Contacts of the helix formed by residues 580 - 592 (chain A) in PDB entry 3RFU
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 SER 580 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A ASP* 1.3 84.5 + - - +
581A LYS* 1.3 54.2 + - - +
582A ARG* 2.8 41.5 + - - -
583A THR* 3.2 16.9 + - - +
584A ALA* 3.5 6.1 + - - +
599A GLU* 4.1 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A ASP 3.1 2.0 + - - -
580A SER* 1.3 69.8 - - - +
582A ARG* 1.3 57.7 + - - +
584A ALA* 3.9 2.5 - - - -
585A GLU* 3.0 39.6 + - + +
596A VAL* 6.4 0.9 - - + -
598A ALA* 3.8 23.8 - - + +
599A GLU* 4.4 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ARG* 2.8 66.3 + - - +
531A GLY* 4.4 16.4 - - - +
533A GLY* 2.6 36.5 + - - -
534A ALA 3.9 2.6 + - - -
535A SER* 4.5 7.3 - - - +
580A SER* 2.8 24.8 + - - -
581A LYS* 1.3 76.2 - - - +
583A THR* 1.3 72.3 + - + +
585A GLU* 3.4 5.1 + - - +
586A ALA* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS* 3.6 22.0 + - - -
533A GLY* 3.9 28.3 - - - +
579A ASP* 3.6 22.9 + - - +
580A SER* 3.5 14.8 - - - +
582A ARG* 1.3 85.4 - - + +
584A ALA* 1.3 66.7 + - - +
586A ALA* 3.1 3.6 + - - +
587A VAL* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS* 4.3 3.6 - - + +
575A MET* 3.7 8.1 - - - +
577A THR* 4.1 15.0 - - + -
579A ASP* 5.1 1.3 - - + +
580A SER 3.5 4.9 + - - +
581A LYS* 3.8 6.1 - - + +
582A ARG 3.2 0.2 - - - -
583A THR* 1.3 82.9 + - - +
585A GLU* 1.3 59.3 + - + +
587A VAL* 3.3 9.5 - - - +
588A ALA* 3.0 31.8 + - - +
596A VAL* 5.2 7.2 - - + -
598A ALA* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A LYS* 3.0 32.3 + - + +
582A ARG* 3.9 4.5 - - - +
584A ALA* 1.3 74.3 - - - +
586A ALA* 1.3 60.6 + - - +
588A ALA* 3.9 3.0 - - - +
589A GLY* 3.0 23.6 + - - -
596A VAL* 3.0 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A GLY 5.1 0.9 - - - +
532A LYS* 3.2 39.7 - - + +
533A GLY* 4.6 0.2 - - - -
582A ARG 3.0 13.1 + - - +
583A THR* 3.1 10.5 + - - +
585A GLU* 1.3 74.2 - - - +
587A VAL* 1.3 63.2 + - - +
589A GLY* 2.8 18.8 + - - -
590A THR* 3.1 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS* 3.6 20.9 - - - +
431A LEU* 4.8 2.9 - - + -
432A THR* 4.0 13.9 - - + -
555A ILE* 3.6 24.5 - - + -
575A MET* 3.6 14.1 - - + -
583A THR 3.0 9.8 + - - +
584A ALA 3.3 12.1 - - - +
586A ALA* 1.3 79.2 - - - +
588A ALA* 1.3 59.7 + - - +
590A THR* 3.0 18.3 + - - -
591A LEU* 3.0 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A MET* 3.7 14.6 - - + -
584A ALA 3.0 22.2 + - - +
585A GLU* 3.9 5.6 - - - +
587A VAL* 1.3 77.7 - - - +
589A GLY* 1.3 60.8 + - - +
592A GLY 3.2 3.6 + - - -
593A ILE* 3.1 41.0 + - + +
596A VAL* 3.3 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A GLU 3.0 12.0 + - - -
586A ALA* 2.8 9.1 + - - -
588A ALA* 1.3 79.8 - - - +
590A THR* 1.3 60.6 + - - +
592A GLY* 4.2 5.2 + - - -
593A ILE 4.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LYS* 5.3 13.0 - - - -
555A ILE* 4.7 7.2 - - - +
560A PRO* 5.9 1.6 - - - +
586A ALA 3.1 12.0 + - - +
587A VAL* 3.0 21.1 + - - +
589A GLY* 1.3 79.6 - - - +
591A LEU* 1.3 65.9 + - - +
592A GLY 3.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU* 3.4 43.7 - - + -
555A ILE* 4.7 12.3 - - + -
559A THR* 3.7 23.1 - - + +
560A PRO* 4.0 24.6 - - + +
563A ILE* 3.6 22.1 - - + +
564A LEU* 4.3 13.2 - - - +
587A VAL* 3.0 32.0 + - + +
589A GLY 3.5 0.2 - - - -
590A THR* 1.3 82.7 - - - +
592A GLY* 1.3 57.7 + - - +
593A ILE* 3.4 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A ILE* 5.3 0.4 - - - -
564A LEU* 5.8 1.8 - - - -
567A GLN* 3.8 23.2 + - - -
588A ALA 3.2 5.1 + - - -
589A GLY 4.2 4.2 + - - -
590A THR 3.5 3.0 + - - -
591A LEU* 1.3 78.5 - - - +
593A ILE* 1.3 66.0 + - - +
594A LYS* 3.4 18.0 + - - +
----------------------------------------------------------
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