Contacts of the strand formed by residues 199 - 207 (chain B) in PDB entry 1G83
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 HIS 199 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLU* 5.9 0.4 - - - +
164B LEU* 4.0 10.5 - - + +
189B ILE 3.4 0.2 - - - +
190B ARG* 3.4 0.9 - - - +
191B ASP* 2.5 56.0 + - - +
193B ASP* 3.4 34.5 + - + +
196B LYS* 4.2 22.9 + - + +
197B GLY 3.0 18.7 + - - +
198B ASP* 1.3 79.8 + - - +
200B VAL* 1.3 76.9 + - - +
201B LYS* 3.3 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 5.4 1.6 + - - -
160B GLU* 3.9 35.9 + - + +
163B LEU* 3.8 19.7 - - + -
164B LEU* 3.8 26.4 - - + +
189B ILE 3.0 17.5 - - - +
190B ARG* 4.7 1.1 - - - -
199B HIS* 1.3 91.1 - - - +
201B LYS* 1.3 67.8 + - - +
202B HIS* 3.4 36.1 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
187B LEU 3.5 0.7 - - - +
188B SER* 3.2 3.8 - - - -
189B ILE* 2.7 37.2 + - + +
191B ASP* 3.2 24.1 + - + +
193B ASP* 4.1 12.9 + - - +
199B HIS* 3.3 32.9 + - + +
200B VAL* 1.3 75.1 - - - +
202B HIS* 1.3 61.2 + - - +
203B TYR* 3.5 27.4 - - + +
239B SER* 2.9 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 3.7 37.3 - - + +
159B ALA* 4.7 1.8 - - + -
160B GLU* 3.7 23.1 + - + +
176B ARG* 3.1 25.7 + - - +
186B SER* 4.9 6.7 - - - +
187B LEU 3.1 5.4 - - - +
188B SER* 2.5 32.5 + - - -
200B VAL* 3.4 28.9 - - + +
201B LYS* 1.3 77.3 - - - +
203B TYR* 1.3 64.5 + - - +
204B LYS 4.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B SER* 3.4 4.7 - - - -
187B LEU* 2.6 49.4 + - + +
189B ILE* 3.5 32.1 - - + -
201B LYS* 3.5 24.8 - - + +
202B HIS* 1.3 79.6 - - - +
204B LYS* 1.3 63.8 + - - +
205B ILE* 3.6 0.7 + - - +
215B ILE* 4.2 26.0 - - + -
216B THR* 5.7 4.3 - - + -
237B GLY 5.4 1.1 - - - -
238B LEU* 3.5 33.8 - - + -
239B SER* 2.9 37.1 + - - -
240B SER 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B SER* 2.9 18.2 + - - -
180B THR* 2.9 28.2 + - - -
181B THR* 3.0 19.8 + - + +
184B ALA* 4.5 5.4 - - + -
185B TYR 3.8 8.5 - - - +
186B SER* 4.7 5.0 + - - +
202B HIS 4.1 1.4 + - - -
203B TYR* 1.3 73.4 - - - +
205B ILE* 1.3 69.1 + - - +
206B ARG* 2.7 57.4 + - + +
215B ILE* 3.9 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE* 4.6 10.1 - - + -
184B ALA* 3.6 5.9 - - - +
185B TYR* 3.0 45.4 + - + +
186B SER 4.5 1.1 - - - -
187B LEU* 4.0 24.2 - - + +
203B TYR 4.1 6.3 - - - +
204B LYS* 1.3 76.3 - - - +
206B ARG* 1.3 70.2 + - - +
207B LYS* 5.1 0.2 - - - +
213B TYR* 3.8 26.7 - - + -
214B TYR 3.6 8.5 - - - +
215B ILE* 4.1 14.8 - - + -
224B LEU* 4.1 20.2 - - + -
227B LEU* 4.0 18.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
181B THR* 6.6 0.2 - - + -
184B ALA* 4.7 7.2 - - - -
204B LYS* 2.7 58.5 + - + +
205B ILE* 1.3 79.6 - - - +
207B LYS* 1.3 65.4 + - - +
213B TYR* 3.5 4.0 - - - -
214B TYR* 3.2 58.4 + - + +
215B ILE* 3.8 5.3 - - - +
216B THR* 3.4 38.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
183B GLY 4.6 14.6 - - - +
184B ALA* 5.7 0.4 - - - +
185B TYR* 6.1 0.2 - - + -
205B ILE 5.1 0.4 - - - +
206B ARG* 1.3 78.6 - - - +
208B LEU* 1.3 83.4 + - - +
209B ASP* 4.0 5.0 + - - +
211B GLY 3.9 13.8 + - - -
212B GLY* 3.7 8.6 - - - +
213B TYR* 2.9 61.4 + - + -
214B TYR* 4.3 4.2 + - - -
222B GLU* 4.2 9.9 + - - -
----------------------------------------------------------
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