Contacts of the helix formed by residues 152 - 172 (chain B) in PDB entry 5IZL
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 152 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU 4.3 3.6 - - - +
151B LEU* 1.3 90.9 - - + +
153B GLU* 1.3 55.5 + - - +
154B GLY 3.2 2.9 - - - +
155B LYS* 3.0 20.4 + - + +
156B ARG* 2.6 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU 3.8 2.2 + - - -
152B PRO* 1.3 72.9 - - - +
154B GLY* 1.3 64.1 + - - +
155B LYS 3.3 0.3 + - - -
156B ARG* 3.3 48.6 + - - +
157B GLN* 4.4 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PRO* 3.2 2.6 + - - +
153B GLU* 1.3 78.6 - - - +
155B LYS* 1.3 58.8 + - - +
157B GLN 5.5 0.2 + - - -
158B ALA* 5.1 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PRO* 3.0 20.9 + - + +
154B GLY* 1.3 76.0 - - - +
156B ARG* 1.3 59.2 + - - +
157B GLN 3.6 1.6 - - - -
158B ALA* 3.3 10.9 + - + +
159B ALA* 2.8 33.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
148B ILE* 3.7 25.1 + - - +
149B ASP* 3.3 16.5 + - - +
151B LEU* 2.5 49.8 + - + +
152B PRO* 2.6 17.9 + - - +
153B GLU* 3.3 42.7 + - - +
155B LYS* 1.3 71.1 - - - +
157B GLN* 1.3 61.5 + - + +
159B ALA* 2.9 19.2 + - - +
160B ILE* 2.9 27.7 + - + +
200B GLN* 4.6 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B GLU* 4.4 9.1 + - - +
155B LYS 3.6 0.2 - - - -
156B ARG* 1.3 80.6 - - + +
158B ALA* 1.3 63.7 + - - +
160B ILE* 3.9 22.3 - - - +
161B ASP* 3.4 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLY 5.1 2.8 + - - +
155B LYS* 3.3 19.1 + - + +
156B ARG 3.1 0.4 - - - -
157B GLN* 1.3 77.9 - - - +
159B ALA* 1.3 58.4 + - - +
161B ASP* 3.1 6.8 + - - +
162B LYS* 2.8 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 5.2 2.2 - - + -
151B LEU* 3.8 24.0 - - + -
155B LYS* 2.8 23.5 + - + +
156B ARG 3.5 3.6 - - - +
158B ALA* 1.3 71.9 - - - +
160B ILE* 1.3 53.8 + - - +
162B LYS* 3.1 7.9 + - - +
163B MET* 2.7 38.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
119B VAL* 4.8 4.0 - - + -
145B LEU* 4.7 4.2 - - + +
148B ILE* 4.0 32.5 - - + -
151B LEU* 4.0 12.5 - - + +
156B ARG* 2.9 28.0 + - + +
157B GLN* 3.9 25.6 - - - +
159B ALA* 1.3 75.7 - - - +
161B ASP* 1.3 50.6 + - - +
163B MET* 3.5 5.1 - - - +
164B THR* 2.4 49.3 + - - +
183B PRO* 3.5 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLN* 3.4 23.6 + - - +
158B ALA* 3.1 6.5 + - - +
160B ILE* 1.3 79.8 - - - +
162B LYS* 1.3 61.1 + - - +
164B THR* 3.7 9.2 - - - -
165B LYS* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ALA 2.8 14.4 + - - +
159B ALA* 3.5 11.0 - - - +
161B ASP* 1.3 75.6 - - - +
163B MET* 1.3 64.1 + - - +
165B LYS* 3.3 12.8 + - - +
166B LYS* 3.3 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 4.8 2.0 - - + -
119B VAL* 4.0 31.2 - - + +
121B LYS 5.2 0.2 - - - -
122B GLY* 3.7 31.9 - - - -
123B MET* 4.7 2.2 - - + +
145B LEU* 4.1 22.2 - - + -
159B ALA 2.7 19.8 + - - +
160B ILE 3.6 2.7 - - - +
162B LYS* 1.3 69.8 - - - +
164B THR* 1.3 67.0 + - - +
166B LYS* 3.1 23.9 + - + -
167B MET* 3.3 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 4.0 13.4 - - - +
160B ILE* 2.4 43.6 + - - +
161B ASP* 3.7 9.3 - - - -
162B LYS 3.3 0.2 - - - -
163B MET* 1.3 72.3 - - - +
165B LYS* 1.3 60.3 + - - +
167B MET* 3.3 1.7 + - - -
168B GLN* 3.2 31.6 + - - +
181B ILE* 3.6 36.5 + - + +
183B PRO* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ASP 3.2 15.6 + - - +
162B LYS* 3.3 5.4 + - - +
163B MET 3.1 1.2 - - - -
164B THR* 1.3 78.7 - - - +
166B LYS* 1.3 59.8 + - - +
167B MET 3.3 0.2 - - - -
168B GLN* 3.7 18.3 - - - +
169B LYS* 3.5 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LYS 3.3 10.3 + - - +
163B MET* 3.1 22.8 + - + +
165B LYS* 1.3 75.2 - - - +
167B MET* 1.3 64.4 + - - +
169B LYS* 4.0 5.5 - - - +
170B THR* 3.2 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 4.7 7.2 - - + -
117B ILE* 4.5 9.2 - - + -
123B MET* 3.8 39.5 - - + +
131B LEU* 5.7 2.0 - - + -
143B VAL* 3.8 36.1 - - + -
145B LEU* 4.6 7.4 - - + -
163B MET* 3.3 28.0 + - + +
164B THR 3.8 1.6 - - - +
166B LYS* 1.3 76.8 - - - +
168B GLN* 1.3 60.3 + - - +
169B LYS 3.1 0.4 - - - -
170B THR* 3.5 7.1 + - - +
171B LEU* 2.8 45.6 + - + +
181B ILE* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B THR* 3.2 25.1 + - - +
165B LYS* 3.7 20.5 - - - +
166B LYS 3.5 0.4 - - - -
167B MET* 1.3 76.2 - - - +
169B LYS* 1.3 64.3 + - - +
171B LEU* 3.6 8.9 - - + +
172B GLU* 3.3 17.8 + - - +
177B ARG 5.5 2.4 - - - +
179B ALA 5.8 1.3 - - - +
181B ILE* 3.9 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LYS 3.5 14.2 + - - +
166B LYS* 4.0 7.2 - - - +
167B MET 3.1 0.6 - - - -
168B GLN* 1.3 74.4 - - - +
170B THR* 1.3 60.2 + - + +
171B LEU 3.0 3.8 - - - -
172B GLU* 2.7 34.8 + - - +
173B ASN* 4.7 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B MET* 5.0 14.0 - - + +
131B LEU* 4.7 12.0 - - - +
166B LYS 3.2 18.9 + - - +
167B MET* 3.5 16.8 + - - +
169B LYS* 1.3 76.5 - - + +
171B LEU* 1.3 62.3 + - - +
172B GLU 3.3 8.0 - - - +
173B ASN* 4.5 8.2 + - - +
174B THR* 4.6 3.1 - - - +
324B TYR* 5.2 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 6.2 0.4 - - + -
131B LEU* 4.5 21.3 - - + -
141B LEU* 3.9 21.8 - - + -
143B VAL* 4.3 15.7 - - + -
167B MET* 2.8 35.9 + - + +
168B GLN* 3.6 9.0 - - + +
170B THR* 1.3 76.3 + - - +
172B GLU* 1.3 60.9 + - - +
174B THR* 2.4 32.8 + - + +
176B PHE* 3.8 17.4 - - + +
177B ARG* 4.8 6.3 - - - +
179B ALA* 3.8 36.8 - - + +
181B ILE* 4.5 6.5 - - + -
----------------------------------------------------------
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 GLN 3.3 11.4 + - - +
169B LYS* 2.7 15.5 + - - +
170B THR 3.3 4.0 - - - +
171B LEU* 1.3 84.9 - - - +
173B ASN* 1.3 91.6 + - + +
174B THR* 3.0 2.9 + - - +
177B ARG* 3.2 30.0 - - - +
----------------------------------------------------------
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