Contacts of the helix formed by residues 589 - 595 (chain A) in PDB entry 2HX4
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 MET 589 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A VAL* 4.2 11.9 - - + -
587A TRP 3.9 0.2 + - - -
588A TYR* 1.3 77.0 - - - +
590A GLY* 1.3 70.9 + - - +
591A THR* 3.3 22.7 - - - +
592A GLU* 2.8 36.2 + - + +
593A ILE* 4.3 0.3 + - - +
649A VAL* 3.1 20.9 - - + +
651A HIS* 3.8 20.0 - - - +
654A ALA* 3.5 26.0 - - - -
655A THR* 5.1 1.8 - - - -
678A TRP 6.1 0.4 - - - +
679A ILE 5.3 2.7 - - - +
681A PRO* 4.4 21.3 - - + -
682A PRO* 5.1 1.8 - - + -
750A HEM 3.7 29.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
588A TYR* 3.9 2.0 + - - -
589A MET* 1.3 69.1 - - - +
591A THR* 1.3 61.9 + - - +
592A GLU 3.0 1.7 + - - -
593A ILE* 3.1 16.3 + - - +
594A GLY* 3.1 10.2 + - - -
634A ASN* 4.1 4.5 - - - -
637A VAL* 4.1 5.3 - - - +
638A LEU* 3.5 27.6 - - - -
648A ILE* 4.0 11.8 - - - +
649A VAL 2.7 14.3 + - - -
650A ASP* 4.6 1.3 - - - +
651A HIS* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 591 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589A MET* 3.3 27.8 - - - +
590A GLY* 1.3 72.6 - - - +
592A GLU* 1.3 61.0 + - - +
593A ILE 3.1 0.2 - - - -
595A VAL* 2.8 36.6 + - + +
596A ARG* 3.2 3.8 + - - +
634A ASN* 3.5 11.8 + - - +
651A HIS* 3.3 41.6 + - + +
681A PRO* 4.6 2.2 - - + -
682A PRO* 3.8 15.5 - - + +
683A MET* 3.9 17.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
588A TYR* 3.7 14.3 - - + -
589A MET* 2.8 41.1 + - + +
591A THR* 1.3 79.2 + - - +
593A ILE* 1.3 56.9 + - - +
596A ARG* 3.3 14.5 - - - +
597A ASP* 2.9 29.9 + - - +
682A PRO* 5.9 0.2 - - - -
750A HEM 3.7 28.5 - - + +
799A 4HX 2.7 67.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 593 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A TRP* 3.5 46.9 - - + +
588A TYR* 3.6 45.3 - - + -
590A GLY 3.1 5.7 + - - +
592A GLU* 1.3 76.7 - - - +
594A GLY* 1.3 62.8 + - - +
595A VAL 3.4 0.2 - - - -
597A ASP* 3.3 7.2 + - - +
598A TYR* 2.8 50.3 + - + +
637A VAL* 4.1 18.2 - - + -
641A PHE* 3.8 20.0 - - + -
648A ILE* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 594 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A GLY 3.1 7.5 + - - -
593A ILE* 1.3 79.9 - - - +
595A VAL* 1.3 58.3 + - - +
598A TYR* 3.7 10.5 - - - +
599A CYS* 3.5 20.1 - - - -
633A ILE* 3.7 4.9 - - - +
634A ASN* 3.4 29.7 + - - -
637A VAL* 3.9 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A THR* 2.8 27.6 + - - +
594A GLY* 1.3 74.3 - - - +
596A ARG* 1.3 59.5 + - - +
599A CYS* 3.1 25.7 + - - +
600A ASP* 3.4 5.4 + - - +
630A LEU* 4.0 17.0 - - + -
634A ASN* 3.3 25.3 + - - +
682A PRO* 3.7 20.0 - - + +
683A MET* 3.5 24.0 - - + -
686B SER* 2.9 27.1 + - - +
687B ILE* 5.0 3.0 - - + +
----------------------------------------------------------
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