Contacts of the helix formed by residues 585 - 599 (chain A) in PDB entry 4N78
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 585 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A GLN* 3.0 42.8 + - - +
502A LYS* 4.0 15.2 + - - +
583A SER 4.3 0.4 + - - -
584A LEU* 1.3 79.5 - - - +
586A GLY* 1.3 66.0 + - - +
587A PRO* 4.2 12.1 - - + +
588A THR* 3.4 17.2 + - + +
589A ILE* 3.1 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 6.5 0.9 - - - -
585A GLU* 1.3 74.6 + - - +
587A PRO* 1.3 74.8 - - - +
589A ILE* 3.2 17.6 + - - +
590A LEU* 3.4 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A GLU* 3.9 11.7 - - + +
586A GLY* 1.3 90.0 - - - +
588A THR* 1.3 64.4 + - + +
590A LEU* 3.3 15.5 + - + +
591A ASP* 3.1 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A GLU* 4.3 20.4 - - + -
495A PRO* 3.9 33.3 - - + +
498A GLN* 4.6 5.2 + - - +
584A LEU* 4.3 10.6 - - - +
585A GLU* 3.4 32.4 + - + -
587A PRO* 1.3 77.6 - - + +
589A ILE* 1.3 64.1 + - - +
591A ASP* 3.1 12.6 + - - +
592A ILE* 2.9 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ILE* 4.3 6.3 - - + -
581A ARG* 3.6 51.6 - - + +
584A LEU* 3.6 24.5 - - + +
585A GLU 3.1 18.2 - - - +
586A GLY* 3.2 10.0 + - - +
588A THR* 1.3 81.6 + - - +
590A LEU* 1.3 61.1 + - + +
592A ILE* 3.3 7.3 + - - +
593A GLU* 2.8 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 590 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A GLY 3.4 12.7 + - - +
587A PRO* 3.3 14.7 + - + +
588A THR 3.2 0.2 - - - -
589A ILE* 1.3 78.8 - - + +
591A ASP* 1.3 58.5 + - - +
593A GLU* 3.8 18.2 - - + +
594A LYS* 2.8 33.1 + - - +
597A ARG* 5.4 2.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
487A PHE* 3.8 5.3 - - + -
491A THR* 4.0 27.8 - - + +
495A PRO* 6.4 0.9 - - + -
587A PRO* 3.1 18.2 + - - +
588A THR* 3.1 16.6 + - - +
590A LEU* 1.3 79.2 - - - +
592A ILE* 1.3 62.1 + - + +
594A LYS* 3.4 11.3 + - - +
595A PHE* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 592 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A PHE* 4.2 17.0 - - + -
492A LEU* 4.7 9.6 - - + -
495A PRO* 5.3 9.6 - - + -
511A LEU* 5.2 2.2 - - + -
566A LEU* 3.7 35.5 - - + +
569A LEU* 4.1 21.3 - - + -
570A ILE* 3.6 21.8 - - + -
584A LEU* 4.5 19.3 - - + -
588A THR* 2.9 23.5 + - - +
589A ILE* 3.8 3.6 - - - +
591A ASP* 1.3 75.3 - - + +
593A GLU* 1.3 59.7 + - - +
595A PHE* 3.4 1.6 + - - +
596A HIS* 2.9 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ILE* 3.8 25.7 - - + +
581A ARG* 2.9 37.6 + - - -
589A ILE* 2.8 34.7 + - + +
590A LEU* 3.8 21.0 - - - +
592A ILE* 1.3 72.5 - - - +
594A LYS* 1.3 56.8 + - - +
596A HIS* 3.8 2.4 + - - +
597A ARG* 2.9 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A LEU 2.8 19.9 + - - +
591A ASP* 3.5 13.2 - - - +
592A ILE 3.1 0.2 - - - -
593A GLU* 1.3 76.3 - - - +
595A PHE* 1.3 63.4 + - - +
597A ARG* 3.2 21.7 + - - +
598A GLU* 3.0 52.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ALA* 3.7 27.8 - - + -
484A LEU* 3.6 26.2 - - + -
487A PHE* 3.7 41.7 - + + -
559A LEU* 5.5 2.0 - - + -
562A VAL* 4.2 11.7 - - + -
563A ARG* 5.4 2.2 - - + -
566A LEU* 3.5 30.5 - - + -
591A ASP 3.1 4.9 + - - +
592A ILE 4.0 1.6 - - - +
594A LYS* 1.3 79.9 - - - +
596A HIS* 1.3 56.6 + - - +
598A GLU* 4.1 6.9 - - - +
599A SER* 2.8 50.5 + - - -
602A TYR* 4.2 22.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU* 4.2 21.1 - - - -
563A ARG* 2.6 79.0 + - + -
566A LEU* 4.7 8.5 - - + -
567A GLU* 3.5 34.3 + - + +
570A ILE* 4.5 15.7 - - + +
592A ILE 2.9 19.3 + - - +
593A GLU* 3.8 7.3 + - - +
595A PHE* 1.3 80.6 - - - +
597A ARG* 1.3 64.3 + - - +
599A SER* 3.2 5.3 + - - -
600A PHE* 3.7 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A MET* 4.2 22.6 - - + +
590A LEU* 5.4 2.6 + - - +
593A GLU* 2.9 41.4 + - - +
594A LYS* 3.2 26.4 + - - +
596A HIS* 1.3 80.5 - - - +
598A GLU* 1.3 67.3 + - + +
600A PHE* 3.2 22.1 - - - +
601A PHE* 4.8 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG* 4.3 27.5 + - - +
391A PHE* 5.4 1.6 - - - -
483A ALA* 6.0 0.5 - - - +
594A LYS* 3.0 48.2 + - + +
595A PHE* 4.1 6.4 - - - +
597A ARG* 1.3 78.4 + - + +
599A SER* 1.3 58.5 + - - +
600A PHE 3.0 9.1 + - - -
601A PHE* 3.6 15.1 + - - +
602A TYR* 3.4 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A LEU* 4.7 3.1 - - - +
563A ARG* 2.8 44.9 + - - +
595A PHE* 2.8 34.6 + - - -
596A HIS* 3.2 4.2 + - - -
598A GLU* 1.3 75.6 - - - +
600A PHE* 1.3 63.3 + - - +
601A PHE 3.2 1.0 + - - -
602A TYR* 3.4 45.9 + - - +
603A THR* 4.8 0.5 + - - -
----------------------------------------------------------
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