Contacts of the helix formed by residues 90 - 98 (chain C) in PDB entry 2UX1
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 THR 90 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 3.8 0.4 - - - -
45A GLN* 3.9 1.8 - - - +
102A GLU* 3.5 30.7 - - + +
103A VAL 3.4 29.6 - - - +
104A LEU* 4.4 4.0 - - + +
89C SER* 1.3 84.7 - - - +
91C LEU* 1.3 64.3 + - - +
92C LYS* 3.9 8.3 + - - +
93C GLU* 2.8 38.6 + - - +
94C PHE* 3.1 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 4.6 4.7 - - - +
38A VAL* 4.0 19.5 - - + -
41A SER* 3.7 22.7 - - - +
91A LEU* 3.9 25.7 - - + +
94A PHE* 3.7 37.0 - - + -
95A SER* 4.1 12.8 - - - +
102A GLU* 2.8 23.7 + - - +
90C THR* 1.3 71.1 - - - +
92C LYS* 1.3 56.9 + - - +
94C PHE* 3.3 19.0 + - + +
95C SER* 2.9 34.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER* 4.7 8.0 + - - +
102A GLU* 4.3 1.9 + - - +
90C THR* 4.1 8.3 - - - +
91C LEU* 1.3 79.3 - - - +
93C GLU* 1.3 64.6 + - + +
95C SER* 4.0 3.0 - - - -
96C GLU* 3.1 61.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.2 27.2 - - + +
105A GLY 5.0 0.7 + - - -
87C PRO 5.1 0.5 - - - +
88C PHE* 3.5 40.0 - - + -
89C SER* 3.0 22.5 + - - -
90C THR* 2.8 34.4 + - - +
92C LYS* 1.3 75.6 - - + +
94C PHE* 1.3 66.2 + - - +
96C GLU* 4.8 2.9 - - - +
97C ASN* 2.8 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 3.9 18.8 - - - -
44A HIS* 6.6 0.4 - - + -
48A TRP* 4.7 8.5 - + - -
91A LEU* 3.7 12.1 - - + -
33C VAL* 3.8 10.1 - - + -
34C ALA* 3.7 19.4 - - - +
37C SER* 3.6 36.8 - - - -
38C VAL* 4.3 1.3 - - + -
73C LEU* 5.7 0.2 - - + -
88C PHE* 3.4 31.0 - - + -
89C SER* 3.8 18.6 - - - -
90C THR 3.1 14.5 + - - -
91C LEU* 3.6 22.0 - - + +
93C GLU* 1.3 76.0 - - - +
95C SER* 1.3 57.3 + - - +
98C SER* 2.9 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 4.1 20.2 - - - +
92A LYS* 4.8 9.3 + - - +
38C VAL* 4.5 9.1 - - - +
91C LEU 2.9 18.3 + - - -
92C LYS* 4.2 3.4 - - - -
94C PHE* 1.3 78.8 - - - +
96C GLU* 1.3 59.5 + - - +
98C SER* 3.9 12.6 + - - +
100C LEU 5.2 1.9 - - - +
101C LYS* 4.7 6.8 + - - -
102C GLU* 4.7 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LYS* 3.1 58.3 + - + +
93C GLU* 4.2 2.9 - - - +
95C SER* 1.3 78.1 - - - +
97C ASN* 1.3 68.2 + - - +
98C SER 4.5 2.3 - - - +
101C LYS* 5.7 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLN* 2.9 26.9 + - - +
34C ALA* 3.9 5.6 - - + -
88C PHE* 3.3 45.8 - - + -
93C GLU* 2.8 36.4 + - - +
96C GLU* 1.3 83.9 + - - +
98C SER* 1.3 61.9 + - - +
99C GLN* 4.4 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLN* 3.9 1.1 - - - +
34C ALA* 3.8 8.7 - - - +
35C ASP* 2.7 22.7 + - - -
38C VAL* 3.5 28.0 - - - +
94C PHE 2.9 19.3 + - - -
95C SER 3.9 6.9 - - - +
96C GLU 3.5 2.6 - - - +
97C ASN* 1.3 79.1 - - - +
99C GLN* 1.3 61.4 + - - +
100C LEU* 3.0 20.0 + - - +
101C LYS* 3.6 16.8 + - - -
----------------------------------------------------------
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