Contacts of the helix formed by residues 149 - 170 (chain B) in PDB entry 2V5Q
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 THR 149 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ARG* 4.1 3.5 - - - +
148B LEU* 1.3 77.3 - - - +
150B GLU* 1.3 66.5 + - - +
151B PRO* 3.6 13.8 - - - +
152B GLU* 2.7 37.3 + - - +
153B ALA* 3.0 19.2 + - - +
322B PRO* 4.9 6.5 - - + -
323B PRO* 4.2 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU 3.8 1.6 + - - -
149B THR* 1.3 71.6 - - - +
151B PRO* 1.4 65.9 - - + +
153B ALA* 3.1 2.1 + - - +
154B ARG* 2.9 58.4 + - - +
245B LEU* 4.0 19.6 - - + +
275B ASN* 3.6 32.7 + - - +
278B ALA* 3.6 25.8 + - - +
304B PHE* 3.7 12.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B THR* 3.4 15.7 - - - +
150B GLU* 1.4 93.6 - - + +
152B GLU* 1.3 56.5 + - + +
154B ARG* 3.3 19.3 + - - +
155B TYR* 2.9 28.6 + - - +
309B TYR* 3.8 35.7 - - + +
311B PRO* 3.6 11.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
145B ARG* 2.9 44.7 + - - -
148B LEU* 4.2 13.0 - - + -
149B THR* 2.7 34.8 + - - +
151B PRO* 1.3 73.8 - - + +
153B ALA* 1.3 65.3 + - - +
155B TYR* 3.3 8.1 + - - +
156B TYR* 3.1 28.3 + - + -
311B PRO* 5.7 0.4 - - + -
314B LEU* 3.9 27.3 - - + +
315B PRO* 5.9 0.2 - - - +
318B CYS* 3.6 15.8 - - - +
323B PRO* 3.8 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 4.3 11.1 - - + +
149B THR 3.0 10.0 + - - +
150B GLU 3.4 7.9 - - - +
152B GLU* 1.3 77.2 - - - +
154B ARG* 1.3 57.7 + - - +
156B TYR* 3.3 1.7 + - - +
157B LEU* 2.9 45.1 + - + +
244B LEU* 4.4 14.4 - - + -
245B LEU* 3.6 32.3 - - + -
304B PHE* 4.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLU* 2.9 41.3 + - - +
151B PRO* 3.4 30.1 - - - +
153B ALA* 1.3 73.6 - - - +
155B TYR* 1.3 65.6 + - - +
157B LEU* 4.3 1.3 - - - -
158B ARG* 2.9 27.5 + - - +
304B PHE* 2.9 57.8 + - + -
305B PHE* 3.7 5.5 - - + -
307B SER* 4.7 3.2 + - - -
308B GLY* 3.6 27.5 + - - +
309B TYR 3.0 28.5 + - - +
310B ILE* 3.5 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ALA* 5.1 1.7 - - - +
151B PRO 2.9 14.7 + - - +
152B GLU* 3.3 9.4 - - - +
154B ARG* 1.3 79.3 - - - +
156B TYR* 1.3 90.4 + + - +
158B ARG* 3.6 5.2 + - - +
159B GLN* 3.1 52.4 + - + +
187B ASP 4.4 4.5 + - - -
188B LEU 3.7 13.0 + - - -
189B GLU* 4.1 8.8 - - - +
310B ILE* 3.9 10.3 - - + +
311B PRO* 3.4 31.4 - - + -
312B ALA 3.6 21.7 + - - -
313B ARG* 3.7 16.0 - - - +
314B LEU* 3.7 24.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 4.0 27.1 - - + -
141B LEU* 3.9 21.4 - - + +
148B LEU* 4.3 15.0 - - + -
152B GLU* 3.1 21.2 + - + +
153B ALA 4.1 2.2 - - - +
155B TYR* 1.3 87.8 - + - +
157B LEU* 1.3 60.5 - - - +
159B GLN* 3.2 6.0 + - - +
160B ILE* 2.9 36.4 + - + +
184B LEU* 3.6 26.1 - - + +
188B LEU* 3.1 36.4 + - - +
190B VAL* 3.8 20.7 - - + +
244B LEU* 4.7 6.5 - - + -
314B LEU* 3.4 27.3 - - + +
318B CYS* 4.2 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ALA* 2.9 35.0 + - + +
156B TYR* 1.3 71.9 - - - +
158B ARG* 1.3 61.7 + - - +
160B ILE* 3.7 8.0 - - + +
161B VAL* 2.9 36.3 + - + +
237B ILE* 4.3 17.5 - - + -
240B ILE* 4.2 14.6 - - + -
241B MET* 3.6 53.8 - - + +
244B LEU* 4.2 8.7 - - + -
245B LEU* 5.2 0.2 - - + -
304B PHE* 4.1 13.0 - - + -
305B PHE* 3.7 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 3.0 47.6 - - - +
162A LEU* 4.1 22.6 - - - +
154B ARG 2.9 18.9 + - - +
155B TYR* 4.0 5.7 + - - +
157B LEU* 1.3 77.3 - - - +
159B GLN* 1.3 58.4 - - - +
161B VAL* 3.4 3.5 + - - +
162B LEU* 2.9 40.9 + - + +
300B LEU* 4.2 14.8 - - + -
305B PHE* 3.3 20.7 - - + -
310B ILE* 3.7 44.1 + - + +
311B PRO 4.7 5.3 + - - -
312B ALA* 5.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B HIS* 3.3 47.9 - - + +
155B TYR* 3.1 54.6 + - + +
156B TYR* 3.2 3.1 + - - +
158B ARG* 1.3 76.3 - - + +
160B ILE* 1.3 61.1 + - - +
162B LEU* 3.7 4.0 - - + +
163B GLY* 2.9 24.6 + - - -
189B GLU* 3.6 10.2 - - - +
190B VAL* 3.0 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 4.0 14.1 - - + -
156B TYR* 2.9 29.9 + - + +
157B LEU* 3.7 11.9 - - + +
159B GLN* 1.3 75.4 - - - +
161B VAL* 1.3 58.1 + - + +
163B GLY 3.5 0.2 + - - -
164B CYS* 2.8 29.1 + - + +
177B LEU* 5.2 4.0 - - + -
182B LEU* 3.7 40.8 - - + -
190B VAL* 4.0 13.0 - - + -
192B ILE* 3.7 12.7 - - + +
237B ILE* 4.0 27.6 - - + -
240B ILE* 4.2 18.2 - - + -
244B LEU* 4.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 2.9 23.0 + - - +
158B ARG* 3.9 3.8 - - - +
160B ILE* 1.3 75.0 - - + +
162B LEU* 1.3 54.7 + - - +
164B CYS* 3.7 0.6 - - - -
165B GLN* 2.7 33.9 + - + +
237B ILE* 4.1 17.3 - - + -
296B ILE* 3.6 36.7 - - + +
299B LEU* 3.9 24.2 - - + -
300B LEU* 3.7 28.7 - - + +
305B PHE* 4.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 4.2 18.2 - - - +
305A PHE 4.9 3.6 - - - +
306A THR* 4.0 33.8 - - + +
310A ILE* 6.2 0.7 - - + -
110B HIS* 3.5 19.8 + - + -
112B HIS* 4.4 12.3 - - + +
158B ARG* 2.9 38.4 + - + +
159B GLN* 3.7 9.2 - - + +
161B VAL* 1.3 75.7 - - - +
163B GLY* 1.3 61.9 + - - +
165B GLN* 3.7 7.3 + - - +
166B TYR* 3.1 18.7 + - - +
300B LEU* 3.9 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B HIS* 3.8 17.4 - - - -
112B HIS* 3.9 11.4 - - - -
113B VAL* 4.1 3.1 - - - +
159B GLN 2.9 16.4 + - - -
160B ILE 3.8 1.6 - - - -
162B LEU* 1.3 76.8 - - - +
164B CYS* 1.3 60.7 + - - +
166B TYR* 3.2 6.4 + - - +
167B LEU* 3.1 23.2 + - - +
192B ILE* 3.8 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE 2.8 18.3 + - - +
161B VAL 3.3 0.2 + - - -
163B GLY* 1.3 73.0 - - - +
165B GLN* 1.3 60.8 + - - +
167B LEU* 3.1 13.3 + - - +
168B HIS* 3.0 53.2 + - - -
177B LEU* 4.0 11.0 - - + -
192B ILE* 3.7 10.9 - - + +
233B ASP* 3.8 20.4 - - - -
237B ILE* 4.0 7.4 - - + -
296B ILE* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A THR* 3.6 25.5 - - - +
161B VAL* 2.7 21.6 + - + +
162B LEU* 3.7 8.5 + - - +
163B GLY 3.3 0.2 - - - -
164B CYS* 1.3 68.5 - - - +
166B TYR* 1.3 65.3 + - - +
168B HIS* 3.3 1.4 + - - +
169B ARG* 3.0 57.8 + - + +
296B ILE* 3.6 26.8 - - + +
297B ASN* 2.8 42.5 + - - +
300B LEU* 3.6 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A SER* 4.4 10.8 - - - -
107B SER 4.1 4.5 + - - -
108B LEU* 3.5 25.0 - - + +
109B ALA* 2.8 45.1 + - - +
110B HIS* 3.5 42.2 - + + +
113B VAL* 4.2 9.4 - - + -
162B LEU 3.1 8.7 + - - +
163B GLY 3.2 7.8 + - - +
165B GLN* 1.3 78.3 - - - +
167B LEU* 1.3 65.4 + - + +
169B ARG* 3.4 4.6 + - - +
170B ASN* 2.7 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 3.7 35.9 - - + -
113B VAL* 4.2 11.0 - - + -
163B GLY 3.1 14.6 + - - +
164B CYS* 3.1 18.8 + - - +
166B TYR* 1.3 77.0 - - + +
168B HIS* 1.3 64.2 + - + +
170B ASN* 3.0 11.8 + - - -
171B ARG 3.1 0.2 + - - -
172B VAL* 3.0 40.6 + - + +
174B HIS* 4.2 18.8 - - + +
192B ILE* 4.2 15.3 - - + -
195B PHE* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B CYS* 3.0 32.6 + - - +
165B GLN 3.3 3.8 + - - +
167B LEU* 1.3 76.0 - - + +
169B ARG* 1.3 59.0 + - + +
171B ARG* 2.9 21.3 + - - +
172B VAL 3.3 18.4 - - - -
230B PHE* 3.4 56.0 + + + +
233B ASP* 2.8 28.0 + - + +
234B VAL* 4.7 4.9 - - + -
296B ILE* 3.7 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASN* 4.8 10.5 + - - +
303A GLU* 5.9 1.2 - - - +
306A THR* 3.8 18.4 + - - +
165B GLN* 3.0 58.7 + - + +
166B TYR* 3.9 6.3 - - - +
168B HIS* 1.3 77.4 - - + +
170B ASN* 1.3 64.7 + - - +
171B ARG* 3.2 7.0 + - - +
296B ILE* 6.0 0.9 - - + -
297B ASN* 3.8 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B SER 5.7 1.3 - - - +
108B LEU* 4.5 16.8 - - + -
166B TYR* 2.7 60.4 + - - +
167B LEU 3.0 5.3 + - - +
169B ARG* 1.3 83.6 - - - +
171B ARG* 1.3 68.8 + - - +
172B VAL* 3.3 4.5 + - + +
200B LYS* 3.1 25.2 + - - +
----------------------------------------------------------
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