Contacts of the helix formed by residues 125 - 133 (chain S) in PDB entry 5JBA
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 ASP 125 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E PHE* 5.2 4.5 - - - -
124S ALA* 1.3 74.7 - - - +
126S LYS* 1.3 60.5 + - - +
127S GLU* 3.2 18.1 + - - +
128S TYR* 2.8 42.8 + - - +
129S THR* 2.8 30.8 + - - -
235S VAL* 3.7 5.4 - - - -
236S ASN* 5.5 2.5 - - - +
239S LYS* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125S ASP* 1.3 75.3 - - - +
127S GLU* 1.3 64.8 + - - +
129S ASN* 3.1 23.5 + - + +
232S SER* 3.3 31.0 + - - +
233S ARG* 3.7 41.5 - - - +
235S VAL* 3.4 15.3 - - + +
236S ASN* 4.7 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E CYS 5.3 2.9 - - - +
125S ASP* 3.2 12.2 + - - +
126S LYS* 1.3 80.0 - - - +
128S TYR* 1.3 82.0 + - - +
129S ASN* 2.9 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 128 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E CYS* 5.3 1.2 - - - +
92E ASN* 2.6 30.9 + - - -
97E GLN 3.5 11.0 - - - -
98E PHE* 3.6 21.1 - + + -
99E CYS* 2.8 40.2 + - - +
124S ALA* 3.7 15.5 - - + -
125S ASP* 2.8 27.9 + - - +
127S GLU* 1.3 91.8 + - - +
129S THR* 1.3 81.6 + + - +
130S PHE* 2.8 61.9 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 129 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123S ILE* 5.0 0.2 - - - +
124S ALA* 3.2 24.7 + - - +
125S ASP 2.8 26.0 + - - -
128S TYR* 1.3 76.3 - - - +
129S ASN* 1.3 57.0 + - - +
130S PHE* 3.4 7.2 + - - +
131S LEU* 2.9 27.7 + - + +
208S PHE* 6.3 0.4 - - - -
209S LEU 3.5 24.0 + - - +
210S THR* 3.7 11.2 - - + +
231S VAL* 4.1 4.3 - - + -
232S SER* 3.5 35.0 - - - +
235S VAL* 3.6 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 129 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126S LYS* 3.1 17.9 + - + +
127S GLU* 3.7 5.3 - - - +
129S THR* 1.3 141.1 + + - +
131S LEU* 3.3 16.7 + - + +
132S LYS* 3.0 55.8 + - + +
230S LYS* 5.0 9.1 - - + -
232S SER* 3.8 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ASN* 5.6 0.9 - - - -
127S GLU* 2.9 41.5 + - + -
128S TYR* 3.2 30.9 + - - -
129S ASN* 1.3 75.0 - + + +
130S PHE* 1.3 72.6 - - - +
132S LYS* 3.1 18.3 - - + -
133S PHE* 3.1 37.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E GLN* 4.5 7.4 - - - -
98E PHE* 4.1 9.2 - + - -
124S ALA* 4.1 11.2 - - + -
128S TYR* 2.8 51.2 + + - +
129S ILE* 1.3 81.0 - + - +
131S LEU* 1.3 62.0 + - - +
133S PHE* 3.2 39.4 + + - +
134S GLY 4.1 0.2 + - - -
135S SER 5.5 0.2 - - - +
201S THR* 3.4 19.2 + - + +
203S VAL* 3.7 33.2 - - + -
208S PHE* 3.5 50.3 - + + -
210S THR* 3.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129S THR* 2.9 36.1 + - + +
130S PHE* 1.3 75.6 - - - +
132S LYS* 1.3 60.1 + - + +
134S GLY* 2.9 22.7 + - - -
135S SER 4.6 0.5 + - - -
162S LEU* 3.7 18.7 - - + +
181S PHE* 3.5 61.2 - - + -
199S HIS* 3.8 15.8 - - + -
201S THR* 4.4 2.0 - - - -
210S THR* 3.7 17.3 - - + +
230S LYS* 4.4 17.7 - - + -
232S SER* 5.8 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