Contacts of the helix formed by residues 588 - 609 (chain A) in PDB entry 4GT4
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 GLU 588 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ALA* 5.6 2.2 - - + -
587A LEU* 1.3 77.0 - - - +
589A PRO* 1.3 75.7 - - + +
590A PRO* 3.3 13.0 - - + +
591A ASP* 2.8 31.7 + - - +
592A PHE* 3.3 9.3 - - - -
651B ASN* 3.3 33.0 - - + +
652B SER* 4.3 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A LEU 4.6 1.3 - - - +
588A GLU* 1.3 88.3 - - + +
590A PRO* 1.3 68.8 - - + +
591A ASP 3.2 0.7 + - - -
592A PHE* 3.5 22.5 + - + +
593A VAL* 3.7 14.2 + - - +
686A PHE* 5.5 0.5 - - - -
802A NO3 4.1 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A GLU* 3.4 13.7 - - + +
589A PRO* 1.3 97.0 - - + +
591A ASP* 1.3 55.8 + - - +
592A PHE 3.3 0.2 - - - -
593A VAL* 3.4 11.2 + - + +
594A HIS* 2.9 30.0 + - - +
651B ASN* 3.4 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ALA 4.5 1.2 - - - +
587A LEU* 3.7 23.3 - - + +
588A GLU* 2.8 35.0 + - - +
590A PRO* 1.3 74.9 - - - +
592A PHE* 1.3 61.4 + - + +
594A HIS* 3.2 8.9 + - - +
595A LEU* 2.9 35.9 + - + +
627A LEU* 4.1 8.9 - - + +
650B GLY* 3.6 10.6 - - - -
651B ASN* 3.1 41.5 + - - +
652B SER 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A LEU* 4.7 4.5 - - + -
587A LEU* 4.2 26.7 - - + -
588A GLU 3.3 24.7 - - - -
589A PRO* 3.7 9.2 - - + +
590A PRO 3.3 0.4 - - - -
591A ASP* 1.3 76.6 - - + +
593A VAL* 1.3 58.6 + - - +
595A LEU* 3.2 12.8 + - + +
596A VAL* 2.9 34.7 + - - +
685A VAL* 3.5 35.2 - - + -
686A PHE* 3.7 27.1 - + + -
688A TYR* 3.6 32.5 - + - -
802A NO3 3.2 33.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A PRO 3.7 14.6 - - - +
590A PRO* 3.4 11.4 + - + +
591A ASP 3.3 0.2 - - - -
592A PHE* 1.3 74.3 - - - +
594A HIS* 1.3 57.2 + - - +
596A VAL* 3.2 8.9 - - - +
597A ALA* 2.9 34.3 + - + +
686A PHE* 4.6 11.2 - - + -
718A PRO* 6.5 0.7 - - + -
720A TRP* 4.5 20.9 - - + -
746A LEU* 4.1 17.0 - - + +
749A TRP 3.3 27.8 - - - +
750A GLY 4.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A PRO 2.9 14.1 + - - +
591A ASP* 3.2 12.5 + - - +
593A VAL* 1.3 76.8 - - - +
595A LEU* 1.3 56.6 + - - +
597A ALA* 3.6 5.6 - - - +
598A GLN* 2.9 70.0 + - + +
626A LYS 4.6 7.3 + - - -
627A LEU* 4.1 20.4 + - + -
628A ASN* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A LEU* 4.0 29.6 - - + -
564A PHE* 5.9 1.3 - - + -
565A LEU* 4.5 9.2 - - + -
587A LEU* 5.6 4.7 - - + -
591A ASP* 2.9 21.5 + - + +
592A PHE* 3.4 15.7 - - + +
594A HIS* 1.3 76.5 - - + +
596A VAL* 1.3 62.0 + - + +
598A GLN* 3.1 8.6 + - - +
599A ILE* 2.9 34.1 + - - +
627A LEU* 3.7 33.7 - - + +
629A VAL* 3.6 30.9 - - + +
685A VAL* 4.4 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A PHE 2.9 21.7 + - - +
593A VAL* 3.2 18.6 - - - +
595A LEU* 1.3 72.3 - - - +
597A ALA* 1.3 59.7 + - - +
599A ILE* 3.5 8.4 + - + +
600A ALA* 2.9 17.7 + - - +
678A TYR* 2.6 22.1 + - + +
681A VAL* 5.4 1.6 - - + -
682A LEU* 3.6 31.9 - - + +
685A VAL* 3.9 33.0 - - + -
686A PHE* 4.4 10.3 - - + -
720A TRP* 6.3 0.4 - - + -
746A LEU* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A VAL* 2.9 20.2 + - + +
594A HIS* 3.6 8.1 - - - +
596A VAL* 1.3 75.1 - - - +
598A GLN* 1.3 60.3 + - + +
600A ALA* 3.2 3.7 + - - +
601A ALA* 2.9 27.9 + - - +
743A HIS* 3.7 11.6 - - + -
746A LEU* 3.7 35.0 - - + +
747A ARG* 5.0 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ASN* 3.0 41.0 + - - +
594A HIS* 2.9 52.4 + - + +
595A LEU* 3.5 7.2 - - - +
597A ALA* 1.3 76.0 - - - +
599A ILE* 1.3 62.4 + - - +
601A ALA* 3.0 6.6 + - - +
602A GLY 2.9 19.8 + - - -
627A LEU 2.9 25.1 + - - -
628A ASN* 3.1 20.0 + - - -
629A VAL* 3.2 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ASN* 5.5 0.2 - - - -
561A LEU* 4.1 18.6 - - + -
595A LEU 2.9 22.3 + - - +
596A VAL* 3.7 9.6 - - - +
598A GLN* 1.3 75.1 - - - +
600A ALA* 1.3 57.1 + - - +
602A GLY 3.3 1.3 + - - +
603A MET* 2.9 29.0 + - + +
616A LEU* 4.5 20.2 - - + -
621A VAL* 4.0 24.0 - - + -
629A VAL* 4.3 11.6 - - + +
631A ILE* 3.6 16.2 - - + +
678A TYR* 3.7 21.1 - - + -
681A VAL* 3.9 23.3 - - + -
685A VAL* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A VAL 2.9 11.0 + - - +
597A ALA 3.4 6.3 - - - +
599A ILE* 1.3 76.4 - - - +
601A ALA* 1.3 56.8 + - - +
603A MET* 3.5 5.3 + - - +
604A GLU* 2.9 28.9 + - - +
678A TYR* 3.4 29.4 - - + +
739A PHE* 4.0 8.8 - - + +
742A ILE* 4.0 17.0 - - + -
743A HIS* 4.0 15.9 - - - +
746A LEU* 4.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A HIS* 3.9 12.1 + - + +
535A ASN* 3.6 14.6 - - - +
597A ALA 2.9 13.8 + - - +
598A GLN* 3.0 10.5 + - - +
600A ALA* 1.3 73.7 - - - +
602A GLY* 1.3 59.3 + - - +
604A GLU* 3.1 6.0 + - - +
605A TYR* 2.9 28.6 + - - +
743A HIS* 3.7 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A HIS* 4.1 2.9 - - - -
535A ASN* 3.9 19.6 - - - +
536A VAL* 4.0 7.7 - - - +
598A GLN 2.9 10.7 + - - -
601A ALA* 1.3 77.3 - - - +
603A MET* 1.3 55.5 + - - +
605A TYR* 3.2 4.2 + - - +
606A LEU* 2.9 32.0 + - - +
631A ILE* 3.5 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A ILE* 2.9 23.2 + - + +
600A ALA 3.9 0.4 - - - +
602A GLY* 1.3 72.6 - - - +
604A GLU* 1.3 61.6 + - - +
606A LEU* 3.9 17.8 - - + +
607A SER* 2.9 30.8 + - - -
611A VAL 5.4 2.2 - - - +
613A HIS* 4.3 11.9 - - + +
616A LEU* 4.0 25.8 - - + -
631A ILE* 3.4 19.3 - - + +
671A ILE* 5.6 2.0 - - + -
674A ASP* 3.8 25.4 - - + +
678A TYR* 4.9 0.2 - - + -
739A PHE* 3.5 52.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A ALA 2.9 13.8 + - - +
601A ALA 3.1 8.3 + - - +
603A MET* 1.3 74.7 - - - +
605A TYR* 1.3 59.7 + - - +
607A SER* 3.0 7.7 + - - -
608A SER* 2.9 40.8 + - - +
739A PHE* 3.7 11.2 - - + +
740A LYS* 3.3 44.2 - - + +
743A HIS* 3.0 35.5 + - - +
801A NO3 4.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 605 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ARG 3.2 11.8 + - - -
531A LEU* 3.8 21.8 - - + -
532A GLN* 2.8 45.2 + - - +
533A HIS* 3.5 42.8 - + + +
536A VAL* 4.2 9.4 - - + -
601A ALA 2.9 9.3 + - - +
602A GLY 3.4 7.4 - - - +
604A GLU* 1.3 77.8 - - - +
606A LEU* 1.3 67.4 + - + +
608A SER* 3.2 6.6 + - - -
609A HIS* 3.0 56.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 606 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 4.0 27.4 - - + -
536A VAL* 4.2 21.5 - - + -
602A GLY 2.9 17.4 + - - +
603A MET* 3.9 28.3 - - + +
605A TYR* 1.3 82.8 - - + +
607A SER* 1.3 59.9 + - - +
609A HIS* 3.1 9.6 + - - -
611A VAL* 2.9 49.0 + - + +
613A HIS* 4.5 10.5 - - + -
631A ILE* 4.2 21.3 - - + -
633A ASP* 4.3 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A MET* 2.9 17.4 + - - +
604A GLU* 3.0 16.5 + - - -
606A LEU* 1.3 76.5 - - - +
608A SER* 1.3 61.4 + - - +
610A HIS* 3.1 19.7 + - - +
611A VAL 4.3 0.4 + - - -
671A ILE* 3.9 33.3 - - - +
739A PHE* 4.1 2.6 - - - -
801A NO3 3.3 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A GLU* 2.9 30.7 + - - +
605A TYR* 3.4 10.0 - - - -
606A LEU 3.2 0.2 - - - -
607A SER* 1.3 78.1 + - - +
609A HIS* 1.3 66.6 + - - +
610A HIS* 3.3 15.2 + - - -
740A LYS* 6.1 0.7 - - - +
801A NO3 5.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A LEU* 5.5 3.3 - - + +
530A ARG* 4.7 12.7 + - + -
531A LEU* 3.9 28.5 - - + -
605A TYR* 3.0 60.0 + + - +
606A LEU 3.1 7.7 + - - +
608A SER* 1.3 81.7 - - - +
610A HIS* 1.3 74.7 + - - +
611A VAL* 3.2 10.6 + - + +
----------------------------------------------------------
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