Contacts of the helix formed by residues 573 - 583 (chain A) in PDB entry 6R4F
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 573 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ARG* 3.9 27.4 - - - +
571A LEU* 3.1 9.7 + - - +
572A ALA* 1.3 77.9 - - - +
574A GLU* 1.3 61.6 + - - +
575A LEU 3.4 0.6 + - - -
576A LYS* 4.9 2.5 + - - +
577A HIS* 3.5 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ILE* 5.2 1.8 - - + -
571A LEU* 2.8 38.1 + - + +
573A GLY* 1.3 78.5 - - - +
575A LEU* 1.3 65.5 + - - +
576A LYS 3.4 1.8 - - - -
577A HIS* 3.0 44.9 + - - +
579A PRO* 3.2 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A MET* 3.6 42.0 - - + -
570A ILE* 4.3 13.7 - - + -
571A LEU 3.8 1.2 + - - -
572A ALA* 3.1 25.4 + - - +
573A GLY 3.4 0.6 - - - -
574A GLU* 1.3 76.0 - - - +
576A LYS* 1.3 59.7 + - - +
577A HIS 2.9 6.2 + - - -
578A GLY 3.1 12.0 + - - -
579A PRO* 4.4 5.2 - - + +
580A LEU* 3.1 50.8 + - + +
605A ALA* 4.0 23.6 - - + +
608A GLN* 4.1 13.7 - - - +
609A VAL* 4.4 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A GLY 4.9 2.5 + - - +
574A GLU 3.4 0.8 - - - -
575A LEU* 1.3 77.6 - - - +
577A HIS* 1.3 67.6 + - + +
578A GLY 3.3 1.7 + - - -
580A LEU* 4.7 13.2 - - + -
608A GLN* 3.5 38.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A GLY 3.5 25.7 + - - -
574A GLU* 3.4 35.6 + - - +
575A LEU 2.9 1.8 + - - -
576A LYS* 1.3 85.0 + - + +
578A GLY* 1.3 54.9 + - - +
579A PRO* 3.6 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A LEU 3.1 2.6 + - - -
576A LYS 3.3 2.8 + - - -
577A HIS* 1.3 79.8 - - - +
579A PRO* 1.3 68.4 - - - +
580A LEU* 3.0 4.8 + - - -
581A ALA* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LEU* 5.3 1.0 - - - +
543A MET* 6.2 0.2 - - - +
570A ILE* 4.2 35.3 - - + +
574A GLU* 3.2 28.0 - - + +
575A LEU* 3.5 5.0 - - + +
577A HIS* 3.6 3.1 - - + +
578A GLY* 1.3 89.0 - - - +
580A LEU* 1.3 60.5 + - - +
581A ALA 2.9 2.4 + - - -
582A LEU* 3.0 27.2 + - + +
583A VAL* 4.5 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A LEU* 3.1 37.9 + - + +
576A LYS* 4.7 13.9 - - + -
578A GLY 3.0 1.4 + - - +
579A PRO* 1.3 75.2 - - - +
581A ALA* 1.3 62.3 + - - +
582A LEU 3.1 0.2 - - - -
583A VAL* 3.1 40.4 + - + +
608A GLN* 4.2 37.9 - - + +
609A VAL* 4.5 7.6 - - + -
612A ARG* 4.4 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A GLY 3.0 14.1 + - - +
579A PRO 2.9 0.6 + - - -
580A LEU* 1.3 77.9 - - - +
582A LEU* 1.3 64.1 + - + +
583A VAL 3.3 5.5 + - - +
584A ASP* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LEU* 4.0 33.0 - - + -
568A GLU* 5.1 7.2 - - - +
570A ILE* 5.3 4.3 - - + -
579A PRO* 3.0 18.9 + - + +
581A ALA* 1.3 80.0 - - + +
583A VAL* 1.3 62.3 + - - +
584A ASP* 3.3 8.8 + - - +
587A MET* 3.4 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LEU* 4.8 3.6 - - + -
543A MET* 4.1 25.4 - - + -
579A PRO 5.1 0.2 - - - +
580A LEU* 3.1 35.2 + - + +
581A ALA 4.1 5.5 - - - +
582A LEU* 1.3 76.8 - - - +
584A ASP* 1.3 64.1 + - - +
587A MET* 4.6 4.3 - - - -
589A VAL* 4.5 9.4 - - + -
609A VAL* 3.6 40.4 - - + +
612A ARG* 3.5 21.9 - - + +
614A GLY* 3.9 7.2 - - - -
----------------------------------------------------------
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