Contacts of the helix formed by residues 450 - 456 (chain A) in PDB entry 1C2O
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 450 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 3.4 12.9 - - - +
228A GLN* 2.7 47.7 + - - +
229A SER* 4.1 4.8 + - - -
331A VAL* 3.7 16.0 - - + +
428A TYR* 3.9 7.2 + - + +
430A PHE* 3.6 39.2 - - + -
448A GLY* 3.5 18.4 + - - -
449A TYR* 1.3 79.2 + - - +
451A ILE* 1.4 69.4 + - - +
452A GLU 3.4 1.6 - - - -
453A PHE* 2.9 16.4 + - - +
454A ILE* 3.0 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP* 4.2 12.8 - - + -
117A TRP* 3.8 12.8 - - + -
132A VAL* 4.1 8.7 - - + +
133A TYR* 3.9 19.5 - - + +
202A GLU* 3.5 44.4 - - + +
228A GLN* 5.0 2.0 - - - +
448A GLY* 2.8 23.8 - - - +
450A GLU* 1.4 79.5 - - + +
452A GLU* 1.3 69.5 + - - +
453A PHE 3.0 0.3 + - - -
454A ILE* 3.1 4.3 + - + +
455A PHE* 2.9 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 4.6 7.1 - - + +
86A TRP* 6.5 0.2 - - + -
132A VAL* 4.5 22.9 - - + +
434A ALA* 4.0 11.4 - - - +
436A THR* 3.9 10.6 + - - -
437A LEU* 4.7 3.1 - - - +
448A GLY 5.1 1.8 - - - +
449A TYR* 3.6 40.6 - - + +
451A ILE* 1.3 75.9 - - + +
453A PHE* 1.3 66.4 + - + +
455A PHE* 3.6 0.9 + - - -
456A GLY 3.1 2.1 + - - -
457A LEU* 3.0 35.0 + - + +
458A PRO* 4.4 1.3 - - - -
465A TYR* 2.6 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A PHE* 3.4 25.6 - + + -
432A HIS* 3.8 15.3 - + - -
434A ALA* 3.4 36.1 - - + -
449A TYR 3.8 15.7 - - - -
450A GLU 2.9 7.9 + - - +
452A GLU* 1.3 78.5 - - + +
454A ILE* 1.3 67.2 + - - +
456A GLY* 2.7 16.5 + - - -
458A PRO* 3.7 26.5 - - + -
465A TYR* 4.0 6.1 - + - -
469A GLU* 3.6 31.0 - - + -
472A PHE* 4.2 11.9 - + - -
473A ALA* 4.1 12.4 - - + +
476A LEU* 3.5 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.5 19.5 - - + +
200A PHE* 4.1 17.9 - - + -
228A GLN* 4.0 20.0 - - - +
430A PHE* 5.5 0.7 - - + -
450A GLU* 3.0 23.3 + - + +
451A ILE* 3.9 5.2 - - + +
453A PHE* 1.3 72.2 - - - +
455A PHE* 1.3 65.7 + - + +
456A GLY 3.2 0.2 + - - -
476A LEU* 3.8 19.1 - - + +
477A MET* 4.0 8.4 - - - +
480A TRP* 3.2 73.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TRP* 3.5 43.5 - + + -
132A VAL 3.3 25.6 - - - +
133A TYR* 3.8 21.1 - - - -
134A ASP 3.7 17.0 - - - +
135A GLY 4.2 0.4 - - - -
137A PHE* 3.5 21.5 - - - +
138A LEU* 3.5 21.3 + - + +
146A LEU* 3.9 24.2 - - + -
200A PHE* 3.5 24.7 - + - -
451A ILE* 2.9 31.9 + - + +
454A ILE* 1.3 76.9 - - + +
456A GLY* 1.3 60.1 + - - +
457A LEU* 3.8 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 3.7 11.2 - - - -
452A GLU 3.1 0.6 + - - -
453A PHE 2.7 21.7 + - - -
455A PHE* 1.3 74.2 - - - +
457A LEU* 1.3 64.8 + - - +
458A PRO* 3.1 5.4 - - - -
459A LEU* 3.0 40.7 + - - +
473A ALA* 4.5 0.7 - - - -
477A MET* 3.9 7.6 - - - -
----------------------------------------------------------
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