Contacts of the helix formed by residues 195 - 206 (chain B) in PDB entry 1SXG
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 LYS 195 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ILE* 4.5 20.0 - - + -
150B SER* 4.4 17.9 + - - +
161B TYR* 3.5 28.9 - - + -
162B GLU* 3.4 28.3 - - + +
190B PRO* 3.3 10.0 + - - +
191B ILE* 3.2 18.4 - - - +
194B ALA* 1.3 88.7 - - + +
196B LYS* 1.3 56.4 + - - +
199B GLY 2.7 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B TYR* 4.4 10.8 - - + +
165B ALA* 3.5 21.2 - - + +
182B PHE* 3.8 17.7 - - + -
191B ILE* 2.9 34.0 + - + +
192B ASN* 3.2 21.7 + - - +
195B LYS* 1.3 70.1 - - - +
197B VAL* 1.3 71.4 + - - +
199B GLY* 2.8 3.8 + - - -
200B TYR* 2.8 18.9 + - - +
221B TYR* 5.7 3.8 - - - -
244B PHE* 5.1 0.9 - - + -
246B GLY* 2.9 39.7 + - - -
247B THR* 4.6 3.2 + - - -
274B PHE* 3.8 34.7 - - + -
275B ASP* 5.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PHE* 3.4 25.3 - - + -
187B LEU* 3.4 32.8 - - + -
192B ASN 2.6 30.6 + - - +
193B HIS* 3.4 11.9 - - + +
196B LYS* 1.3 70.1 - - - +
198B LYS* 1.3 55.8 + - - +
200B TYR* 2.8 28.2 + - + +
201B LYS* 2.9 42.6 + - + +
216B ILE* 4.5 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLU* 2.7 31.1 + - - +
193B HIS 3.4 6.2 + - - +
194B ALA* 2.9 32.8 - - - +
197B VAL* 1.3 79.0 - - - +
199B GLY* 1.3 62.5 + - - +
201B LYS* 3.0 21.4 + - + +
202B ARG* 3.0 51.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLU* 3.1 36.1 + - - -
165B ALA* 4.0 0.7 - - - -
166B PHE* 3.2 30.5 - - - +
195B LYS 2.7 17.1 + - - -
196B LYS 2.8 5.0 + - - -
198B LYS* 1.3 72.7 - - - +
200B TYR* 1.3 58.6 + - - +
202B ARG* 4.0 1.1 - - - +
203B ALA 3.6 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA* 4.1 0.2 - - - +
169B VAL* 3.5 33.2 - - + -
180B ILE* 2.5 38.0 + - + -
181B ALA* 3.4 21.1 - - - -
182B PHE* 3.5 23.1 + + + -
196B LYS 2.8 8.5 + - - +
197B VAL* 2.8 15.5 + - + +
199B GLY* 1.3 78.7 - - - +
201B LYS* 1.3 76.5 + - + +
203B ALA* 3.2 14.1 - - - +
204B LEU* 3.4 28.9 + - + +
211B VAL* 6.0 2.0 - - + -
212B ARG 5.0 1.1 + - - -
215B TYR* 3.9 6.8 + - - +
216B ILE* 3.4 26.9 - - + +
244B PHE* 4.5 12.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 2.9 38.5 + - + +
198B LYS* 3.0 16.1 + - + +
200B TYR* 1.3 81.4 - - + +
202B ARG* 1.3 64.4 + - + +
203B ALA 2.7 3.6 + - - -
204B LEU* 2.9 15.8 + - - +
205B THR* 2.6 24.7 + - + +
211B VAL* 3.6 38.1 - - + +
213B ASP* 5.7 4.6 + - - +
216B ILE* 4.8 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLU* 2.8 28.6 + - - +
163B GLN* 3.2 14.8 + - - +
166B PHE* 3.0 33.0 - - + -
198B LYS* 3.0 53.3 - - + +
199B GLY* 4.0 0.9 - - - +
201B LYS* 1.3 79.1 - - + +
203B ALA* 1.3 66.1 + - - +
205B THR* 3.1 7.2 + - - -
206B GLU* 2.9 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PHE* 4.0 23.1 - - + +
169B VAL* 3.2 37.5 - - + -
170B GLN* 4.3 7.8 - - - +
173B ILE* 4.7 4.3 - - + -
199B GLY 3.6 6.6 + - - +
200B TYR 3.2 8.0 + - - +
201B LYS 2.7 4.2 + - - -
202B ARG* 1.3 81.2 - - - +
204B LEU* 1.3 65.7 + - - +
206B GLU* 3.1 8.7 + - - +
207B SER* 3.6 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 4.3 4.9 - - + +
173B ILE* 4.4 2.2 - - + +
178B LYS 3.8 21.8 - - - +
180B ILE* 3.9 34.3 - - + +
200B TYR* 3.4 45.5 - - + +
201B LYS* 2.9 9.6 + - - +
203B ALA* 1.3 78.1 - - - +
205B THR* 1.3 60.0 + - - +
207B SER* 3.2 6.2 + - - -
209B LEU* 2.9 49.6 + - + +
210B PRO 3.9 16.2 - - - +
211B VAL* 4.7 9.0 - - + -
212B ARG 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LYS* 2.6 30.2 + - + +
202B ARG* 3.1 11.4 + - - -
204B LEU* 1.3 70.6 - - - +
206B GLU* 1.3 51.0 + - - +
207B SER 2.7 16.5 + - - -
208B GLY* 2.7 15.6 + - - -
209B LEU 3.9 8.5 - - - +
211B VAL* 3.4 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PHE* 3.0 41.4 - - + -
170B GLN* 5.3 1.9 - - - +
202B ARG* 2.9 33.0 + - + +
203B ALA 3.1 3.3 + - - +
205B THR* 1.3 71.0 - - - +
207B SER* 1.3 60.6 + - - +
208B GLY 3.6 0.2 - - - -
----------------------------------------------------------
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