Contacts of the helix formed by residues 193 - 203 (chain A) in PDB entry 2XYX
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 193 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 4.6 8.7 - - + -
187A LEU* 4.0 29.6 - - + +
190A PHE* 5.4 5.8 - - + +
192A MET* 1.4 78.9 - - - +
194A LYS* 1.3 59.0 + - - +
195A LYS* 3.8 3.8 + - - +
196A LYS* 3.1 25.3 + - - +
197A ALA* 3.1 27.4 + - - +
296A SER* 5.1 2.2 - - - -
345A ASP* 3.4 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TYR* 4.5 1.0 + - - -
193A THR* 1.3 69.9 - - - +
195A LYS* 1.4 54.3 + - - +
197A ALA* 4.3 1.1 - - - -
198A ARG* 2.8 60.8 + - + +
296A SER* 3.7 33.3 - - - +
338A PHE* 5.4 2.8 + - - -
339A ASN* 4.0 29.0 + - - +
342A GLU* 4.2 6.7 - - - +
343A LEU* 2.7 43.1 + - - +
344A ASP* 4.7 2.2 - - - -
345A ASP* 2.7 23.4 + - - +
348A LEU* 4.0 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A THR* 4.1 4.3 - - - +
194A LYS* 1.4 76.8 - - - +
196A LYS* 1.4 61.0 + - - +
198A ARG* 4.0 3.1 - - - +
199A SER* 3.1 26.3 + - - -
345A ASP* 3.2 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASN 4.3 8.6 + - - +
192A MET* 3.7 29.6 - - - +
193A THR* 3.1 20.1 + - - +
195A LYS* 1.4 75.5 - - - +
197A ALA* 1.3 61.1 + - - +
199A SER* 2.8 23.2 + - - +
200A ILE* 3.3 24.8 + - + +
307A ASN* 3.1 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A MET* 3.6 5.5 - - - -
193A THR 3.1 19.0 + - - +
194A LYS 3.8 2.2 - - - +
195A LYS 3.4 0.2 - - - -
196A LYS* 1.3 76.3 - - - +
198A ARG* 1.3 57.3 + - - +
200A ILE* 3.5 0.6 + - - -
201A LEU* 3.1 28.5 + - - +
296A SER* 3.3 26.7 - - - +
297A ILE* 3.9 13.5 - - + -
304A LEU* 3.6 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LYS* 2.8 43.1 + - + +
195A LYS* 4.1 3.8 - - - +
197A ALA* 1.3 70.2 - - - +
199A SER* 1.4 59.0 + - - +
201A LEU* 3.7 16.4 - - - +
202A THR* 2.9 40.7 + - - +
295A ALA 3.2 8.4 + - - -
296A SER 2.9 26.1 + - - -
297A ILE 4.0 1.4 - - - -
298A VAL 2.7 36.6 + - - +
299A ASN* 4.3 12.9 - - - +
300A LYS* 5.4 4.6 - - - +
339A ASN* 4.4 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LYS* 3.1 15.8 + - - -
196A LYS* 2.8 23.7 + - - +
198A ARG* 1.4 74.4 - - - +
200A ILE* 1.4 54.9 + - - +
202A THR* 5.0 1.3 - - - -
203A GLY 2.8 42.9 + - - +
204A LYS 4.1 9.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
192A MET* 4.3 7.2 - - + -
196A LYS* 3.3 40.2 + - + +
197A ALA 3.8 4.9 - - - +
199A SER* 1.4 78.4 + - - +
201A LEU* 1.3 65.0 + - - +
202A THR 3.4 1.6 + - - -
203A GLY* 3.7 7.5 + - - -
209A ALA 5.9 0.4 - - - +
210A PRO* 3.9 24.6 - - + +
304A LEU* 3.7 17.7 - - + -
307A ASN 4.9 0.4 - - - +
308A GLY* 3.7 38.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ALA 3.1 14.0 + - - +
198A ARG* 3.7 23.1 - - - +
200A ILE* 1.3 76.4 - - - +
202A THR* 1.3 62.2 + - - +
210A PRO* 6.0 1.6 - - + -
297A ILE 4.4 9.2 - - - +
299A ASN* 3.6 41.1 - - + +
304A LEU* 3.7 34.5 - - + -
311A PHE* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ARG* 2.9 21.5 + - - +
199A SER* 4.5 1.8 - - - -
200A ILE 4.0 0.9 - - - -
201A LEU* 1.3 79.6 - - - +
203A GLY* 1.3 60.5 + - - +
204A LYS* 5.0 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 2.8 24.0 + - - +
200A ILE* 3.7 6.2 + - - -
202A THR* 1.3 78.5 - - - +
204A LYS* 1.4 85.3 + - - +
----------------------------------------------------------
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