Contacts of the helix formed by residues 151 - 172 (chain B) in PDB entry 2QNJ
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 LYS 151 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG* 4.5 33.8 + - + +
150B MET* 1.3 73.3 - - - +
152B GLU* 1.3 61.9 + - - +
153B LYS* 3.1 12.8 - - + +
154B GLU* 2.8 18.6 + - + +
155B ALA* 2.7 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG* 6.4 0.2 - - - +
150B MET 3.7 2.1 + - - +
151B LYS* 1.3 71.1 - - - +
153B LYS* 1.3 72.0 + - + +
155B ALA* 3.6 8.6 - - - +
156B ARG* 2.8 35.7 + - - +
247B VAL* 4.7 11.6 - - + +
275B TYR* 3.9 5.9 - - + +
276B MET* 3.8 7.3 - - - +
277B SER* 2.8 45.5 + - - -
280B CYS* 4.1 8.9 - - - +
306B TRP* 2.7 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LYS* 3.1 10.9 - - + -
152B GLU* 1.3 86.8 + - - +
154B GLU* 1.3 64.3 + - - +
156B ARG* 3.2 39.2 + - - +
157B SER* 3.1 20.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TYR* 4.0 8.9 + - - -
149B ARG 5.2 0.2 - - - +
150B MET* 3.5 44.4 - - + +
151B LYS* 2.8 18.3 + - + +
153B LYS* 1.3 80.0 - - - +
155B ALA* 1.3 61.9 + - - +
157B SER* 3.3 13.0 + - - -
158B LYS* 3.3 30.3 + - - +
190B MET* 3.9 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B MET* 4.1 20.1 - - + +
151B LYS 2.7 18.2 + - - +
152B GLU* 3.6 4.5 - - - +
154B GLU* 1.3 72.7 - - - +
156B ARG* 1.3 57.8 + - - +
158B LYS* 3.2 4.7 + - - +
159B PHE* 2.8 29.8 + - - +
246B LEU* 4.1 12.7 - - + +
247B VAL* 3.6 30.5 - - + -
306B TRP* 4.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLU* 2.8 24.7 + - - +
153B LYS* 3.5 42.9 - - - +
155B ALA* 1.3 72.4 - - - +
157B SER* 1.3 57.2 + - - +
159B PHE 4.5 0.2 - - - +
160B ARG* 2.9 43.1 + - + +
306B TRP* 2.7 73.8 + - + +
307B ILE 3.6 18.8 - - - +
309B ALA* 3.2 39.1 + - - +
311B HIS* 4.2 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS 3.1 11.4 + - - -
154B GLU* 3.6 10.8 - - - -
155B ALA 3.3 0.4 - - - -
156B ARG* 1.3 77.5 - - - +
158B LYS* 1.3 79.8 + - - +
160B ARG* 3.7 8.6 - - - +
161B GLN* 3.4 29.7 + - - +
311B HIS* 5.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B MET* 4.3 18.6 - - + -
154B GLU* 3.3 24.1 + - - +
155B ALA 3.2 5.3 + - - +
157B SER* 1.3 97.1 + - - +
159B PHE* 1.3 60.1 + - - +
161B GLN* 3.1 19.7 + - - +
162B ILE* 2.9 32.2 + - - +
186B LEU* 4.5 5.6 - - + -
189B ASP 5.5 0.2 + - - -
190B MET* 2.8 50.7 + - - +
191B ASN* 5.3 3.8 + - - -
192B ILE* 3.9 18.7 - - + +
246B LEU* 4.6 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ALA 2.8 19.8 + - - +
156B ARG 4.1 2.9 - - - +
158B LYS* 1.3 70.0 - - - +
160B ARG* 1.3 57.8 + - - +
162B ILE* 4.1 11.0 - - + +
163B VAL* 2.7 66.1 + - + +
239B LEU* 3.3 35.7 - - + -
242B ILE* 4.4 5.8 - - + -
243B LEU* 3.6 32.1 - - + -
246B LEU* 3.9 18.5 - - + +
283B LEU* 4.6 0.7 - - + -
287B PHE* 3.6 28.9 - + - -
306B TRP* 4.2 16.8 - + + -
307B ILE* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 2.9 24.7 + - + +
157B SER* 3.7 7.4 - - - +
159B PHE* 1.3 76.1 - - - +
161B GLN* 1.3 63.6 + - + +
163B VAL* 3.8 1.9 - - - +
164B SER* 2.9 25.9 + - - -
307B ILE* 3.0 38.7 + - + +
308B ASN* 2.8 30.5 + - - +
311B HIS* 3.5 34.0 + - - -
314B ASP* 2.8 35.5 + - - -
316B LEU* 3.4 38.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 3.3 38.9 + - - +
157B SER* 3.4 19.3 + - - +
158B LYS* 3.1 14.4 + - - +
160B ARG* 1.3 76.3 - - + +
162B ILE* 1.3 57.5 + - - +
164B SER* 3.6 4.8 - - - -
165B ALA* 2.9 31.9 + - - +
191B ASN* 3.1 28.1 + - - -
192B ILE* 3.2 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LYS 2.9 27.6 + - - +
159B PHE* 3.1 15.2 + - + +
161B GLN* 1.3 76.3 - - - +
163B VAL* 1.3 58.6 + - - +
165B ALA* 3.7 0.5 - - - +
166B VAL* 2.9 37.0 + - + +
184B LEU* 4.0 26.5 - - + -
192B ILE* 3.7 33.4 - - + -
194B ILE* 4.4 11.7 - - + -
239B LEU* 4.0 24.9 - - + -
242B ILE* 4.2 13.0 - - + -
246B LEU* 4.2 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B PHE* 2.7 55.7 + - + +
160B ARG 3.9 2.2 - - - +
162B ILE* 1.3 72.2 - - - +
164B SER* 1.3 59.5 + - - +
167B GLN* 2.9 29.5 + - - +
239B LEU* 4.1 15.0 - - + -
287B PHE* 4.5 5.6 - - + -
298B LEU* 4.0 16.9 - - + +
301B ILE* 5.3 1.8 - - + -
302B MET* 3.7 28.9 - - + +
307B ILE* 4.0 10.5 - - + -
316B LEU* 4.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B HIS* 2.7 26.9 + - - -
160B ARG 2.9 19.6 + - - -
161B GLN* 3.6 6.7 - - - -
163B VAL* 1.3 78.8 - - - +
165B ALA* 1.3 52.9 + - - +
167B GLN* 3.3 7.1 + - - +
168B TYR* 2.8 35.7 + - - +
302B MET* 5.3 3.1 - - - -
316B LEU* 4.2 18.9 - - - +
317B LYS 5.0 1.9 + - - -
318B PRO* 6.5 0.2 - - - -
319B PHE* 3.9 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B HIS* 3.4 19.2 + - + +
114B ASN* 4.2 5.8 - - + -
115B ILE* 3.8 20.0 - - + +
161B GLN 2.9 19.8 + - - +
162B ILE 3.7 0.2 - - - +
164B SER* 1.3 73.4 + - - +
166B VAL* 1.3 61.8 + - - +
168B TYR* 3.2 4.5 + - - +
169B CYS* 3.1 26.3 + - - -
194B ILE* 3.5 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 2.9 26.5 + - + +
165B ALA* 1.3 69.5 - - - +
167B GLN* 1.3 66.3 + - - +
169B CYS* 3.3 7.2 + - - +
170B HIS* 3.0 48.5 + - + +
179B LEU* 5.7 2.0 - - + -
184B LEU* 6.1 1.1 - - + -
194B ILE* 3.9 17.9 - - + -
197B PHE* 4.2 22.0 - - + -
235B ASP* 4.5 3.1 - - + -
239B LEU* 3.9 28.7 - - + -
298B LEU* 3.7 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL 2.9 20.1 + - - +
164B SER* 3.7 3.7 - - - +
166B VAL* 1.3 78.8 - - - +
168B TYR* 1.3 69.0 + - - +
170B HIS* 3.0 15.6 + - + +
171B GLN* 3.0 25.3 + - - +
298B LEU* 3.5 23.9 - - + +
299B GLU* 4.2 12.4 - - - +
302B MET* 3.6 27.1 - - + -
318B PRO* 3.7 35.3 - - - +
319B PHE 4.1 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE 3.2 8.5 + - - -
110B LEU* 4.2 13.2 - - + -
111B ASN 3.0 36.1 + - - -
112B HIS* 3.7 20.0 - + + -
115B ILE* 3.7 21.1 - - + -
164B SER 2.8 19.9 + - - +
165B ALA 3.2 2.9 + - - +
167B GLN* 1.3 79.8 + - - +
169B CYS* 1.3 63.1 + - - +
171B GLN* 3.4 7.0 + - + +
172B LYS* 3.3 50.0 + - + +
319B PHE* 3.8 33.4 - + + -
321B GLU* 3.1 27.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 4.2 17.9 - - - -
115B ILE* 3.8 20.0 - - - -
165B ALA 3.1 18.6 + - - -
166B VAL* 3.5 8.7 - - - +
167B GLN 3.2 0.2 - - - -
168B TYR* 1.3 75.7 - - - +
170B HIS* 1.3 62.0 + - - +
172B LYS* 3.4 8.7 + - - +
174B ILE* 2.9 34.2 + - + +
194B ILE* 5.9 0.7 - - - -
197B PHE* 3.6 44.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B VAL* 3.0 34.4 + - + +
167B GLN* 3.0 11.2 + - + +
169B CYS* 1.3 73.7 - - - +
171B GLN* 1.3 58.1 + - - +
173B ARG* 2.7 25.5 + - - +
174B ILE 3.6 16.6 - - - +
175B VAL* 4.2 6.8 - - + +
197B PHE* 4.6 1.3 - + - -
232B PRO* 3.6 34.0 - - + +
235B ASP* 2.8 38.4 + - + +
236B VAL* 4.8 2.6 - - + +
298B LEU* 3.9 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG* 4.6 7.6 + - - -
167B GLN* 3.0 27.1 + - - +
168B TYR* 3.7 12.6 - - + +
169B CYS 3.3 0.2 - - - -
170B HIS* 1.3 75.7 - - - +
172B LYS* 1.3 60.1 + - + +
173B ARG* 3.2 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG* 2.5 31.6 + - - +
274A PHE* 3.5 9.2 - - + -
109B ILE* 3.8 28.7 - - + +
110B LEU* 5.0 2.2 - - + -
168B TYR* 3.3 55.3 + - + +
169B CYS* 3.8 7.9 - - - +
170B HIS 3.1 0.8 - - - -
171B GLN* 1.3 77.4 - - + +
173B ARG* 1.3 64.8 + - - +
174B ILE* 3.1 15.7 + - + -
321B GLU* 3.7 12.0 + - - +
----------------------------------------------------------
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