Contacts of the helix formed by residues 202 - 211 (chain B) in PDB entry 1GPU
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 202 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA* 2.8 25.2 + - - +
200B ASP 3.9 0.2 + - - -
201B GLU* 1.3 70.0 - - - +
203B VAL* 1.3 62.3 + - - +
204B ALA* 3.4 11.1 + - - +
205B LYS* 3.1 38.1 + - + +
206B ARG* 3.0 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU* 3.9 19.3 - - + -
184B TYR* 4.1 24.7 - - + +
199B PHE* 3.9 28.3 - - + -
201B GLU* 3.3 20.9 + - - +
202B ASP* 1.3 72.6 + - - +
204B ALA* 1.3 64.7 + - - +
206B ARG* 3.2 5.9 + - - +
207B TYR* 2.9 39.0 + - + -
243B LEU* 4.1 13.5 - - + -
245B LYS* 5.2 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ASP* 3.3 8.8 + - - +
203B VAL* 1.3 79.3 - - - +
205B LYS* 1.3 64.5 + - - +
207B TYR* 3.3 0.7 + - - -
208B GLU* 2.9 32.0 + - - +
214B VAL* 3.6 23.0 - - + +
216B TYR* 3.1 34.1 - - + +
243B LEU* 5.4 0.4 - - - -
245B LYS* 4.9 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS* 2.9 73.3 - - + +
208A GLU* 3.4 36.6 + - - +
209A ALA* 3.7 13.5 - - + +
202B ASP* 3.1 30.5 + - + +
204B ALA* 1.3 78.1 - - - +
206B ARG* 1.3 62.4 + - - +
208B GLU* 3.3 3.5 + - - -
209B ALA* 3.0 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ARG* 4.1 9.9 - - + +
209A ALA* 3.8 11.8 - - + +
210A TYR* 3.7 30.5 - - - -
160B LEU* 3.3 32.5 + - - +
165B SER* 5.4 0.6 + - - -
166B SER* 3.2 17.6 + - - +
201B GLU* 2.7 31.4 + - - +
202B ASP 3.0 13.6 + - - +
203B VAL* 3.5 10.1 - - - +
205B LYS* 1.3 77.4 - - - +
207B TYR* 1.3 84.6 + - - +
209B ALA* 3.0 21.0 + - - +
210B TYR* 2.9 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 5.1 2.4 - - + +
155B LEU* 4.8 4.7 - - + +
160B LEU* 3.6 25.2 - - + +
165B SER* 4.1 8.1 + - - -
169B SER* 2.7 38.1 + - - -
203B VAL* 2.9 23.8 + - + +
206B ARG* 1.3 104.3 + - - +
208B GLU* 1.3 63.6 + - - +
210B TYR* 3.1 15.9 + + - +
212B TRP* 3.0 68.0 + + + +
214B VAL* 3.8 18.8 - - + -
243B LEU* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS* 3.4 31.3 + - - +
204B ALA* 2.9 25.6 + - - +
205B LYS* 4.3 3.3 + - - -
207B TYR* 1.3 75.9 - - - +
209B ALA* 1.3 56.8 - - - +
211B GLY* 3.0 18.2 + - - -
212B TRP 3.4 14.0 - - - +
214B VAL* 3.8 27.1 + - + +
216B TYR* 4.9 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLU* 3.3 4.5 - - + -
202A ASP* 2.8 51.4 + - - +
205A LYS* 3.7 14.5 - - + +
206A ARG* 3.7 19.1 - - + +
205B LYS 3.0 12.4 + - - +
206B ARG 3.0 13.0 + - - +
208B GLU* 1.3 78.1 - - - +
210B TYR* 1.3 60.1 + - + +
211B GLY* 3.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A SER* 4.7 0.7 + - - -
200A ASP* 5.1 2.3 - - - +
201A GLU* 3.5 34.3 - - + +
206A ARG* 3.7 19.9 - - - -
166B SER* 3.3 23.7 + - - -
169B SER* 3.7 31.0 - - - +
170B SER* 3.6 21.7 - - - +
173B GLY* 3.2 22.7 - - - -
174B HIS* 3.9 1.9 + - - -
206B ARG* 2.9 56.7 + - + -
207B TYR* 3.1 22.2 + + - +
209B ALA* 1.3 76.9 - - + +
211B GLY* 1.3 58.1 + - - +
212B TRP* 3.6 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLY* 4.6 7.6 - - - +
208B GLU 3.0 13.5 + - - -
209B ALA 3.2 1.0 - - - -
210B TYR* 1.3 80.7 - - - +
212B TRP* 1.3 63.7 + - - +
240B LYS* 3.4 30.9 - - - +
241B PRO* 4.1 4.7 - - - +
----------------------------------------------------------
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