Contacts of the helix formed by residues 1042 - 1052 (chain C) in PDB entry 1UKJ
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 THR1042 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040C PHE* 3.4 9.8 - - - +
1041C PRO* 1.3 88.6 - - + +
1043C VAL* 1.3 64.4 + - - +
1044C GLU* 3.3 17.8 + - - +
1045C TYR* 2.9 25.6 + - - +
1046C GLY 3.3 13.3 + - - -
1830D ASN* 3.4 17.5 - - - +
1837D ARG* 3.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1043 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040C PHE* 5.5 0.7 - - - -
1042C THR* 1.3 71.3 - - - +
1044C GLU* 1.3 70.7 + - - +
1046C GLY* 3.1 3.6 + - - +
1047C ALA* 2.8 28.2 + - - +
1826D ARG* 3.7 23.3 - - + -
1829D MET* 3.5 31.4 - - + -
1830D ASN* 2.6 24.6 - - - +
1837D ARG* 3.8 5.6 - - - +
1853D SER* 3.7 19.9 - - - +
1854D MET* 3.4 37.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1044 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042C THR* 3.1 11.5 - - - +
1043C VAL* 1.3 84.5 - - + +
1045C TYR* 1.3 63.9 + - - +
1047C ALA* 2.9 10.4 + - - +
1048C ALA* 2.9 22.1 + - - +
1826D ARG* 3.7 23.4 - - - +
1830D ASN* 2.7 26.0 - - - +
1853D SER 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1045 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039C THR 5.1 2.2 - - - -
1040C PHE* 3.7 13.7 - + + -
1041C PRO* 3.5 37.7 - - + -
1042C THR* 2.9 20.4 + - - +
1044C GLU* 1.3 72.1 - - - +
1046C GLY* 1.3 66.9 + - - +
1048C ALA* 3.1 9.4 + - - +
1049C CYS* 2.9 39.4 + - - -
1054C GLN* 3.0 40.8 - - - +
1055C ALA 3.1 19.9 + - - -
1056C GLY* 3.7 8.8 - - - -
1057C HIS 5.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1046 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040C PHE* 3.5 36.8 - - - -
1042C THR 3.3 5.1 + - - -
1043C VAL* 3.1 7.8 + - - -
1045C TYR* 1.3 80.7 - - - +
1047C ALA* 1.3 61.4 + - - +
1049C CYS* 3.2 2.6 + - - +
1050C PHE* 2.9 34.7 + - - -
1854D MET* 5.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1047 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043C VAL 2.8 12.4 + - - +
1044C GLU* 3.2 11.7 - - - +
1046C GLY* 1.3 72.7 - - - +
1048C ALA* 1.3 68.9 + - - +
1050C PHE* 3.3 2.1 + - - +
1051C ALA* 3.0 25.3 + - - +
1053C GLU* 5.5 0.4 - - - -
1853D SER 3.8 12.8 - - - +
1854D MET 3.5 14.5 + - - +
1857D SER* 3.6 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1048 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044C GLU 2.9 12.0 + - - +
1045C TYR* 3.2 11.2 - - - +
1047C ALA* 1.3 77.4 - - - +
1049C CYS* 1.3 51.9 + - - +
1051C ALA* 3.0 1.4 + - - +
1052C GLY 2.7 32.2 + - - -
1053C GLU* 3.0 27.5 + - + +
1054C GLN* 3.3 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1049 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040C PHE* 4.6 4.7 - - + -
1045C TYR* 2.9 49.1 + - - +
1046C GLY* 3.4 10.3 - - - +
1048C ALA* 1.3 75.7 - - - +
1050C PHE* 1.3 66.5 + - - +
1052C GLY* 2.9 15.4 + - - -
1054C GLN* 3.7 22.0 - - - +
1056C GLY* 4.0 17.9 - - - +
1057C HIS 4.4 5.2 - - - -
1058C PHE* 4.4 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1050 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040C PHE* 3.7 26.0 - + - -
1046C GLY 2.9 30.9 + - - +
1047C ALA 3.7 3.8 - - - +
1049C CYS* 1.3 73.2 - - - +
1051C ALA* 1.3 59.8 + - - +
1058C PHE* 3.6 44.0 - + + -
1839D VAL* 3.4 31.2 - - + -
1854D MET* 3.5 26.2 - - + +
1855D THR* 3.5 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1051 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047C ALA 3.0 12.2 + - - +
1048C ALA 3.4 6.1 - - - +
1050C PHE* 1.3 80.3 - - - +
1052C GLY* 1.3 58.3 + - - +
1053C GLU* 3.4 29.2 - - + +
1858D SER* 6.4 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1052 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048C ALA 2.7 7.5 + - - -
1049C CYS 2.9 10.2 + - - -
1051C ALA* 1.3 75.2 - - - +
1053C GLU* 1.3 64.0 + - - +
1054C GLN 3.3 7.7 + - - +
----------------------------------------------------------
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