Contacts of the helix formed by residues 152 - 168 (chain D) in PDB entry 2QJK
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 152 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D PHE* 4.7 2.0 - - - -
150D PRO 3.4 2.5 - - - -
151D TRP* 1.3 76.4 - - - +
153D GLN* 1.3 66.0 + - - -
155D SER* 3.1 7.5 + - - -
156D PHE 2.9 17.7 + - - -
279D ASN* 3.0 19.7 - - - -
281D ILE 3.3 14.1 - - - -
282D GLU* 4.5 0.9 - - - -
283D ALA* 3.3 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D GLY* 1.3 70.0 - - - +
154D MET* 1.3 72.9 + - + +
155D SER 2.8 1.4 + - - -
156D PHE* 3.1 7.4 + - - +
157D TRP* 3.3 30.1 + - - -
278D ASP 3.3 12.0 + - - +
279D ASN* 3.1 2.4 + - - -
281D ILE* 3.0 41.0 + - + +
282D GLU 3.7 4.0 - - - +
283D ALA* 3.6 0.5 - - - +
284D ASN* 2.8 37.8 + - - +
287D ARG* 3.4 21.0 + - - +
289D PRO* 3.4 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SMA 3.9 7.3 - - - +
147D TYR* 3.5 33.9 - - + +
153D GLN* 1.3 75.1 - - - +
155D SER* 1.3 58.2 + - - +
157D TRP* 5.2 1.1 - - - -
158D GLY* 3.0 28.5 + - - +
276D HIS* 3.7 44.0 - - + +
278D ASP* 3.6 21.3 - - + +
279D ASN* 3.0 11.6 + - - +
289D PRO* 3.7 28.3 - - + -
292D ILE* 3.8 29.8 - - + -
293D VAL 3.9 7.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
147D TYR* 2.8 25.4 + - - -
148D VAL* 3.2 31.4 + - - +
150D PRO* 4.1 1.2 - - - +
151D TRP* 3.6 3.6 + - - -
152D GLY 3.1 24.2 + - - -
153D GLN 2.8 1.8 + - - -
154D MET* 1.3 78.6 - - - +
156D PHE* 1.3 64.8 + - - +
158D GLY* 4.1 0.2 - - - -
159D ALA* 3.2 20.3 + - - +
279D ASN* 2.9 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLY 4.9 6.3 - - - -
151D TRP* 4.0 23.1 - + - -
152D GLY 2.9 14.7 + - - +
153D GLN 3.8 2.9 - - - +
155D SER* 1.3 73.2 - - - +
157D TRP* 1.3 107.2 + + + +
159D ALA* 2.8 18.1 + - - +
160D THR* 2.9 18.1 + - - -
186D VAL* 3.2 50.3 - - + -
283D ALA* 3.8 15.7 - - + -
284D ASN 4.1 6.1 - - - -
285D PRO* 3.4 40.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PRO* 5.1 4.7 - - + -
133C GLY 4.2 2.7 - - - -
134C CYS* 3.9 23.3 - - - -
135C SER* 4.0 11.2 - - - -
153D GLN* 3.3 21.5 + - - +
154D MET 4.7 0.2 - - - +
156D PHE* 1.3 91.9 - + - +
158D GLY* 1.3 66.9 + - - +
160D THR* 2.8 36.5 + - + -
161D VAL* 2.9 16.1 + - - +
284D ASN 3.3 22.3 + - - -
285D PRO 3.6 16.8 - - - -
287D ARG 2.6 32.7 + - - -
288D THR* 3.3 24.7 - - + -
289D PRO* 3.5 21.5 - - + -
292D ILE* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SMA 3.2 34.6 + - - -
144D PHE* 4.4 4.0 - - - -
147D TYR* 6.2 0.9 - - - -
154D MET 3.0 16.9 + - - -
155D SER 4.1 0.4 - - - -
157D TRP* 1.3 77.0 - - - +
159D ALA* 1.3 55.1 + - - +
161D VAL* 3.3 1.9 + - - +
162D ILE* 2.9 37.4 + - - +
292D ILE* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D PHE* 3.8 14.8 - - + -
148D VAL* 4.1 20.6 - - + +
155D SER 3.2 12.9 + - - +
156D PHE* 2.8 12.2 + - - +
158D GLY* 1.3 70.9 - - - +
160D THR* 1.3 58.7 + - - +
163D THR* 2.8 38.9 + - - +
186D VAL* 4.1 18.6 - - + -
190D THR* 5.8 0.4 - - + -
194D PHE* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU 3.4 5.4 - - - +
133C GLY* 3.9 31.2 - - - +
134C CYS 4.5 0.4 - - - +
156D PHE* 2.9 20.9 + - - -
157D TRP* 2.8 31.5 + - + -
159D ALA* 1.3 76.2 - - - +
161D VAL* 1.3 57.9 + - + +
163D THR* 2.8 18.4 + - - -
164D GLY* 3.1 9.5 + - - -
177D GLN* 5.0 0.9 + - - -
186D VAL* 3.7 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 3.8 34.9 - - + +
134C CYS* 3.7 30.3 - - - +
152C HIS* 4.4 1.3 - - + -
2D SMA 3.3 54.1 - - + +
157D TRP 2.9 11.6 + - - +
158D GLY 3.6 6.7 - - - +
160D THR* 1.3 76.5 - - - +
162D ILE* 1.3 63.0 + - - +
164D GLY* 2.9 15.4 + - - -
165D LEU* 3.0 14.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SMA 3.6 91.1 - - + +
144D PHE* 3.6 41.1 - - + -
158D GLY 2.9 19.0 + - - +
161D VAL* 1.3 73.9 - - + +
163D THR* 1.3 66.3 + - - +
165D LEU* 3.4 16.2 + - + +
166D PHE* 3.4 17.3 - - - -
298D PHE* 4.9 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SMA 5.8 0.7 - - + -
144D PHE* 5.3 1.6 - - + -
159D ALA 2.8 25.4 + - - +
160D THR* 2.8 15.2 + - - -
162D ILE* 1.3 78.1 - - - +
164D GLY* 1.3 62.1 + - - +
166D PHE* 3.1 19.5 + - - +
177D GLN* 3.4 21.4 + - - +
180D LEU* 4.3 21.8 - - + -
181D LEU* 3.5 39.4 - - + +
186D VAL* 4.8 0.4 - - + -
190D THR* 4.8 1.1 - - + -
194D PHE* 4.4 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 3.6 21.4 - - - +
160D THR 3.1 12.1 + - - -
161D VAL 2.9 10.3 + - - -
163D THR* 1.3 74.6 + - - +
165D LEU* 1.3 56.0 + - - -
166D PHE 2.9 1.8 - - - -
167D GLY* 2.5 28.9 + - - -
168D ALA 3.3 4.0 + - - -
177D GLN* 3.1 15.2 + - - -
329D LYS* 4.9 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 3.8 31.2 - - + -
2D SMA 4.5 17.9 - - + +
161D VAL* 3.0 10.7 + - + +
162D ILE* 3.6 26.2 - - + +
163D THR 3.3 0.4 - - - -
164D GLY* 1.3 73.5 - - - +
166D PHE* 1.3 67.7 + - + +
168D ALA* 3.1 18.8 - - - +
169D ILE* 4.0 4.0 + - - +
305D LEU* 4.1 19.1 - - + -
333D VAL* 4.1 16.3 - - + +
336D MET* 3.6 26.7 - - + -
337D PHE* 4.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SMA 4.0 38.6 - - + -
162D ILE* 3.4 21.5 - - + -
163D THR 3.1 9.4 + - - +
164D GLY 2.8 1.2 + - - -
165D LEU* 1.3 79.9 - - + +
167D GLY* 1.3 62.6 + - - +
168D ALA 2.9 5.8 + - - -
169D ILE* 2.8 34.0 + - + +
173D GLY* 3.3 11.9 - - - -
176D ILE* 3.6 30.9 - - + +
177D GLN* 4.8 4.0 - - - +
180D LEU* 4.0 16.2 - - + -
337D PHE* 4.7 15.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D THR 3.6 2.6 + - - -
164D GLY 2.5 19.3 + - - -
166D PHE* 1.3 73.9 - - - +
168D ALA* 1.3 57.1 - - - -
169D ILE 3.4 7.3 + - - +
173D GLY* 3.6 16.9 - - - -
174D HIS* 4.6 2.1 + - - -
177D GLN* 3.8 19.4 - - - +
329D LYS* 4.3 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 5.4 0.4 - - + -
164D GLY 3.3 3.0 + - - +
165D LEU* 3.1 17.2 + - - +
166D PHE 2.9 0.6 - - - -
167D GLY* 1.3 77.4 - - - +
169D ILE* 1.3 64.5 + - - +
170D PRO* 3.3 4.9 - - - +
329D LYS* 4.0 26.9 - - + +
330D PHE* 3.5 24.1 - - + +
333D VAL* 3.5 26.0 - - + -
----------------------------------------------------------
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