Contacts of the helix formed by residues 403 - 408 (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 GLY 403 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E CYS* 3.9 0.9 - - - -
173E THR* 3.3 34.6 - - - +
175E LYS* 4.4 2.0 - - - -
401E GLN 4.0 0.4 - - - -
402E PHE* 1.3 69.9 - - - +
404E GLY* 1.3 59.0 + - - +
405E GLY 3.1 0.8 - - - +
406E THR 3.0 2.9 + - - -
407E LEU* 2.9 32.3 + - - +
1477E CAP 2.8 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 404 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E LYS* 4.4 0.2 - - - +
403E GLY* 1.3 71.2 - - - +
405E GLY* 1.3 55.5 + - - +
406E THR 3.1 0.2 - - - -
408E GLY* 2.8 30.5 + - - -
462E TRP* 3.6 1.0 - - - -
1477E CAP 2.7 20.4 + - - -
65K THR* 3.9 13.6 - - - +
66K TRP* 3.8 4.0 - - - +
67K THR* 3.3 25.6 - - - +
69K VAL* 4.2 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 405 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382E ILE 4.0 10.9 + - - -
383E HIS* 4.9 1.8 - - - -
384E VAL* 5.7 0.2 - - - +
402E PHE* 4.0 7.4 - - - -
403E GLY 3.1 4.9 - - - +
404E GLY* 1.3 74.3 - - - +
406E THR* 1.3 58.2 + - - +
409E HIS* 5.6 0.3 - - - -
416E GLY* 4.3 4.3 - - - +
420E ASN* 3.2 19.6 + - - +
462E TRP* 3.5 28.3 - - - -
66K TRP* 3.8 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 406 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E CYS* 3.8 4.3 - - - -
192E CYS* 4.0 14.1 - - - -
197E LEU* 3.9 22.9 - - + +
402E PHE* 2.7 24.5 + - - +
403E GLY 3.0 2.7 + - - -
405E GLY* 1.3 77.0 - - - +
407E LEU* 1.3 58.5 + - - +
408E GLY 3.1 4.0 - - - -
409E HIS* 3.2 25.2 + - - +
412E GLY 3.8 8.1 - - - +
413E ASN* 3.5 23.9 - - - +
416E GLY* 3.8 2.8 + - - -
417E ALA 3.7 9.6 - - - +
420E ASN* 3.1 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E CYS* 3.5 24.9 - - - -
173E THR 3.6 12.6 - - - +
174E ILE* 4.2 3.4 - - + -
175E LYS* 3.6 30.7 - - + +
188E ALA* 4.3 8.1 - - + -
192E CYS* 4.1 4.9 - - - -
403E GLY 2.9 25.8 + - - +
406E THR* 1.3 75.9 - - - +
408E GLY* 1.3 57.7 + - - +
409E HIS 3.5 0.7 - - - -
413E ASN* 3.4 35.0 - - - +
13K PHE* 4.4 0.2 - - - -
69K VAL* 3.4 16.4 - - + -
70K TRP* 3.2 34.2 + - - +
71K THR* 3.8 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 408 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404E GLY 2.8 19.9 + - - -
407E LEU* 1.3 78.3 - - - +
409E HIS* 1.3 65.1 + - - +
410E PRO* 3.5 0.7 - - - +
462E TRP* 3.6 17.0 - - - -
13K PHE* 3.8 2.4 - - - -
15K ALA* 3.4 20.1 - - - +
16K GLY 4.5 1.0 + - - -
67K THR* 4.4 2.0 - - - -
68K THR 3.2 22.1 - - - +
69K VAL* 4.2 0.4 - - - +
----------------------------------------------------------
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