Contacts of the helix formed by residues 574 - 589 (chain B) in PDB entry 5OF4
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 574 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ASP* 1.3 71.8 - - - +
575B ALA* 1.3 59.4 + - - +
576B GLU 3.3 1.3 - - - -
577B THR* 3.3 12.1 - - - +
578B SER* 3.0 27.5 + - - -
603B LYS* 5.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 575 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ASP* 3.7 7.8 - - + +
574B GLY* 1.3 78.5 - - - +
576B GLU* 1.3 70.3 + - - +
578B SER* 2.3 27.5 + - - -
579B VAL* 2.9 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B ILE 5.4 2.3 - - - +
570B GLU* 4.5 2.6 - - - +
571B THR* 3.8 41.4 + - + +
573B ASP* 4.1 24.3 - - + +
574B GLY 3.3 0.2 - - - -
575B ALA* 1.3 83.6 - - - +
577B THR* 1.3 60.2 + - - +
579B VAL* 4.0 14.1 - - - +
580B ALA* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B GLU* 3.4 22.2 + - - +
571B THR 4.3 1.8 + - - -
573B ASP 3.3 15.5 + - - -
574B GLY* 3.3 16.2 - - - +
576B GLU* 1.3 76.9 - - - +
578B SER* 1.3 58.2 + - - +
580B ALA* 3.9 0.5 - - - +
581B LEU* 2.9 38.4 + - + +
604B VAL* 4.5 18.3 - - + +
608B ILE* 5.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B GLY 3.0 13.4 + - - -
575B ALA* 2.3 32.0 + - - -
577B THR* 1.3 79.8 - - - +
579B VAL* 1.3 62.0 + - - +
581B LEU* 3.4 7.4 + - - +
582B GLU* 2.9 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B ALA* 2.9 17.6 + - + +
576B GLU* 4.0 15.0 - - - +
577B THR 3.4 0.2 - - - -
578B SER* 1.3 85.7 + - - +
580B ALA* 1.3 59.1 + - - +
582B GLU* 3.9 6.5 - - - +
583B LYS* 3.0 56.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B PHE* 3.7 33.6 - - + +
569B ILE 4.7 8.7 - - - +
570B GLU* 4.2 16.6 - - - +
576B GLU 3.0 18.2 + - - +
579B VAL* 1.3 79.6 - - + +
581B LEU* 1.3 56.3 + - - +
583B LYS* 3.7 5.7 - - - -
584B TYR* 2.9 28.8 + - - +
596B LEU* 4.4 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B GLU* 5.3 1.1 + - - +
577B THR* 2.9 26.0 + - + +
578B SER* 3.8 7.0 - - - +
580B ALA* 1.3 74.8 - - - +
582B GLU* 1.3 67.1 + - + +
584B TYR* 3.1 8.4 + - + +
585B GLN* 3.1 47.9 + - + +
596B LEU* 5.5 4.7 - - + -
608B ILE* 3.8 51.8 - - + -
610B PHE* 5.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B SER* 2.9 32.4 + - - +
579B VAL* 3.9 7.0 - - - +
581B LEU* 1.3 78.0 - - + +
583B LYS* 1.3 59.9 + - + +
585B GLN* 3.5 5.9 + - - +
586B GLU* 2.9 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B PHE* 3.4 32.0 - - + -
579B VAL* 3.0 41.7 + - + +
580B ALA* 3.8 3.8 - - - +
582B GLU* 1.3 78.5 - - + +
584B TYR* 1.3 56.1 + - - +
586B GLU* 4.5 4.0 - - - +
587B ALA* 2.8 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B GLY* 3.1 17.3 - - - -
535B ILE 3.5 5.2 + - - -
536B VAL* 4.1 0.7 - - + +
568B PHE* 3.4 7.8 - + + -
580B ALA 2.9 19.6 + - - +
581B LEU* 3.1 8.9 + - + +
583B LYS* 1.3 74.5 - - - +
585B GLN* 1.3 70.2 + - + +
588B CYS* 3.0 47.7 + - - -
594B ALA 3.1 29.8 - - - -
596B LEU* 3.6 35.2 - - + -
610B PHE* 3.6 33.4 - + - -
614B TYR* 4.1 18.2 - + - -
615B GLY* 3.1 23.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B LEU* 3.1 37.8 + - + +
582B GLU* 4.3 5.6 - - - +
584B TYR* 1.3 78.9 - - + +
586B GLU* 1.3 60.7 + - + +
588B CYS 3.9 0.2 - - - -
589B GLU* 3.0 40.1 + - - +
608B ILE* 5.1 9.3 + - - +
614B TYR* 3.1 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B GLU* 2.9 29.8 + - - +
583B LYS* 4.4 3.2 - - - +
585B GLN* 1.3 78.5 - - + +
587B ALA* 1.3 59.6 + - - +
589B GLU* 4.2 7.8 - - - +
590B ASN* 3.2 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B LEU* 5.2 4.3 - - + -
568B PHE* 4.2 5.8 - - + -
583B LYS 2.8 20.7 + - - +
584B TYR 4.1 1.1 - - - +
586B GLU* 1.3 78.2 - - - +
588B CYS* 1.3 59.9 + - - +
589B GLU 3.5 0.4 - - - -
590B ASN* 3.0 15.0 - - - +
592B ARG* 3.0 29.2 - - + +
594B ALA* 4.0 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 588 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ASP* 3.4 26.3 - - - +
584B TYR* 3.0 47.6 + - - +
585B GLN 4.3 0.4 - - - +
587B ALA* 1.3 76.5 - - - +
589B GLU* 1.3 58.0 + - - +
590B ASN 3.1 10.7 + - - +
592B ARG 4.0 5.1 - - - +
593B GLY 3.0 25.8 - - - -
594B ALA* 4.4 0.4 - - - -
613B HIS 4.3 3.5 - - - +
614B TYR* 3.5 21.5 - - + -
206E ARG* 4.1 16.6 - - - +
207E VAL* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 589 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B GLN* 3.0 26.3 + - - +
586B GLU* 4.2 7.9 - - - +
587B ALA 3.5 0.2 - - - -
588B CYS* 1.3 77.0 - - - +
590B ASN* 1.3 69.0 + - - +
613B HIS* 5.2 5.1 - - + +
614B TYR* 4.0 28.8 - - + -
183E TYR* 5.6 4.0 - - - -
206E ARG* 4.8 17.7 + - - +
207E VAL* 3.4 13.5 - - - +
210E VAL* 6.0 1.2 - - - +
----------------------------------------------------------
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