Contacts of the strand formed by residues 149 - 157 (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 ILE 149 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D VAL* 5.0 1.1 - - + -
145D SER* 3.4 22.9 - - - -
148D GLU* 1.3 74.7 - - - +
150D CYS* 1.3 65.4 + - - +
151D LEU* 3.6 37.2 - - + -
168D CYS* 3.1 4.2 - - - +
169D ASP* 2.8 45.8 + - + +
170D THR* 4.9 0.2 - - - +
179D VAL* 3.9 22.7 - - + -
197D LYS* 4.2 2.0 - - + -
201D LYS* 3.4 17.2 - - - +
202D GLY* 3.8 19.5 - - - -
203D HIS 3.6 9.6 - - - +
204D ILE* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D ILE* 1.3 73.6 - - - +
151D LEU* 1.3 61.9 + - - +
167D PHE 3.4 4.0 - - - -
168D CYS* 2.1 44.4 - - - -
170D THR* 4.7 0.2 - - - -
197D LYS* 3.4 4.0 - - - -
198D ASP* 3.0 47.9 + - + +
201D LYS* 2.9 35.6 + - + +
202F ILE* 4.3 5.2 - - - -
203F GLN 4.9 3.8 - - - -
204F GLY* 5.0 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D VAL* 4.1 13.0 - - + -
141D PHE* 3.6 28.3 - - + -
143D VAL* 3.3 44.2 - - + -
149D ILE* 3.6 31.0 - - + -
150D CYS* 1.3 75.0 - - - +
152D SER* 1.3 59.3 + - - +
166D GLY* 3.2 2.9 - - - -
167D PHE* 2.7 43.9 + - - +
179D VAL* 3.8 5.2 - - + -
195D VAL* 4.1 10.3 - - + -
196D GLU 3.4 7.0 - - - +
197D LYS* 3.7 16.6 - - + -
204D ILE* 4.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLN* 4.3 16.6 + - - -
141D PHE* 4.8 1.8 - - - -
151D LEU* 1.3 76.0 - - - +
153D ILE* 1.3 70.2 + - - +
154D VAL* 3.5 9.0 + - - +
164D SER 3.6 13.5 + - - -
165D LEU 2.7 21.7 + - - -
166D GLY* 4.2 3.8 - - - -
167D PHE* 5.4 0.2 - - - -
195D VAL* 3.5 5.3 - - - -
196D GLU 2.9 36.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D PHE* 4.0 22.9 - - + +
140D THR 4.4 1.1 - - - +
141D PHE* 3.6 35.1 - - + -
152D SER* 1.3 73.1 + - - +
154D VAL* 1.3 59.2 + - - +
164D SER* 3.3 26.7 - - - -
165D LEU 3.8 4.6 + - - +
167D PHE* 5.5 4.4 - - + -
182D GLY* 3.9 25.1 - - - +
183D MET* 4.5 17.3 - - + +
185D LEU* 4.2 14.9 - - + +
193D VAL* 3.9 25.4 - - + -
194D TRP 3.6 4.3 - - - +
195D VAL* 4.5 8.5 - - + -
214D PHE* 5.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLN* 4.3 9.9 - - - +
152D SER* 3.8 19.7 - - - +
153D ILE* 1.3 78.1 - - - +
155D SER* 1.3 67.0 + - - +
161D VAL* 3.4 34.1 - - + -
162D ARG 3.5 11.9 - - - +
163D ARG* 4.3 6.1 - - - +
164D SER* 5.1 0.4 - - - -
185D LEU* 5.5 0.4 - - - -
193D VAL* 3.3 6.4 - - - +
194D TRP* 2.8 52.5 + - + +
196D GLU* 4.0 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ARG* 5.5 1.2 + - - -
154D VAL* 1.3 81.8 - - - +
156D SER* 1.3 57.9 + - - +
161D VAL* 3.7 1.2 - - - -
162D ARG* 2.8 69.3 + - - +
185D LEU* 4.4 17.7 - - - +
187D LEU* 4.6 0.4 - - - -
192D GLN 3.1 12.6 - - - -
193D VAL* 4.0 13.5 - - - -
194D TRP* 3.8 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D ARG* 5.0 1.3 + - - -
155D SER* 1.3 75.7 - - - +
157D SER* 1.3 59.9 + - - +
159D GLY* 4.4 9.6 + - - -
160D GLN 3.1 26.0 - - - -
161D VAL* 4.4 1.1 - - - -
162D ARG* 3.9 5.6 + - - +
191D ASP* 3.3 28.2 - - - +
192D GLN* 2.9 30.8 + - - +
194D TRP* 3.8 14.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C SER 4.7 1.1 - - - -
156D SER* 1.3 72.3 - - - +
158D ARG* 1.3 85.8 + - - +
159D GLY 3.2 0.7 - - - -
160D GLN* 3.1 22.7 + - - +
162D ARG* 3.5 25.5 - - - +
188D GLN* 4.0 14.6 + - - +
191D ASP* 2.9 21.5 + - - +
1223D SEP 4.1 10.8 + - - +
----------------------------------------------------------
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