Contacts of the helix formed by residues 154 - 173 (chain B) in PDB entry 4R1Z
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 SER 154 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS* 3.4 27.8 - - - +
146B CYS 5.6 0.9 - - - -
148B PHE 3.4 9.2 - - - -
153B VAL* 1.4 80.1 + - - +
155B ILE* 1.3 68.1 + - - +
156B GLU* 2.7 8.1 + - - +
157B LYS* 2.5 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 3.5 35.0 - - + +
146B CYS* 4.6 5.6 - - - +
148B PHE* 3.6 29.7 + - + +
154B SER* 1.3 94.9 + - - +
156B GLU* 1.3 55.8 + - - +
158B ILE* 2.7 36.9 + - + +
159B ILE* 2.9 31.9 + - + +
191B VAL* 4.7 5.8 - - + +
195B LEU* 4.8 5.8 - - + -
458B LEU* 4.4 15.7 - - + -
461B MET* 4.9 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 2.7 11.9 + - - +
155B ILE* 1.3 76.6 - - - +
157B LYS* 1.3 59.3 + - - +
159B ILE* 3.5 7.4 + - - +
160B CYS* 3.1 31.2 + - - -
354B GLN* 3.1 31.8 - - - +
355B LEU* 3.4 44.8 + - + +
356B SER 4.9 1.6 + - - -
461B MET* 5.5 0.2 - - - -
465B LEU* 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LYS* 6.1 2.6 - - - +
153B VAL* 3.2 39.7 + - + +
154B SER 2.5 19.5 + - - +
156B GLU* 1.3 70.3 - - - +
158B ILE* 1.3 66.8 + - + +
160B CYS* 3.2 5.0 + - - +
161B ARG* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B PHE* 3.5 36.1 - - + -
153B VAL* 3.7 22.4 - - + -
155B ILE* 2.7 20.1 + - + +
157B LYS* 1.3 77.6 - - - +
159B ILE* 1.3 60.8 + - - +
161B ARG* 3.5 32.6 - - - +
162B GLU* 3.3 21.2 + - + +
191B VAL* 3.9 23.6 - - + +
194B ALA* 3.7 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ILE* 2.9 29.7 + - + +
156B GLU* 3.9 3.1 - - - +
158B ILE* 1.3 75.3 - - - +
160B CYS* 1.3 57.4 + - - +
162B GLU* 3.1 5.9 + - - +
163B ALA* 2.8 24.2 + - + +
191B VAL* 3.9 26.9 - - + -
458B LEU* 4.3 2.7 - - + -
461B MET* 3.8 30.5 - - + -
462B GLU* 3.9 24.2 - - + +
465B LEU* 3.3 38.8 - - + -
466B PHE* 4.3 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLU* 3.1 30.2 + - - +
157B LYS* 3.9 4.9 - - - +
159B ILE* 1.3 74.7 - - - +
161B ARG* 1.3 58.1 + - - +
163B ALA* 2.9 8.3 + - - +
164B SER* 2.6 38.0 + - - -
353B PRO 4.2 4.7 - - - -
354B GLN* 5.9 0.2 - - - -
465B LEU* 4.1 19.7 - - - -
469B TRP* 3.6 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LYS* 2.9 18.3 + - + +
158B ILE* 3.5 33.3 + - - +
160B CYS* 1.3 74.3 - - - +
162B GLU* 1.3 81.6 + - - +
164B SER* 3.5 6.2 + - - -
165B SER* 2.7 36.9 + - - -
190B ASN* 4.0 17.6 + - - +
194B ALA* 4.5 5.9 - - - +
200B SER* 3.3 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ILE 3.3 13.2 + - - +
159B ILE 3.1 8.6 + - - +
160B CYS 3.0 0.6 - - - -
161B ARG* 1.3 111.3 + - - +
163B ALA* 1.3 61.7 + - - +
165B SER* 3.4 15.5 + - - -
166B MET* 2.9 27.7 + - - +
186B ARG* 5.0 1.9 + - - -
187B ALA* 3.7 38.8 - - + +
190B ASN* 3.2 36.0 + - + +
191B VAL* 4.4 6.1 - - + +
200B SER* 4.7 0.9 + - - -
466B PHE* 4.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 2.8 14.8 + - + +
160B CYS* 3.5 7.6 - - - +
162B GLU* 1.3 73.3 - - - +
164B SER* 1.3 54.9 + - - +
166B MET* 2.9 6.0 + - - +
167B CYS* 2.7 40.5 + - - -
465B LEU 5.1 0.4 - - - -
466B PHE* 3.7 25.0 - - + +
469B TRP* 3.5 36.3 - - + -
470B ILE* 5.7 1.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
160B CYS 2.6 20.2 + - - -
161B ARG* 3.5 6.5 - - - -
163B ALA* 1.3 70.3 - - - +
165B SER* 1.3 65.9 + - - +
167B CYS* 2.9 15.8 + - - +
168B GLU* 3.3 19.0 + - - +
469B TRP* 3.5 27.7 - - - -
473B ARG* 5.3 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ARG* 2.7 24.4 + - - -
162B GLU* 3.4 22.5 + - - -
164B SER* 1.3 70.9 + - - +
166B MET* 1.3 57.9 + - - +
168B GLU* 3.1 32.4 + - - +
169B VAL* 3.8 5.5 + - - +
186B ARG* 4.9 13.5 + - - -
187B ALA* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLU 2.9 16.6 + - - +
163B ALA* 2.9 8.2 + - - +
165B SER* 1.3 74.7 - - - +
167B CYS* 1.3 63.0 + - - +
168B GLU 3.2 2.5 - - - -
169B VAL* 2.8 32.9 - - + +
170B LEU* 3.5 16.3 + - + +
180B LEU* 4.4 24.0 - - + +
183B GLU* 3.9 14.8 - - + +
184B LEU* 3.4 59.9 - - + +
187B ALA* 4.4 9.9 - - + -
466B PHE* 5.2 3.6 - - + -
470B ILE* 5.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ALA 2.7 29.6 + - - -
164B SER* 2.9 8.9 + - - +
166B MET* 1.3 73.5 - - - +
168B GLU* 1.3 52.3 + - - +
170B LEU* 3.3 3.1 + - - -
171B THR* 2.7 32.5 + - - -
469B TRP* 4.0 22.4 - - - -
470B ILE* 4.6 9.0 - - - -
473B ARG* 3.2 39.7 - - - +
474B PHE* 3.2 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 3.3 15.2 + - - +
165B SER* 3.1 28.0 + - - +
167B CYS* 1.3 78.4 - - - +
169B VAL* 1.3 59.8 + - - +
171B THR* 3.2 11.6 + - - -
172B GLU* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B SER 3.9 2.5 - - - +
166B MET* 2.8 52.7 - - + +
168B GLU* 1.3 80.5 - - - +
170B LEU* 1.3 56.9 + - + +
172B GLU* 3.6 12.0 - - - +
173B SER* 2.7 45.3 + - - +
183B GLU* 3.3 30.7 - - + +
203B ARG* 4.9 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 3.8 25.6 - - + +
167B CYS* 3.3 8.7 + - - +
168B GLU 3.3 0.6 - - - -
169B VAL* 1.3 84.0 - - + +
171B THR* 1.3 66.1 + - - +
173B SER* 3.2 24.9 - - - +
174B GLN* 3.6 10.2 + - - +
178B VAL* 5.0 2.9 - - + -
180B LEU* 4.1 39.3 - - + -
470B ILE* 4.7 17.7 - - + -
474B PHE* 3.5 28.0 - - + -
476B LEU* 5.4 1.8 - - + -
504B ALA* 3.5 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B CYS* 2.7 18.3 + - - +
168B GLU* 3.2 15.0 + - - +
170B LEU* 1.3 74.8 - - - +
172B GLU* 1.3 63.3 + - - +
174B GLN* 3.4 32.6 - - - +
473B ARG* 5.4 2.8 - - - -
474B PHE* 3.6 8.7 - - - -
506B VAL* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLU 2.8 15.2 + - - +
169B VAL* 3.6 12.2 - - - +
171B THR* 1.3 78.9 - - - +
173B SER* 1.3 63.3 + - - +
174B GLN* 2.7 18.0 + - - +
203B ARG* 5.0 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 2.7 30.8 + - - +
170B LEU* 3.2 12.2 - - - +
172B GLU* 1.3 77.5 + - - +
174B GLN* 1.3 58.3 + - - +
175B ASN 4.1 0.7 + - - -
176B SER* 3.7 12.8 + - - +
178B VAL* 3.9 38.6 - - - +
504B ALA* 4.5 6.8 + - - +
----------------------------------------------------------
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