Contacts of the helix formed by residues 194 - 201 (chain A) in PDB entry 5JEI
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 SER 194 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.4 8.0 - - - -
110A GLY 2.7 36.0 + - - +
112A SER* 3.3 14.1 - - - -
192A LEU 3.4 0.2 + - - -
193A GLU* 1.3 71.7 - - - +
195A THR* 1.3 55.8 + - - +
197A ASN* 3.5 1.5 - - - +
198A GLU* 2.8 55.1 + - - +
210A LYS* 4.1 0.9 - - - -
214A ASN* 3.6 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 3.1 15.6 + - - -
107A MET* 3.6 23.6 - - + -
108A SER 3.4 25.8 - - - +
109A LEU* 3.7 10.6 - - + +
193A GLU* 3.8 1.9 - - - +
194A SER* 1.3 75.4 + - - +
196A MET* 1.3 66.4 + - - -
198A GLU* 3.5 6.4 + - - +
199A TYR* 3.1 8.0 + - - +
220A TYR* 2.8 24.3 + - + -
251A LYS* 4.5 9.9 - - - +
255A TRP* 2.8 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 3.7 26.5 - - + +
14A SER 4.5 5.2 - - - +
16A TYR* 3.2 36.6 - - + -
61A TYR* 3.8 4.5 - - - +
89A PRO* 4.0 5.2 - - + -
174A THR* 4.2 7.4 - - + -
192A LEU* 3.8 16.6 - - + -
193A GLU* 3.0 15.6 + - - +
195A THR* 1.3 79.4 + - - +
197A ASN* 1.3 65.1 + - - +
199A TYR* 3.2 7.7 + - - +
200A ILE* 3.0 28.4 + - + +
220A TYR* 3.2 22.0 - - - +
301A FWD 3.1 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 2.9 26.0 + - - +
113A ILE 3.0 29.7 + - - -
114A MET* 3.5 21.5 - - - +
192A LEU* 3.6 22.3 - - + +
193A GLU 3.0 5.8 + - - +
194A SER* 3.3 8.5 + - - +
196A MET* 1.3 74.7 - - - +
198A GLU* 1.3 58.6 + - + +
200A ILE* 3.3 2.8 + - - +
201A GLU* 3.1 29.6 + - - +
208A THR* 5.4 0.3 + - - -
209A MET* 3.9 1.0 - - - -
210A LYS* 3.5 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A SER* 2.8 33.2 + - - +
195A THR* 4.0 7.5 - - - +
197A ASN* 1.3 69.8 - - - +
199A TYR* 1.3 63.7 + - - +
201A GLU* 3.5 24.2 - - - +
202A GLN* 3.2 22.7 + - - +
210A LYS* 3.4 32.7 - - + +
214A ASN* 5.3 1.0 + - - -
251A LYS* 4.7 5.5 + - - -
255A TRP* 3.9 7.0 - - + -
256A TYR* 4.1 17.6 + - + +
304A PG4 4.5 8.6 + - - +
314A NA 3.1 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 3.8 29.0 - - - -
15A PRO* 3.6 40.8 - - + +
18A MET* 4.4 3.1 - - - +
195A THR 3.1 8.3 + - - +
196A MET* 3.5 7.9 - - - +
198A GLU* 1.3 74.8 - - - +
200A ILE* 1.3 80.0 + - + +
202A GLN* 2.9 27.2 + - - +
203A ARG* 3.5 45.2 + - + +
254A TRP 3.6 15.3 - - - -
255A TRP* 3.5 26.4 - - - +
311A PEG 4.1 13.2 + - - -
312A EDO 5.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A MET* 3.9 15.0 - - + -
174A THR* 5.0 4.7 - - + -
178A VAL* 3.8 44.4 - - + -
182A ARG* 3.9 11.2 + - - +
196A MET* 3.0 21.9 + - + +
197A ASN 3.3 0.9 + - - +
199A TYR* 1.3 98.3 - - + +
201A GLU* 1.3 57.5 + - - +
202A GLN 3.1 0.2 - - - -
203A ARG* 3.0 32.0 + - + +
208A THR* 3.4 18.6 + - - +
312A EDO 4.2 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 5.6 0.9 + - - -
197A ASN 3.1 13.2 + - - +
198A GLU* 3.5 24.4 - - - +
200A ILE* 1.3 76.2 - - - +
202A GLN* 1.3 58.9 + - - +
203A ARG 3.3 1.8 - - - -
206A CYS* 4.9 3.1 - - - +
208A THR* 3.5 25.4 + - - +
209A MET* 3.4 7.3 - - - +
210A LYS* 2.9 28.2 + - - +
261A CYS* 3.3 17.6 - - - +
304A PG4 2.6 42.6 + - - +
310A ETE 3.3 31.4 - - - +
----------------------------------------------------------
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