Contacts of the helix formed by residues 198 - 207 (chain B) in PDB entry 1PG3
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 LEU 198 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 3.3 36.7 - - + +
139B MET 4.5 0.7 - - - -
140B PRO* 3.6 37.0 - - + -
164B GLY* 4.1 19.7 - - - +
185B THR* 3.4 10.3 - - - +
186B ALA* 3.2 15.0 - - + +
187B ASP 3.4 5.2 + - - +
188B GLU 4.1 2.5 - - - -
189B GLY* 3.8 17.7 - - - +
196B ILE* 3.7 13.5 - - + +
197B PRO* 1.3 83.8 - - - +
199B LYS* 1.3 68.7 + - - +
200B LYS 3.3 1.3 - - - +
201B ASN* 3.3 2.5 + - - -
202B VAL* 3.1 25.1 + - - +
991B COA 5.7 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B THR* 4.2 12.1 - - + -
186B ALA 3.1 16.0 + - - +
187B ASP* 3.3 15.8 + - - +
198B LEU* 1.3 78.4 - - - +
200B LYS* 1.3 58.0 + - - +
202B VAL* 2.9 7.6 + - + +
203B ASP* 2.8 56.8 + - - +
217B VAL* 4.8 4.7 - - + -
219B VAL* 3.7 30.3 - - + -
227B ILE* 3.7 27.1 - - + -
228B ASP 2.8 27.5 + - - -
229B TRP* 4.3 1.8 - - - -
234B ASP* 3.2 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ASP 4.8 0.8 + - - -
197B PRO* 4.4 21.8 - - + -
198B LEU 3.3 1.2 - - - +
199B LYS* 1.3 79.6 - - - +
201B ASN* 1.3 61.5 + - - +
203B ASP* 3.2 13.5 + - + +
204B ASP* 2.9 45.9 + - - +
227B ILE* 5.5 4.1 - - + +
228B ASP* 5.2 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 3.0 29.2 + - + +
166B PHE 4.1 0.6 + - - -
168B PRO* 3.6 34.4 - - + +
171B VAL* 5.4 1.3 - - + -
197B PRO* 3.4 29.4 + - - +
198B LEU 3.3 7.9 + - - +
199B LYS 3.2 0.6 - - - -
200B LYS* 1.3 78.3 - - - +
202B VAL* 1.3 61.6 + - - +
204B ASP* 3.2 2.8 + - - +
205B ALA* 2.8 29.7 + - - +
805B EDO 3.5 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 3.6 21.3 - - + -
171B VAL* 5.1 5.6 - - + -
175B ILE* 5.7 2.0 - - + -
183B VAL* 3.8 27.1 - - + -
185B THR* 3.9 18.6 - - + -
198B LEU 3.1 16.1 + - - +
199B LYS* 2.9 10.2 + - + +
201B ASN* 1.3 76.8 - - - +
203B ASP* 1.3 65.3 + - - +
205B ALA* 3.0 8.6 + - + +
206B LEU* 2.9 40.2 + - + +
217B VAL* 4.4 12.8 - - + -
233B ARG* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LYS* 2.8 51.3 + - - +
200B LYS* 3.4 15.1 - - + +
202B VAL* 1.3 79.2 - - - +
204B ASP* 1.3 66.2 + - - +
205B ALA 3.3 0.7 + - - -
206B LEU* 3.3 9.5 + - - +
207B LYS* 3.2 26.7 + - - +
228B ASP* 3.9 19.8 + - + +
233B ARG* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PRO* 3.8 22.7 - - + +
200B LYS* 2.9 42.1 + - - +
201B ASN* 3.6 5.9 - - - +
203B ASP* 1.3 78.2 - - - +
205B ALA* 1.3 62.4 + - - +
207B LYS* 3.0 43.8 + - - +
208B ASN* 4.2 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PRO* 3.3 26.2 - - - +
171B VAL* 3.8 22.2 - - + -
172B ALA* 3.7 13.2 - - + +
175B ILE* 5.0 0.7 - - + -
201B ASN 2.8 16.7 + - - +
202B VAL* 3.0 6.0 + - - +
204B ASP* 1.3 78.5 - - - +
206B LEU* 1.3 66.6 + - + +
207B LYS 3.1 0.2 - - - -
208B ASN* 3.2 23.6 + - - +
211B VAL* 3.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE* 4.0 17.5 - - + -
183B VAL* 4.9 1.1 - - + -
202B VAL* 2.9 24.8 + - + +
203B ASP 3.3 3.3 + - - +
205B ALA* 1.3 72.5 - - - +
207B LYS* 1.3 59.4 + - - +
208B ASN 3.0 12.8 + - - +
211B VAL* 3.4 35.5 - - + +
214B VAL* 3.5 34.8 - - + -
217B VAL* 3.9 11.2 - - + -
233B ARG* 3.3 39.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ASP* 3.2 21.3 - - - +
204B ASP* 3.0 37.7 + - - +
205B ALA 3.1 1.6 - - - -
206B LEU* 1.3 76.5 - - - +
208B ASN* 1.3 62.5 + - - +
209B PRO* 3.1 8.8 - - - +
----------------------------------------------------------
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