Contacts of the helix formed by residues 123 - 126 (chain E) 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 123 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E GLU* 4.6 10.8 + - - +
119E SER 5.0 2.2 + - - -
122E GLY* 1.3 82.9 - - - +
124E VAL* 1.3 67.6 + - - +
125E PHE 3.2 4.3 + - - -
126E GLY* 3.2 10.8 + - - -
127E PHE* 3.7 7.1 - - + -
177K LYS* 3.9 3.2 - - - +
204K GLU* 3.0 21.7 + - - -
294K HIS* 3.3 19.6 - - - -
296K ALA* 4.4 0.3 - - - -
298K HIS* 5.9 2.0 - - - -
299K ALA* 5.2 1.6 - - - +
335K LEU* 3.4 24.9 - - + +
1478R CAP 3.0 51.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E PHE* 4.5 0.7 - - + -
56E ALA 4.4 0.2 - - - +
57E VAL* 3.4 45.3 - - + +
60E GLU* 3.8 29.4 - - + +
61E SER* 3.9 3.8 - - - +
120E ILE 3.7 24.9 - - - +
121E VAL* 4.7 0.4 - - - -
122E GLY 3.9 0.4 - - - +
123E ASN* 1.3 77.1 - - - +
125E PHE* 1.3 67.5 + - + +
126E GLY 3.1 2.4 + - - -
127E PHE* 3.4 19.8 + - + +
130E LEU* 3.5 18.9 - - + +
133E LEU* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E PHE* 4.1 7.4 - + - -
121E VAL* 3.5 45.5 - - + +
123E ASN 3.2 1.4 + - - -
124E VAL* 1.3 86.6 - - + +
126E GLY* 1.3 56.9 + - - +
127E PHE 3.5 0.4 - - - -
130E LEU* 4.0 4.1 - - - +
133E LEU* 3.2 53.6 - - + -
134E ARG* 4.0 0.2 - - - -
135E LEU 4.0 9.2 - - - -
307E HIS* 3.8 13.6 - + + -
308E GLY 3.3 22.2 - - - -
309E ILE* 4.6 0.2 - - + -
299K ALA* 3.4 24.9 - - + +
300K VAL* 3.7 19.5 - - + +
303K ARG* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E ASN 3.2 8.1 + - - -
124E VAL 3.1 0.8 - - - -
125E PHE* 1.3 77.2 - - - +
127E PHE* 1.3 60.0 + - - +
298K HIS* 5.6 2.7 - - - -
299K ALA* 3.3 18.2 - - - +
303K ARG* 3.4 10.3 - - - -
335K LEU* 3.5 11.5 - - - -
336K GLU* 2.9 32.7 + - - +
----------------------------------------------------------
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