Contacts of the strand formed by residues 448 - 453 (chain D) in PDB entry 4OMC
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 ARG 448 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C ARG* 4.4 0.4 - - - +
446D PRO* 4.0 8.3 + - + +
447D GLN* 1.3 82.0 - - - +
449D LYS* 1.3 61.6 + - - +
477D GLU 4.2 1.2 + - - -
478D PRO* 3.1 29.6 + - - +
479D ASN* 3.8 8.7 - - - +
480D HIS* 2.8 47.2 + - - +
481D ILE* 4.0 11.4 - - + -
571D TYR* 3.2 5.7 - - - -
572D GLY 2.8 38.4 + - - +
573D THR* 4.5 5.2 - - - +
574D ALA* 3.5 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 449 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C LEU* 4.1 12.5 + - - +
272C GLU* 2.6 40.8 + - - +
273C ALA* 5.9 0.2 - - - +
276C ARG* 3.9 29.2 - - - +
448D ARG* 1.3 76.8 - - - +
450D CYS* 1.3 60.2 + - - +
451D ILE* 4.1 17.1 + - + +
479D ASN* 3.3 23.6 - - - +
481D ILE* 4.5 0.2 - - - -
569D VAL* 3.9 18.2 - - + -
570D LEU 3.3 3.8 - - - +
571D TYR* 3.5 28.7 - - + -
602D FMT 2.8 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 450 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D LYS* 1.3 73.7 - - - +
451D ILE* 1.3 61.0 + - - +
452D ILE* 3.9 17.0 + - - -
473D ALA* 3.5 10.3 - - - -
474D CYS* 2.0 58.8 - - - -
479D ASN* 3.8 11.7 - - - +
481D ILE* 4.0 11.4 - - + +
568D LEU 3.7 1.6 - - - +
569D VAL* 3.6 2.1 - - - -
570D LEU* 2.8 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 451 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ALA* 4.2 13.9 - - + -
237C ALA* 3.8 30.3 - - + +
238C ARG* 3.7 38.0 + - + +
269C LEU* 4.0 25.4 - - + +
449D LYS* 4.1 26.2 + - + +
450D CYS* 1.3 74.9 - - - +
452D ILE* 1.3 68.3 + - - +
474D CYS* 4.5 2.9 - - - -
479D ASN* 5.6 0.2 + - - -
567D THR* 3.8 22.9 - - + -
568D LEU 3.7 2.9 - - - -
569D VAL* 4.6 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 452 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450D CYS* 3.9 17.3 - - - +
451D ILE* 1.3 79.2 - - - +
453D ASP* 1.3 64.5 + - - +
454D ILE* 3.4 21.7 + - + +
469D LYS* 4.7 8.5 - - - -
471D VAL* 3.8 34.5 - - + -
473D ALA* 4.5 3.1 - - - +
474D CYS 5.7 0.2 - - - +
567D THR* 4.0 2.2 - - - -
568D LEU* 2.8 46.8 + - + +
570D LEU* 3.9 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 453 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C THR* 4.0 17.2 + - - +
234C ALA* 3.9 25.5 - - + +
238C ARG* 6.0 1.4 - - - +
451D ILE* 4.1 2.8 + - - +
452D ILE* 1.3 74.7 - - - +
454D ILE* 1.3 62.1 + - - +
455D LEU* 3.9 9.2 + - - +
469D LYS* 5.3 3.8 + - - -
565D LYS* 4.1 11.6 - - - +
566D PHE 3.5 8.7 + - - +
567D THR* 2.8 26.7 + - - +
----------------------------------------------------------
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