Contacts of the helix formed by residues 578 - 604 (chain A) in PDB entry 5CGD
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 PRO 578 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A LEU* 3.8 20.2 - - + -
576A GLY 3.6 9.4 - - - +
577A ASP* 1.3 89.4 - - - +
579A ALA* 1.3 64.6 + - + +
580A PRO 3.6 0.7 - - - -
581A ILE* 3.2 24.7 - - + +
582A ALA* 3.3 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A ASP* 3.6 11.9 - - - +
578A PRO* 1.3 78.6 - - + +
580A PRO* 1.4 75.1 - - + +
582A ALA* 3.2 5.4 + - - +
583A ALA* 3.1 23.2 + - - +
730A TYR* 3.9 4.7 - - - +
800A ILE* 3.8 32.6 - - + +
804A PHE* 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A PRO* 4.3 9.4 - - + +
572A TYR* 3.9 24.7 - - + -
577A ASP* 3.5 22.4 - - - +
579A ALA* 1.4 94.2 - - + +
581A ILE* 1.3 60.5 + - - +
583A ALA* 3.7 3.0 + - + +
584A VAL* 3.2 28.2 + - - +
636A ILE* 4.2 16.0 - - + +
729A VAL* 3.7 27.6 - - + -
730A TYR* 3.7 7.6 - - + +
800A ILE* 4.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A PRO* 3.9 27.1 - - + +
570A VAL* 4.5 11.4 - - + -
573A LEU* 3.9 31.2 - - + -
577A ASP 4.9 0.2 - - - +
578A PRO* 3.2 26.9 - - + +
580A PRO* 1.3 80.7 - - - +
582A ALA* 1.3 66.2 + - + +
584A VAL* 3.6 2.7 + - + +
585A VAL* 3.2 30.7 + - + +
4002A OLA 4.0 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A PRO 3.3 16.2 - - - +
579A ALA* 3.2 5.8 + - - +
581A ILE* 1.3 81.8 - - + +
583A ALA* 1.3 58.9 + - - +
585A VAL* 3.5 6.1 + - - +
586A PHE* 3.0 30.4 + - - +
804A PHE* 4.5 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A ALA 3.1 15.0 + - - +
580A PRO* 4.1 6.5 - - + +
581A ILE 3.4 0.2 - - - -
582A ALA* 1.3 75.8 - - - +
584A VAL* 1.3 57.6 + - - +
586A PHE* 3.6 4.8 - - - +
587A ALA* 3.0 27.4 + - - +
632A THR* 3.7 9.9 + - + +
636A ILE* 4.9 4.0 - - + -
800A ILE* 4.9 3.6 - - + -
803A CYS* 4.0 33.2 - - + -
804A PHE* 4.0 15.6 - - + -
807A SER* 5.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A PRO* 4.4 12.8 - - + -
580A PRO 3.2 18.9 + - - +
581A ILE* 3.8 6.5 - - + +
582A ALA 3.2 0.4 - - - -
583A ALA* 1.3 75.4 - - - +
585A VAL* 1.3 56.2 + - - +
587A ALA* 3.0 6.9 + - - +
588A CYS* 2.7 55.5 + - - -
632A THR* 4.6 3.6 - - - +
633A PHE* 3.9 20.2 - - + -
636A ILE* 4.4 21.3 - - + -
4002A OLA 4.2 13.7 - - + -
4004A OLA 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A ILE* 3.2 28.6 + - + +
582A ALA* 3.9 5.4 - - - +
584A VAL* 1.3 76.2 - - - +
586A PHE* 1.3 58.6 + - - +
588A CYS* 3.2 7.9 + - - +
589A LEU* 2.8 48.8 + - + +
4002A OLA 4.3 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ALA 3.0 17.9 + - - +
583A ALA* 3.6 7.2 - - - +
585A VAL* 1.3 78.6 - - - +
587A ALA* 1.3 57.3 + - - +
589A LEU* 3.4 9.2 + - + +
590A GLY* 2.9 24.2 + - - -
629A TYR* 4.3 3.0 - + - -
804A PHE* 4.2 27.8 - + + -
807A SER* 3.8 29.8 - - - +
808A LEU* 4.2 12.8 - - + -
811A THR* 3.4 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ALA 3.0 12.6 + - - +
584A VAL 3.4 4.0 - - - +
586A PHE* 1.3 76.9 - - - +
588A CYS* 1.3 59.4 + - - +
590A GLY* 3.2 1.0 + - - -
591A LEU* 2.9 34.1 + - - +
629A TYR* 3.4 28.8 - - + +
632A THR* 3.2 31.4 - - + +
633A PHE* 3.8 10.5 - - + -
807A SER* 4.7 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A VAL* 2.7 44.6 + - - +
585A VAL 3.2 4.7 + - - +
587A ALA* 1.3 72.0 - - - +
589A LEU* 1.3 59.0 + - - +
591A LEU* 3.3 8.0 + - - +
592A LEU* 3.0 35.9 + - + +
633A PHE* 3.8 13.7 - - - -
4002A OLA 3.9 23.1 - - + -
4004A OLA 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A VAL* 2.8 35.9 + - + +
586A PHE* 3.8 9.0 - - + +
588A CYS* 1.3 75.5 - - - +
590A GLY* 1.3 56.9 + - - +
592A LEU* 3.8 8.0 - - + +
593A ALA* 3.1 29.1 + - - +
4002A OLA 3.8 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A PHE* 2.9 10.4 + - - -
587A ALA 3.2 4.7 + - - -
588A CYS 3.1 0.4 - - - -
589A LEU* 1.3 75.3 - - - +
591A LEU* 1.3 55.2 + - - +
593A ALA* 3.3 5.9 + - - +
594A THR* 2.8 35.9 + - - -
629A TYR* 3.5 37.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
587A ALA 2.9 17.0 + - - +
588A CYS* 3.8 6.7 - - - +
590A GLY* 1.3 75.5 - - - +
592A LEU* 1.3 57.7 + - - +
594A THR* 3.4 4.3 + - - -
595A LEU* 2.8 31.9 + - - +
626A CYS* 3.6 43.5 - - - +
629A TYR* 3.7 12.1 - - + -
630A LEU* 3.7 23.8 - - + -
633A PHE* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A CYS* 3.0 21.0 + - + +
589A LEU* 3.8 10.8 - - + +
590A GLY 3.3 0.2 - - - -
591A LEU* 1.3 77.0 - - + +
593A ALA* 1.3 56.6 + - - +
595A LEU* 3.3 17.6 + - + +
596A PHE* 2.9 29.7 + - - +
4002A OLA 3.8 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A LEU 3.1 18.4 + - - +
590A GLY* 3.7 5.4 - - - +
592A LEU* 1.3 77.1 - - - +
594A THR* 1.3 57.4 + - - +
596A PHE* 3.5 6.3 + - - +
597A VAL* 3.0 34.9 + - + +
814A LEU* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A GLY 2.8 22.1 + - - -
591A LEU* 3.8 6.1 - - - -
593A ALA* 1.3 75.3 - - - +
595A LEU* 1.3 57.3 + - - +
597A VAL* 4.0 3.4 - - - +
598A THR* 2.5 46.4 + - - +
622A LEU* 3.7 35.9 - - + +
625A ILE* 3.9 4.5 - - + +
626A CYS* 4.4 16.2 - - + +
629A TYR* 3.6 11.4 - - - -
814A LEU* 3.4 16.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
591A LEU 2.8 18.6 + - - +
592A LEU* 3.5 19.5 - - + +
594A THR* 1.3 76.5 - - - +
596A PHE* 1.3 63.4 + - - +
598A THR* 3.5 5.8 + - - -
599A VAL* 3.1 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A LEU 2.9 17.2 + - - +
593A ALA* 3.6 7.9 - - - +
594A THR 3.3 0.2 - - - -
595A LEU* 1.3 78.4 - - - +
597A VAL* 1.3 72.6 + - + +
599A VAL* 3.3 5.2 + - - +
600A VAL* 3.1 47.3 + - + +
822A VAL* 4.0 16.4 - - + -
826A LEU* 4.2 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A ALA* 3.0 18.0 + - + +
594A THR* 4.0 3.1 - - - +
596A PHE* 1.3 89.3 - - + +
598A THR* 1.3 62.5 + - - +
600A VAL* 3.4 7.3 + - - +
601A PHE* 3.3 46.1 + - + -
622A LEU* 4.0 12.6 - - + -
814A LEU* 4.3 16.6 - - + -
818A PHE* 3.8 18.2 - - + -
819A VAL* 5.2 9.9 - - + -
822A VAL* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A THR* 2.5 31.2 + - - +
595A LEU* 3.8 7.6 - - + -
597A VAL* 1.3 74.9 - - - +
599A VAL* 1.3 65.1 + - + +
601A PHE* 3.2 5.8 + - - +
602A ILE* 3.2 35.4 + - + +
619A TYR* 5.0 9.5 - - + -
622A LEU* 3.7 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A LEU* 3.1 33.8 + - + +
596A PHE* 3.8 5.6 - - - +
598A THR* 1.3 76.5 - - + +
600A VAL* 1.3 64.8 + - + +
602A ILE* 3.1 15.1 + - + +
603A ILE* 3.0 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A PHE* 3.1 44.2 + - + +
597A VAL* 3.5 10.5 - - - +
599A VAL* 1.3 79.3 - - + +
601A PHE* 1.3 63.3 + - + +
603A ILE* 4.9 3.1 - - + -
604A TYR* 3.1 42.1 + - + +
822A VAL* 4.3 17.0 - - + -
825A ILE* 3.8 29.6 - - + -
826A LEU* 4.8 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A VAL* 3.3 24.0 + - + -
598A THR* 3.2 7.5 + - - +
599A VAL 3.2 0.4 - - - -
600A VAL* 1.3 81.0 - - + +
602A ILE* 1.3 64.7 - - - +
604A TYR 4.7 1.8 - - - +
605A ARG* 3.3 26.3 + - - +
610A VAL* 3.6 39.4 - - + +
615A ARG* 5.6 0.2 - - - -
618A CYS* 5.6 6.7 - - + -
619A TYR* 4.1 16.9 + + + -
622A LEU* 4.0 14.4 - - + -
818A PHE* 3.4 29.6 - + - -
821A LYS* 3.9 38.4 - - + -
822A VAL* 4.2 19.5 - - + -
825A ILE* 5.1 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 602 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A THR* 3.2 26.6 + - + +
599A VAL* 3.1 17.1 + - + +
601A PHE* 1.3 77.0 - - - +
603A ILE* 1.3 70.9 + - + +
605A ARG* 3.8 33.3 + - - +
619A TYR* 4.0 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 603 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A VAL* 3.0 35.0 + - + +
600A VAL* 5.0 1.6 - - - -
602A ILE* 1.3 83.1 - - + +
604A TYR* 1.3 89.9 + - + +
605A ARG* 3.3 4.9 + - - +
606A ASP* 4.5 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 604 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A VAL* 3.1 34.7 + - + +
601A PHE 3.6 3.8 - - - -
603A ILE* 1.3 101.3 - - + +
605A ARG* 1.3 60.9 + - - +
606A ASP* 3.2 4.7 + - - +
607A THR* 3.6 19.0 + - - +
610A VAL* 3.4 20.1 - - - +
825A ILE* 3.4 32.4 - - + +
826A LEU* 4.2 24.7 - - + +
----------------------------------------------------------
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