Contacts of the helix formed by residues 154 - 175 (chain D) in PDB entry 4J1R
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 PRO 154 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D TYR* 3.6 27.4 - - + +
152D THR* 3.5 3.8 - - + +
153D LEU* 1.4 91.0 - - + +
155D VAL* 1.3 66.2 + - - +
156D ILE* 3.0 18.4 - - + -
157D TYR* 2.9 29.6 + - + +
158D VAL* 3.3 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D THR* 6.2 2.5 - - + -
153D LEU 3.4 3.5 + - - +
154D PRO* 1.3 71.4 - - + +
156D ILE* 1.3 62.2 + - - +
158D VAL* 3.2 10.4 + - + +
159D LYS* 2.9 46.7 + - - +
251D LEU* 5.7 6.5 - - + -
310D PRO* 4.1 31.2 - - + -
339D PHE* 4.1 16.4 - - + -
342D GLU* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D PRO* 4.0 17.3 - - + -
155D VAL* 1.3 80.2 - - - +
157D TYR* 1.3 64.7 + - + +
159D LYS* 3.4 5.9 + - + +
160D LEU* 3.1 30.8 + - + +
342D GLU* 3.6 32.9 + - + +
343D LEU* 4.2 20.6 - - + -
348D VAL* 4.6 10.5 - - + -
349D LYS 5.0 5.8 - - - +
350D LEU* 5.9 0.4 - - + -
351D PRO* 4.1 31.2 - - + -
356D THR* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D TYR* 4.6 7.6 - - - -
153D LEU* 3.9 31.0 - - + -
154D PRO* 2.9 29.1 + - + +
156D ILE* 1.3 74.8 - - + +
158D VAL* 1.3 66.2 + - - +
160D LEU* 3.3 18.8 + - + +
161D TYR* 3.0 54.4 + + + -
194D ALA* 5.2 6.3 - - + -
350D LEU* 5.6 0.2 - - + -
351D PRO* 3.3 44.8 - - + +
352D ASN* 4.9 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D LEU* 3.7 29.8 - - + +
154D PRO 3.7 11.9 - - - +
155D VAL* 3.2 12.3 + - + +
157D TYR* 1.3 78.1 - - - +
159D LYS* 1.3 62.6 + - - +
161D TYR* 4.0 0.6 - - - -
162D MET* 3.0 28.3 + - + +
247D LEU* 3.7 30.1 - - + -
250D LEU* 4.1 28.3 - - + +
251D LEU* 4.5 10.5 - - + -
339D PHE* 4.0 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D VAL* 2.9 40.0 + - - +
156D ILE* 3.7 5.8 - - + +
158D VAL* 1.3 74.5 - - - +
160D LEU* 1.3 63.0 + - - +
163D TYR* 3.1 23.0 + - - +
312D GLU* 4.8 8.4 + - - -
338D SER 5.7 0.4 + - - -
339D PHE* 3.3 45.2 + - + +
340D PHE* 3.1 21.0 - - + -
342D GLU* 2.5 49.1 + - + +
343D LEU* 3.5 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ILE* 3.1 26.0 + - + +
157D TYR* 3.6 23.3 - - + +
159D LYS* 1.3 78.9 - - - +
161D TYR* 1.3 71.3 + - + +
163D TYR* 3.8 1.6 - - - +
164D GLN* 3.2 34.5 + - - +
194D ALA* 4.0 14.6 - - + -
343D LEU* 4.0 24.2 - - + -
350D LEU* 3.7 27.4 - - + -
351D PRO* 5.5 0.2 - - + -
356D THR* 4.8 4.7 - - + -
357D PRO* 4.6 16.8 - - + -
359D LEU* 4.4 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D VAL* 4.5 16.8 - - + -
142D VAL* 4.9 10.4 - - + +
153D LEU* 4.3 15.0 - - + -
157D TYR* 3.0 47.6 + + + +
158D VAL* 4.1 4.0 - - - +
160D LEU* 1.3 82.9 - - + +
162D MET* 1.3 65.6 + - + +
164D GLN* 3.4 8.0 + - - +
165D LEU* 3.0 22.5 + - - +
187D LEU* 6.2 0.9 - - + -
189D LEU* 3.7 43.7 - - + +
191D PRO* 5.8 3.5 - - - +
194D ALA* 4.2 25.3 - - + +
196D LEU* 3.6 18.3 - - + +
250D LEU* 5.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D VAL* 3.0 21.7 + - + +
161D TYR* 1.3 76.3 - - - +
163D TYR* 1.3 58.0 + - - +
165D LEU* 3.1 19.5 + - + +
166D PHE* 2.9 61.9 + - + -
187D LEU* 6.0 0.7 - - - -
243D ALA 3.3 23.1 - - - +
246D VAL* 4.0 14.8 - - - -
247D LEU* 3.8 43.7 - - + -
250D LEU* 4.3 6.7 - - + -
339D PHE* 4.9 0.4 - - + -
340D PHE* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D LYS 3.1 20.0 + - - +
160D LEU* 3.8 2.9 - - - +
162D MET* 1.3 77.3 - - - +
164D GLN* 1.3 58.8 + - - +
166D PHE* 3.2 4.8 + - - -
167D ARG* 3.0 42.4 + - - +
335D CYS* 3.7 36.2 - - + -
340D PHE* 3.6 30.2 - + + -
343D LEU* 3.9 13.7 - - + -
344D ARG* 4.2 9.1 + - - -
359D LEU* 2.9 55.2 + - + -
360D PHE* 4.3 9.2 - + - -
362D PHE* 3.1 22.8 - + - -
377D LEU* 4.4 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ASN* 3.0 38.9 + - - +
160D LEU* 3.2 28.8 + - - +
161D TYR* 3.8 5.1 - - - +
163D TYR* 1.3 77.2 - - - +
165D LEU* 1.3 61.3 + - - +
167D ARG* 3.3 5.5 + - - +
168D SER* 3.1 18.4 + - - -
194D ALA 2.9 24.2 + - - -
195D VAL* 3.4 9.4 - - - +
196D LEU* 2.9 39.3 + - + +
357D PRO* 4.4 8.1 - - - +
359D LEU* 4.2 23.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
161D TYR 3.0 14.0 + - - +
162D MET* 3.1 34.3 + - + +
164D GLN* 1.3 73.8 - - - +
166D PHE* 1.3 66.5 + - - +
168D SER* 2.9 26.0 + - - +
169D LEU* 3.0 29.7 + - + +
182D ILE* 4.5 14.6 - - + -
187D LEU* 3.9 39.3 - - + -
196D LEU* 3.8 9.1 - - + +
198D LEU* 4.6 2.5 - - + -
243D ALA* 4.0 20.0 - - + -
246D VAL* 4.8 2.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
162D MET* 2.9 56.6 + - + +
163D TYR* 4.4 0.7 - - - -
165D LEU* 1.3 75.5 - - + +
167D ARG* 1.3 57.7 + - - +
169D LEU* 4.1 7.9 - - + -
170D ALA* 2.8 27.2 + - - +
240D VAL* 5.2 5.8 - - + -
243D ALA* 3.8 22.2 - - + -
316D LEU* 4.7 4.9 - - + -
320D LEU* 3.7 29.6 - - + -
331D PRO* 3.3 24.0 - - + +
334D ALA* 3.6 27.8 - - + -
335D CYS* 3.4 21.1 - - - -
340D PHE* 3.9 24.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D HIS* 3.8 8.3 + - + -
107D CYS* 4.1 6.8 - - - -
108D ASN* 3.7 19.2 + - - +
163D TYR* 3.0 39.6 + - + +
164D GLN* 3.4 10.1 - - - +
165D LEU 3.1 0.2 - - - -
166D PHE* 1.3 76.7 - - - +
168D SER* 1.3 63.0 + - - +
170D ALA* 3.1 8.0 + - - +
171D TYR* 3.0 22.9 + - - +
335D CYS* 4.0 9.2 - - - -
358D ALA 3.4 7.5 + - - -
359D LEU* 3.0 25.4 + - - +
360D PHE 3.7 0.2 - - - +
361D ASN* 2.9 49.6 + - - +
362D PHE* 3.9 17.6 - - + -
366D GLU* 3.1 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D HIS* 4.0 9.8 - - - -
108D ASN* 3.3 26.9 + - - -
109D ILE* 3.6 13.9 - - - -
164D GLN 3.1 8.8 + - - -
165D LEU* 2.9 18.5 + - - +
167D ARG* 1.3 79.8 - - - +
169D LEU* 1.3 56.9 + - - +
171D TYR* 3.3 4.3 - - - +
172D ILE* 2.9 34.3 + - - +
196D LEU* 5.1 0.5 - - - +
198D LEU* 3.7 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D LEU* 3.0 26.7 + - + +
166D PHE* 3.5 13.5 - - + +
168D SER* 1.3 75.6 + - - +
170D ALA* 1.3 58.3 + - - +
171D TYR 3.1 1.3 - - - -
172D ILE* 3.8 21.3 - - + -
173D HIS* 2.9 52.9 + - + +
182D ILE* 3.8 16.2 - - + -
198D LEU* 3.8 16.8 - - + -
239D ASP* 4.2 25.6 - - + +
240D VAL* 4.7 2.0 - - + +
243D ALA* 4.3 15.0 - - + -
331D PRO* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D PHE 2.8 19.9 + - - +
167D ARG* 3.1 8.5 + - - +
169D LEU* 1.3 73.5 - - - +
171D TYR* 1.3 61.5 + - - +
173D HIS* 4.1 2.4 - - - +
174D SER* 3.3 21.8 + - - -
331D PRO* 3.4 18.4 - - + +
332D LEU* 4.0 30.5 - - + +
335D CYS* 5.9 0.2 - - - -
366D GLU* 4.6 13.9 - - + +
369D SER* 5.7 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D LYS 3.9 2.9 + - - -
104D LEU* 3.5 26.3 - - + -
105D ASP* 2.9 39.7 + - - +
106D HIS* 3.6 30.7 - + + +
109D ILE* 3.5 19.5 - - + -
167D ARG 3.0 12.0 + - - +
168D SER* 3.3 10.1 - - - +
170D ALA* 1.3 77.7 - - - +
172D ILE* 1.3 60.7 + - - +
174D SER* 2.4 26.5 + - - -
175D PHE* 3.2 33.7 - + - -
363D THR* 5.1 3.8 - - + -
365D GLN* 4.2 14.4 - - + -
366D GLU* 3.9 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D LEU* 3.9 23.1 - - + -
109D ILE* 3.7 22.7 - - + -
168D SER 2.9 21.1 + - - +
169D LEU* 3.5 30.3 - - + +
171D TYR* 1.3 76.5 - - - +
173D HIS* 1.3 70.1 + - + +
175D PHE* 3.3 13.5 + - - +
177D ILE* 3.0 44.9 + - + +
179D HIS* 4.0 24.2 - - + +
198D LEU* 4.1 8.1 - - + -
201D PHE* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D LEU* 2.9 33.7 + - + +
170D ALA* 4.1 4.5 - - - +
172D ILE* 1.3 80.9 - - + +
174D SER* 1.3 63.4 + - - +
176D GLY* 3.1 14.2 + - - +
177D ILE 3.1 18.3 + - - +
236D SER* 3.2 45.3 + - - +
239D ASP* 3.1 34.9 - - + +
240D VAL* 4.8 3.0 - - + +
331D PRO* 3.5 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D ALA 3.3 11.7 + - - -
171D TYR* 2.4 23.5 + - - -
173D HIS* 1.3 80.0 - - - +
175D PHE* 1.3 58.6 + - - +
176D GLY 3.2 0.9 + - - -
365D GLN* 3.0 47.6 + - - +
366D GLU 5.5 0.7 - - - -
368D SER* 4.4 12.6 + - - -
369D SER* 5.7 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D LYS* 4.6 29.6 - - + +
104D LEU* 4.1 13.9 - - + -
171D TYR* 3.2 66.6 - + - -
172D ILE 3.3 2.4 + - - +
173D HIS 3.2 0.4 - - - -
174D SER* 1.3 79.2 + - - +
176D GLY* 1.3 59.1 + - - +
177D ILE* 3.7 22.7 - - + -
206D GLN* 3.0 28.0 + - - +
365D GLN* 3.8 23.3 - - + +
----------------------------------------------------------
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