Contacts of the strand formed by residues 186 - 192 (chain O) in PDB entry 2GTL
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 186 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O CYS* 4.2 28.0 - - + +
118O THR* 4.6 6.7 - - - +
119O LYS* 5.4 1.3 - - + +
180O PRO* 3.3 6.6 - - - +
181O PRO* 3.1 27.0 - - + +
184O ASP* 3.0 38.4 + - + +
185O GLY* 1.3 78.4 - - - +
187O GLY* 1.3 57.8 + - - +
204O ILE* 4.2 12.8 - - + -
205O VAL 3.3 15.3 - - - +
206O HIS* 4.3 13.9 - - + +
213O CYS* 3.9 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 187 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178O ILE 3.7 11.4 - - - -
180O PRO* 4.1 9.1 - - - +
181O PRO* 4.6 2.2 - - - -
185O GLY 4.1 0.8 + - - -
186O LEU* 1.3 75.0 - - - +
188O LEU* 1.3 58.3 + - - -
204O ILE* 3.3 5.9 - - - +
205O VAL* 2.7 48.3 + - - +
207O GLU* 4.4 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125O MET* 5.3 5.6 - - - -
127O LEU* 4.0 26.5 - - + -
148O ILE* 5.2 8.3 - - + -
176O LEU* 4.7 1.6 - - + -
177O THR* 4.3 0.5 - - - +
178O ILE* 2.8 54.0 + - + +
181O PRO* 5.7 0.6 - - - +
187O GLY* 1.3 71.4 - - - -
189O VAL* 1.3 88.0 + - - +
190O GLY* 4.3 2.7 - - - +
200O PHE* 5.0 3.6 - - + -
202O GLY* 3.7 12.6 - - - -
203O HIS 3.1 28.9 - - - +
204O ILE* 4.4 10.8 - - + +
218O PHE* 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175O ARG* 3.9 30.7 - - + +
176O LEU 3.7 3.8 - - - -
177O THR* 3.9 20.2 - - + -
188O LEU* 1.3 83.5 - - - +
190O GLY* 1.3 59.5 + - - +
191O GLU* 4.1 1.6 + - + +
201O VAL 3.9 1.4 - - - +
203O HIS* 2.8 40.2 + - + +
205O VAL* 4.1 22.9 - - + -
207O GLU* 4.8 4.7 - - - +
210O GLU* 5.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 190 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175O ARG* 3.5 2.6 - - - -
176O LEU* 3.0 51.4 + - - +
188O LEU* 4.3 1.6 - - - +
189O VAL* 1.3 74.6 - - - +
191O GLU* 1.3 61.0 + - - -
192O PHE* 4.0 1.7 + - - -
200O PHE* 3.7 13.9 - - - -
201O VAL 3.3 13.7 - - - -
202O GLY* 4.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52O HIS* 5.0 8.4 + - - +
56O GLU* 4.1 15.1 - - - +
173O ASP* 3.6 28.8 - - - +
174O HIS 3.6 1.6 - - - -
175O ARG* 3.4 33.7 + - + +
189O VAL* 4.1 2.5 + - + -
190O GLY* 1.3 73.0 - - - -
192O PHE* 1.3 67.9 + - - +
193O ASP 3.9 0.5 + - - -
200O PHE* 4.0 10.8 - - - +
201O VAL* 3.6 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 192 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52O HIS* 4.5 6.4 + - - -
101O PRO* 3.5 36.3 - - + -
102O THR* 4.0 11.4 - - + -
108O PHE* 4.1 14.1 - + - -
169O TYR* 4.0 7.9 - + - -
173O ASP 4.7 0.3 - - - +
174O HIS* 2.6 41.5 + - + +
176O LEU* 5.1 6.5 - - + -
190O GLY 5.1 2.9 - - - -
191O GLU* 1.3 80.9 - - - +
193O ASP* 1.3 66.8 + - - +
194O GLY* 3.2 1.5 + - - +
197O PHE* 3.6 48.7 - + + -
199O ARG 4.1 7.9 - - - -
200O PHE* 3.5 42.2 - + + -
----------------------------------------------------------
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