Contacts of the helix formed by residues 54 - 60 (chain W) in PDB entry 1UW9
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 ASN 54 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C GLU 5.3 2.0 + - - -
56C SER* 5.5 4.0 + - - +
58C ILE* 3.7 24.1 - - + +
59C ARG* 2.9 47.5 + - + +
226V TYR* 5.8 2.2 - - - -
229V GLN* 4.9 5.0 + - - +
53W SER* 1.3 82.7 - - - +
55W GLU* 1.3 67.0 + - - +
56W SER 3.3 2.9 - - - -
57W ALA* 3.0 21.0 + - + +
67W TYR* 5.7 1.8 - - - -
68W TYR* 4.0 7.8 - - - +
69W ASP* 3.5 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 4.0 8.1 - - - +
54J ASN* 5.4 1.0 + - - -
49W LYS* 4.5 5.2 + - - -
53W SER* 2.4 34.0 + - - -
54W ASN* 1.3 76.0 - - - +
56W SER* 1.3 63.7 + - - +
57W ALA 3.3 0.5 + - - -
58W ILE* 3.3 24.4 + - - +
69W ASP* 3.2 7.7 + - - +
70W ASN* 4.7 3.5 + - - +
1141W EDO 2.8 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226H TYR* 3.5 28.6 - - - +
54J ASN* 5.5 5.4 + - - +
55W GLU* 1.3 72.3 - - - +
57W ALA* 1.3 56.4 + - - +
58W ILE* 3.0 7.4 - - - -
59W ARG* 2.9 32.7 + - - +
60W PHE* 3.8 6.9 - - - -
67W TYR* 3.4 17.8 + - - -
69W ASP* 2.7 32.2 + - - -
1141W EDO 4.1 6.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 3.8 29.6 - - + +
59C ARG* 4.8 4.0 - - + +
54W ASN* 3.0 19.4 + - + +
56W SER* 1.3 72.0 - - - +
58W ILE* 1.3 64.7 + - - +
59W ARG 3.0 2.0 - - - -
60W PHE* 3.0 45.0 + - + +
64W SER* 4.3 11.9 - - - -
67W TYR* 4.8 4.6 - - + -
69W ASP* 4.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 3.8 21.5 - - + +
54J ASN* 3.8 38.6 - - + +
55J GLU* 4.0 9.2 - - - +
57J ALA* 3.8 16.5 - - - +
58J ILE* 3.8 44.4 - - + +
64J SER* 5.4 0.2 - - - -
55W GLU 3.3 18.6 + - - +
56W SER 3.0 1.4 - - - +
57W ALA* 1.3 77.2 - - - +
59W ARG* 1.3 62.7 + - + +
60W PHE 3.3 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226H TYR* 3.0 45.5 + - - +
229H GLN* 6.1 0.2 - - - -
258H LYS 5.1 0.2 - - - +
259H GLU 4.0 1.0 - - - +
260H LEU 4.3 1.8 - - - +
261H GLY* 3.0 26.3 + - - -
54J ASN* 2.7 54.1 + - + +
57J ALA* 4.7 5.2 - - + +
62J SER* 5.8 2.4 - - - -
64J SER* 2.8 62.1 + - - +
66J LEU 4.0 1.0 - - - +
67J TYR* 2.9 22.6 + - - -
68J TYR* 3.6 21.8 + - - -
56W SER* 2.9 15.1 + - - +
58W ILE* 1.3 81.6 - - + +
60W PHE* 1.3 61.2 + - - +
61W GLY 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H THR* 4.1 1.6 - - + -
226H TYR* 4.0 9.2 - + - -
259H GLU 3.2 4.0 - - - +
260H LEU* 3.4 42.6 - - + -
61J GLY 5.0 5.6 - - - +
62J SER* 5.3 2.9 - - - -
56W SER 3.8 13.0 - - - -
57W ALA* 3.0 31.5 + - + +
58W ILE 3.3 3.5 - - - +
59W ARG* 1.3 81.9 - - - +
61W GLY* 1.3 72.4 + - - +
63W VAL* 3.9 10.5 - - + -
64W SER* 4.0 18.2 - - - +
67W TYR* 3.6 57.9 - + + -
----------------------------------------------------------
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