4.9 3.1 - - + -
573C GLU* 3.4 44.6 - - + +
576C VAL* 4.3 26.0 - - - -
609C ILE* 2.9 19.3 + - - +
612C THR* 1.3 99.9 + - - +
614C PRO* 1.4 66.5 - - - +
615C GLY 3.6 1.1 - - - -
616C ALA* 3.4 14.9 - - + +
----------------------------------------------------------
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