Contacts of the strand formed by residues 135 - 145 (chain D) in PDB entry 2JG8
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 GLY 135 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D VAL 3.6 1.4 + - - -
134D PRO* 1.3 74.8 - - - +
136D TYR* 1.3 65.6 + - - -
137D TYR* 3.4 10.7 - - - -
186D GLN* 3.4 3.4 - - - -
187D LEU 2.9 33.9 + - - -
218D LEU* 4.3 2.5 - - - -
220D PHE 3.3 11.2 - - - -
221D PRO* 3.9 0.4 - - - -
222D SER* 3.5 17.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLY* 1.3 74.5 - - - -
137D TYR* 1.3 55.0 + - - +
184D VAL* 4.1 18.2 - - + -
185D LEU 3.7 1.8 - - - -
186D GLN* 3.2 47.3 + - + -
218D LEU* 3.5 2.1 - - - +
219D ILE* 2.5 42.7 + - + +
220D PHE* 2.8 57.0 + + + +
222D SER* 4.6 5.6 - - - -
89F LYS* 3.6 14.8 + - - -
93F VAL* 3.9 11.7 - - + -
117F THR* 3.5 22.7 + - - -
119F PRO* 3.5 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D PRO* 4.0 13.5 - - + +
129D PHE* 3.6 30.1 - + - -
131D CYS* 4.0 12.2 - - - -
132D THR 4.6 1.7 + - - -
133D VAL* 2.4 44.5 + - - +
135D GLY 3.4 17.9 - - - -
136D TYR* 1.3 74.1 - - - +
138D TYR* 1.3 59.4 + - - +
139D PHE* 3.4 22.9 - + + -
183D MET 3.8 0.2 - - - +
184D VAL* 3.1 6.6 - - - +
185D LEU 2.8 34.0 + - - +
187D LEU* 4.0 13.5 - - + -
217D PHE* 3.2 19.5 - - - -
218D LEU* 3.5 31.1 - - + +
219D ILE* 3.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D TYR* 1.3 73.5 - - - +
139D PHE* 1.3 74.9 + - - +
140D THR* 3.9 16.1 + - + -
182D GLY* 3.8 14.6 + - - -
183D MET* 3.2 32.5 - - - -
184D VAL* 3.7 12.3 - - + -
216D GLY* 3.0 5.5 - - - -
217D PHE* 2.9 70.2 + + + -
219D ILE* 3.9 9.7 - - + +
142E TYR* 5.2 3.6 - + - -
139F TYR* 4.8 8.3 - + - -
141F VAL* 3.3 27.8 - - + +
143F HIS* 4.0 11.1 + - - -
210F SER* 4.0 14.5 + - - -
212F PHE* 3.8 10.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D PHE* 3.9 12.6 - + - -
129D PHE* 3.6 48.2 - + + -
137D TYR* 3.4 28.0 - + + -
138D TYR* 1.3 78.3 - - - +
140D THR* 1.3 62.0 - - - +
153D ILE* 4.2 20.0 - - + -
182D GLY* 2.9 24.1 - - - -
183D MET* 2.9 15.7 + - + +
185D LEU* 3.8 23.8 - - + -
187D LEU* 3.7 13.9 - - + -
193D VAL* 4.0 19.1 - - + -
214D PHE* 4.3 8.3 - + + -
215D SER 3.5 4.3 - - - +
216D GLY* 3.8 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D TYR* 3.9 16.7 - - + -
139D PHE* 1.3 77.4 - - - +
141D PHE* 1.3 62.2 + - - +
142D GLN* 3.4 17.6 + - - +
153D ILE* 4.4 1.7 - - - +
181D GLY 2.8 20.6 + - - -
182D GLY* 3.9 1.2 - - - -
214D PHE* 3.5 5.5 - - - -
215D SER* 2.9 50.6 + - - +
216D GLY* 6.0 0.2 - - - -
217D PHE* 5.9 1.1 - - + -
142E TYR* 3.4 27.5 + - + +
184E GLY* 5.9 0.2 - - - -
143F HIS* 4.1 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D PHE* 5.0 0.2 - - + -
140D THR* 1.3 74.9 + - - +
142D GLN* 1.3 71.0 + - - +
143D VAL* 3.9 8.5 - - + -
151D LEU* 3.6 46.7 - - + -
152D SER 4.8 0.9 - - - -
153D ILE* 3.6 41.3 - - + -
167D PHE* 3.8 30.3 - + + -
179D VAL* 3.8 13.9 - - + -
180D SER* 3.2 36.2 - - - -
181D GLY 3.0 17.5 + - - +
195D VAL* 4.3 12.1 - - + -
213D VAL 3.3 12.8 - - - +
214D PHE* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D THR* 3.4 35.4 + - - +
141D PHE* 1.3 79.2 + - - +
143D VAL* 1.3 60.5 + - - +
178D VAL* 3.8 15.3 - - + -
179D VAL 3.4 6.3 - - - -
180D SER* 4.3 1.7 - - - -
211D ASP 4.4 2.8 - - - +
212D SER* 3.3 4.7 - - - -
213D VAL* 2.9 43.2 + - - +
215D SER* 5.4 1.0 + - - -
142E TYR* 4.3 4.9 + - - -
170E PHE* 4.2 9.6 - - + -
182E THR* 3.6 33.6 + - + +
183E GLY* 3.9 3.6 - - - -
184E GLY* 3.1 34.4 + - - +
143F HIS* 5.6 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D VAL* 5.5 0.9 - - + -
111D PHE* 4.0 27.6 - - + -
141D PHE* 3.9 11.4 - - + -
142D GLN* 1.3 78.1 - - - +
144D LEU* 1.3 65.6 + - - +
145D SER* 3.8 0.5 + - - -
149D ILE* 5.0 2.5 - - + -
151D LEU* 3.3 36.8 - - + -
177D GLN 3.6 0.5 - - - +
178D VAL* 3.3 5.5 - - - +
179D VAL* 2.9 39.8 + - + +
195D VAL* 5.4 0.2 - - + -
204D ILE* 3.8 30.7 - - + -
211D ASP 5.2 0.2 - - - -
212D SER* 3.6 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D GLN 4.3 0.4 + - - -
143D VAL* 1.3 73.9 - - - +
145D SER* 1.3 60.6 + - - +
176D PHE* 3.9 26.5 - - + -
177D GLN 3.6 12.3 - - - +
178D VAL* 3.8 7.0 - - + +
204D ILE* 3.6 9.7 - - - +
205D TYR* 2.8 51.8 + - + +
210D ALA* 3.2 36.6 - - + -
211D ASP 3.9 8.3 - - - +
212D SER* 2.8 17.9 + - - +
171E CYS 3.0 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D VAL 5.0 0.7 - - - -
144D LEU* 1.3 74.7 - - - +
146D GLN* 1.3 71.4 + - - +
147D TRP 3.3 13.7 + - - -
149D ILE* 3.4 30.5 - - - +
169D ASP* 5.5 0.9 - - - -
175D LEU 3.6 0.2 - - - +
176D PHE* 3.4 5.7 - - - -
177D GLN* 2.8 38.9 + - - +
203D HIS* 2.8 31.0 + - - +
204D ILE* 4.9 0.2 - - - -
205D TYR* 4.2 2.0 - - - +
----------------------------------------------------------
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