Contacts of the helix formed by residues 573 - 587 (chain B) in PDB entry 2GRP
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 CYS 573 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ASN* 3.9 11.2 - - - -
535B LEU* 4.2 8.5 - - - -
536B TYR* 3.7 31.4 - - + +
539B LEU* 4.0 17.8 - - + +
569B ALA 3.7 3.8 + - - +
570B LEU 3.0 9.1 + - - +
572B SER* 1.3 89.4 + - - +
574B SER* 1.3 63.1 + - - +
575B PHE* 3.3 3.5 + - - -
576B ALA* 3.4 7.4 + - + -
577B ARG* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 574 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B LEU 3.5 4.4 + - - -
571B GLU* 2.8 23.9 + - - -
572B SER 3.5 2.0 + - - -
573B CYS* 1.3 72.4 - - - +
575B PHE* 1.3 60.5 + - - +
577B ARG* 4.0 6.1 + - - +
578B HIS* 2.7 58.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 575 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B TYR* 5.2 12.6 - + + -
540B MET* 5.3 10.1 - - + -
573B CYS 3.3 1.2 - - - -
574B SER* 1.3 78.9 - - - +
576B ALA* 1.3 65.0 + - - +
578B HIS* 3.3 7.4 + - - +
579B SER* 2.9 41.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B TYR* 3.9 21.0 - - + +
539B LEU* 3.7 31.1 - - + +
540B MET* 3.9 26.5 - - - +
543B ASN* 5.9 0.3 - - - +
573B CYS* 3.4 6.1 + - + +
574B SER 3.4 0.4 - - - -
575B PHE* 1.3 81.7 - - - +
577B ARG* 1.3 63.9 + - - +
579B SER* 3.3 3.9 + - - -
580B LEU* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B LEU* 3.9 9.6 - - + +
563B VAL* 2.8 34.0 + - + +
564B THR* 3.4 12.0 + - - -
565B LYS 2.9 30.1 + - - -
566B PRO* 4.0 4.9 - - - +
567B ASN 4.2 0.6 - - - +
570B LEU* 3.6 31.4 - - + +
571B GLU* 3.8 29.3 + - - +
573B CYS 3.0 18.7 + - - +
574B SER* 3.5 8.0 + - - +
576B ALA* 1.3 79.2 - - - +
578B HIS* 1.3 73.7 + - - +
580B LEU* 3.4 4.6 + - - +
581B LEU* 3.1 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B SER* 2.7 50.8 + - - +
575B PHE* 3.8 7.0 - - + +
577B ARG* 1.3 84.8 - - - +
579B SER* 1.3 58.5 + - - +
581B LEU* 3.4 9.9 + - - +
582B GLN* 2.9 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B MET* 5.0 8.6 - - - +
543B ASN* 3.5 13.5 - - - -
575B PHE* 2.9 34.2 + - - -
576B ALA* 3.6 9.9 - - - -
577B ARG 3.3 0.2 - - - -
578B HIS* 1.3 77.1 - - - +
580B LEU* 1.3 56.3 + - - +
582B GLN* 3.3 8.1 + - - +
583B THR* 2.9 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B LEU* 3.7 40.6 - - + +
542B LEU* 4.0 23.6 - - + +
543B ASN* 3.3 26.8 + - + +
546B VAL* 4.4 5.2 - - + -
559B LEU* 4.6 3.8 - - + -
563B VAL* 3.9 24.9 - - + -
576B ALA 3.0 17.6 + - - +
577B ARG* 3.7 4.7 - - - +
578B HIS 3.3 0.2 - - - -
579B SER* 1.3 76.6 - - - +
581B LEU* 1.3 58.1 + - - +
583B THR* 3.2 1.6 + - - -
584B LEU* 2.8 44.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
560B LEU* 4.1 13.2 - - + +
563B VAL* 3.6 29.2 - - + +
564B THR* 3.3 37.2 - - + -
577B ARG* 3.1 34.5 + - + +
578B HIS* 3.8 10.3 - - - +
580B LEU* 1.3 71.2 - - - +
582B GLN* 1.3 68.8 + - - +
584B LEU* 3.0 8.4 + - + -
585B TYR* 2.9 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B HIS* 2.9 25.0 + - + +
579B SER* 3.6 7.0 - - - +
581B LEU* 1.3 77.5 - - - +
583B THR* 1.3 63.1 + - - +
585B TYR* 3.3 41.2 + - + +
586B LYS* 3.6 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ASN* 2.6 32.1 + - - +
546B VAL* 3.4 28.5 - - + -
547B GLN* 3.7 24.9 + - + -
579B SER 2.9 8.7 + - - -
580B LEU* 3.5 4.3 - - - -
582B GLN* 1.3 75.1 - - - +
584B LEU* 1.3 65.3 + - - +
586B LYS* 3.0 32.3 + - - +
587B VAL* 3.4 10.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B VAL* 4.1 23.6 - - + -
556B ALA* 4.0 33.8 - - + +
559B LEU* 4.2 11.0 - - + +
560B LEU* 3.6 48.4 - - + +
563B VAL* 4.8 0.4 - - + -
580B LEU* 2.8 41.0 + - + +
581B LEU* 3.0 13.9 + - + +
583B THR* 1.3 73.5 - - - +
585B TYR* 1.3 62.2 + - - +
586B LYS 3.2 0.9 + - - -
587B VAL* 3.2 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B LEU* 3.9 26.9 - - + -
564B THR* 4.8 5.0 - - + +
581B LEU* 2.9 43.1 + - + +
582B GLN* 3.4 42.4 - - + +
583B THR 3.1 0.2 - - - -
584B LEU* 1.3 75.8 - - - +
586B LYS* 1.3 61.6 + - + +
587B VAL* 3.7 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B GLN* 5.8 1.8 + - - -
582B GLN* 3.7 18.6 - - - +
583B THR* 3.0 22.3 + - - +
585B TYR* 1.3 79.0 - - + +
587B VAL* 1.3 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B VAL* 4.0 27.4 - - + +
547B GLN* 6.2 0.2 - - + -
551B PHE* 5.2 2.5 - - + -
553B LYS* 3.6 48.9 + - + +
556B ALA* 3.8 22.0 - - + -
583B THR* 3.4 16.7 + - + +
584B LEU* 3.2 30.7 + - + +
585B TYR 4.4 3.3 - - - +
586B LYS* 1.3 82.9 - - - +
----------------------------------------------------------
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