Contacts of the helix formed by residues 579 - 595 (chain A) in PDB entry 1N54
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 579 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A PHE* 3.9 23.2 + - - +
576A LEU 4.9 1.4 + - - -
577A ALA 4.3 0.2 - - - -
578A GLU* 1.3 84.6 + - - +
580A ASP* 1.3 61.7 + - - +
581A GLU* 4.1 11.8 - - - +
582A GLY* 3.2 14.6 + - - -
583A LYS* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A SER* 1.3 73.7 - - - +
581A GLU* 1.3 64.8 + - + +
583A LYS* 3.8 8.2 - - - +
584A LEU* 3.0 24.5 + - - +
615A ASP* 3.6 26.7 - - - +
617A ALA* 4.6 6.1 - - - +
618A ALA* 4.4 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A PHE* 4.1 37.6 - - + +
579A SER* 3.2 8.0 - - - +
580A ASP* 1.3 79.0 - - + +
582A GLY* 1.3 58.4 + - - +
584A LEU* 3.4 10.7 - - - +
585A HIS* 3.1 24.8 + - - +
588A ARG* 4.2 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A PHE* 3.9 19.5 - - - -
544A ILE* 4.2 10.1 - - - +
576A LEU 5.0 0.4 - - - -
577A ALA* 3.9 11.7 - - - -
579A SER* 3.2 13.3 + - - -
581A GLU* 1.3 76.6 - - - +
583A LYS* 1.3 63.8 + - - +
584A LEU 3.0 1.8 - - - -
585A HIS* 3.1 2.8 + - - +
586A VAL* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574A LYS* 5.4 5.8 - - - +
577A ALA* 2.6 39.4 + - + +
578A GLU* 3.7 15.2 + - - +
579A SER 2.8 17.5 + - - +
580A ASP* 3.4 9.8 + - - +
582A GLY* 1.3 76.9 - - - +
584A LEU* 1.3 61.3 + - - +
586A VAL* 3.9 1.1 - - - +
587A LEU* 3.3 26.4 + - - +
612A GLN 5.0 5.3 + - - -
613A ILE 4.0 16.8 - - - +
614A VAL* 3.7 22.6 - - + +
615A ASP* 3.9 30.5 - - - +
618A ALA* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A ASP 3.0 17.0 + - - +
581A GLU* 3.4 9.4 - - - +
582A GLY 3.0 0.2 - - - -
583A LYS* 1.3 77.2 - - - +
585A HIS* 1.3 64.7 + - - +
587A LEU* 3.2 10.9 + - - +
588A ARG* 3.0 40.1 + - - +
618A ALA* 3.6 28.2 - - - +
621A ASN* 3.9 15.9 - - + +
622A TRP* 3.6 28.0 - - + +
625A SER* 5.8 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A PHE* 4.6 7.9 - + + -
541A PRO* 3.2 39.3 + - + +
544A ILE* 3.9 18.4 - - + -
545A GLU* 4.5 7.7 + - - +
581A GLU 3.1 10.8 + - - +
582A GLY* 3.1 12.3 + - - +
584A LEU* 1.3 77.2 - - - +
586A VAL* 1.3 59.1 + - - +
588A ARG* 2.5 62.1 + - + +
589A VAL* 2.8 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ILE* 4.1 22.2 - - + +
548A VAL* 4.3 20.1 - - + +
573A PHE* 4.6 18.2 - - + -
576A LEU* 6.0 1.6 - - + -
577A ALA* 3.8 21.3 - - + +
582A GLY 2.9 21.1 + - - +
583A LYS* 3.9 7.9 - - - +
585A HIS* 1.3 78.4 - - - +
587A LEU* 1.3 58.7 + - - +
589A VAL* 3.1 2.8 + - - +
590A MET* 2.8 27.4 + - + +
608A MET* 3.9 29.2 - - + -
613A ILE* 5.1 2.0 - - + +
614A VAL* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A LYS 3.3 20.2 + - - +
584A LEU* 3.2 10.1 + - - +
585A HIS 3.1 0.6 - - - -
586A VAL* 1.3 79.1 - - - +
588A ARG* 1.3 56.5 + - - +
590A MET* 3.4 29.1 - - + +
591A PHE* 3.0 31.0 + - - +
605A VAL* 4.3 19.3 - - + -
608A MET* 4.1 17.7 - - + -
614A VAL* 4.3 10.1 - - + -
618A ALA* 4.3 4.3 - - + -
619A VAL* 4.2 21.8 - - + +
622A TRP* 3.9 37.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A PHE* 5.9 1.8 - - - -
581A GLU 4.2 5.3 + - - -
584A LEU* 3.0 35.4 + - - +
585A HIS* 2.5 64.5 + - + +
587A LEU* 1.3 69.7 - - - +
589A VAL* 1.3 66.2 + - + +
591A PHE* 3.3 7.0 + - - +
592A GLU* 2.9 35.2 + - + +
622A TRP* 4.7 9.2 - - - +
625A SER* 5.6 2.2 - - - -
627A GLU* 3.3 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ILE* 4.7 3.4 - - + -
545A GLU* 4.0 31.6 - - + +
548A VAL* 4.4 10.8 - - + -
549A GLN* 3.5 35.2 - - + +
585A HIS* 2.8 45.2 + - + +
586A VAL 3.7 3.6 - - - +
588A ARG* 1.3 71.9 - - + +
590A MET* 1.3 57.5 + - - +
592A GLU* 2.6 33.8 + - + +
593A VAL* 2.8 13.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A VAL* 4.2 12.0 - - + +
552A LEU* 4.0 17.3 - - + -
586A VAL* 2.8 16.9 + - + +
587A LEU* 3.4 41.1 - - + +
589A VAL* 1.3 76.1 - - - +
591A PHE* 1.3 55.5 + - - +
593A VAL* 3.0 10.9 + - - +
594A TRP* 2.8 28.7 + - - +
601A ILE* 3.6 28.7 - - + +
604A LEU* 4.1 21.5 - - + -
605A VAL* 3.9 13.5 - - + -
608A MET* 3.6 20.2 - - + -
622A TRP* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A LEU 3.0 19.4 + - - +
588A ARG* 3.5 6.5 - - - +
590A MET* 1.3 75.3 - - - +
592A GLU* 1.3 67.1 + - - +
593A VAL 2.9 4.7 + - - -
594A TRP 4.4 1.6 - - - +
595A ARG* 2.6 78.9 + - + +
601A ILE* 4.6 12.8 - - + -
622A TRP* 4.2 16.6 - + + +
627A GLU* 3.4 36.6 - - + -
628A LEU* 3.7 24.9 - - + -
631A ASP* 3.9 21.3 - - - -
636A PHE* 5.1 10.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ILE* 3.4 30.0 - - - +
545A GLU* 6.2 0.4 - - - +
549A GLN* 5.2 5.3 + - - +
588A ARG* 2.9 33.9 + - + +
589A VAL* 2.6 21.0 + - + +
591A PHE* 1.3 77.2 - - - +
593A VAL* 1.3 57.3 + - + -
595A ARG* 4.0 25.4 + - - +
627A GLU* 4.2 20.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
482A THR 4.2 0.9 - - - +
483A CYS* 3.4 32.9 - - - -
484A ILE* 2.9 43.1 + - - +
549A GLN* 3.6 39.7 - - + +
552A LEU* 4.6 12.3 - - + -
589A VAL* 2.8 23.2 + - + +
590A MET* 3.3 9.6 - - - +
591A PHE 2.9 0.2 - - - -
592A GLU* 1.3 79.2 - - - +
594A TRP* 1.3 71.9 + - + +
595A ARG 3.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A PRO 3.8 15.5 - - - -
482A THR 4.8 0.9 - - - -
483A CYS* 3.7 26.9 - - + -
552A LEU* 3.5 41.3 - - + +
556A ALA* 3.3 50.0 - - + -
562A SER* 5.0 0.4 - - - -
590A MET* 2.8 17.0 + - - +
591A PHE 3.5 0.7 - - - -
593A VAL* 1.3 77.2 - - + +
595A ARG* 1.3 49.9 + - - +
596A ASN 2.6 7.6 + - - -
597A HIS* 2.6 75.6 + + + +
600A MET* 3.5 29.6 - - + +
601A ILE* 3.3 15.8 - - + +
604A LEU* 3.8 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ILE* 3.6 29.8 - - + -
591A PHE* 2.6 61.2 + - + +
592A GLU* 4.0 25.6 + - - +
593A VAL 3.6 0.2 - - - -
594A TRP* 1.3 69.5 - - - +
596A ASN* 1.3 62.0 + - - +
597A HIS 3.3 2.0 + - - -
598A PRO* 5.0 4.2 - - - +
601A ILE* 4.2 10.9 - - - +
627A GLU 4.9 3.0 + - - -
630A ARG* 4.8 18.2 - - - +
631A ASP* 4.4 16.0 + - - +
634A ARG* 5.7 1.9 + - - -
----------------------------------------------------------
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