Contacts of the helix formed by residues 154 - 174 (chain B) in PDB entry 4EOZ
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 TYR 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ARG* 3.3 47.6 + - - +
94B LEU* 4.0 25.0 - - + +
149B ASP 4.2 5.1 + - - -
150B GLN 3.6 17.0 - - - +
151B VAL 3.4 11.2 + - - +
153B ARG* 1.3 76.4 - - - +
155B GLY* 1.3 71.6 + - - +
156B CYS* 4.0 15.9 - - + -
157B ILE* 3.1 17.8 + - + -
158B ARG 2.8 20.1 + - - -
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Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ARG 3.4 4.5 + - - -
154B TYR* 1.3 80.5 - - - +
156B CYS* 1.3 62.2 + - - +
158B ARG* 3.8 6.2 - - - +
159B ASP* 3.1 27.2 + - - +
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Residues in contact with CYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 3.7 17.5 - - + -
97B LEU* 3.3 36.1 - - - -
154B TYR* 3.5 11.7 - - + -
155B GLY* 1.3 73.2 - - - +
157B ILE* 1.3 64.3 + - - +
159B ASP* 3.4 8.2 + - - +
160B HIS* 3.1 21.5 + - - +
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG* 3.8 30.5 - - + +
93B VAL* 3.6 38.1 - - + -
94B LEU* 3.7 18.4 - - + +
97B LEU* 4.9 0.9 - - + -
101B PHE* 3.9 13.9 - - + -
105B LEU* 4.6 9.0 - - + -
151B VAL* 3.1 33.7 - - + +
152B VAL* 4.4 6.5 - - - +
154B TYR* 3.1 8.3 + - + +
156B CYS* 1.3 76.3 - - - +
158B ARG* 1.3 58.7 + - - +
160B HIS* 3.1 4.8 + - - +
161B LEU* 2.8 31.5 + - + +
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Residues in contact with ARG 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B VAL 3.3 19.0 + - - +
153B ARG* 3.7 39.2 + - - +
154B TYR 2.8 19.4 + - - +
155B GLY* 3.8 4.7 - - - +
157B ILE* 1.3 72.7 - - - +
159B ASP* 1.3 68.1 + - - +
161B LEU* 3.6 5.0 + - - +
162B ARG* 3.2 28.0 + - + +
203B GLU* 4.2 11.7 + - - -
204B ASP* 3.4 39.2 + - + +
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Residues in contact with ASP 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B GLY 3.1 19.5 + - - +
156B CYS* 3.7 7.1 - - - +
158B ARG* 1.3 80.2 - - - +
160B HIS* 1.3 56.6 + - - +
162B ARG* 2.5 37.5 + - - +
163B GLN* 3.0 44.5 + - - +
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Residues in contact with HIS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 3.7 20.6 - - + +
98B ASN* 3.2 49.9 + - - -
101B PHE* 3.5 40.6 - + + +
156B CYS* 3.1 13.8 + - - +
157B ILE 3.1 4.0 + - - +
159B ASP* 1.3 75.9 - - - +
161B LEU* 1.3 66.3 + - - +
163B GLN* 4.0 16.8 + - + +
164B THR* 2.6 43.8 + - - -
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 3.5 16.3 - - + -
102B LEU* 4.4 7.2 - - + -
105B LEU* 4.0 21.5 - - + -
152B VAL* 4.3 14.4 - - + +
157B ILE* 2.8 22.3 + - + +
158B ARG* 3.8 4.7 - - - +
160B HIS* 1.3 74.7 - - - +
162B ARG* 1.3 63.2 + - - +
164B THR* 3.8 1.1 - - - -
165B LEU* 3.1 48.9 + - + +
186B ALA* 4.3 11.9 - - + -
189B MSE 4.0 22.4 - - + -
190B LEU* 4.1 20.6 - - + -
204B ASP* 6.2 2.0 - - + -
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ARG* 3.2 18.8 + - + +
159B ASP* 2.5 34.3 + - - +
161B LEU* 1.3 81.0 - - - +
163B GLN* 1.3 85.5 + - - +
165B LEU* 4.1 5.3 - - - +
166B LEU* 3.1 51.9 + - + +
204B ASP 3.8 22.6 + - - +
205B PHE* 5.4 1.1 - - + -
208B PRO* 4.0 17.7 - - + +
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Residues in contact with GLN 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ASP* 3.0 27.3 + - - +
160B HIS* 3.9 21.5 + - + +
162B ARG* 1.3 97.7 + - - +
164B THR* 1.3 58.9 + - - +
166B LEU* 4.0 4.7 - - - +
167B ASP* 2.7 36.8 + - - +
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Residues in contact with THR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 4.1 3.4 - - + -
102B LEU* 3.4 37.9 - - + -
160B HIS* 2.6 43.7 + - - -
161B LEU 3.8 2.5 - - - -
163B GLN* 1.3 78.7 - - - +
165B LEU* 1.3 62.5 + - - +
167B ASP* 3.7 4.7 - - - +
168B MSE 3.0 34.4 + - + +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 4.2 15.9 - - + -
161B LEU* 3.1 38.6 + - + +
162B ARG* 4.1 5.2 - - - +
164B THR* 1.3 78.8 - - - +
166B LEU* 1.3 64.1 + - - +
168B MSE 3.2 7.3 + - - +
169B ILE* 3.1 28.2 + - + +
183B ILE* 4.0 26.9 - - + +
186B ALA* 3.7 28.0 - - + -
187B CYS* 4.9 3.6 - - - -
190B LEU* 4.9 6.5 - - + -
205B PHE* 3.8 37.2 - - + -
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ARG* 3.1 34.7 + - + +
163B GLN* 4.0 4.9 - - - +
165B LEU* 1.3 77.1 - - - +
167B ASP* 1.3 58.3 + - - +
169B ILE* 3.4 4.4 + - + +
170B ALA* 3.0 30.3 + - - +
205B PHE* 3.9 32.1 - - + +
208B PRO* 3.9 28.5 - - + +
209B PHE* 4.5 4.5 - - - +
212B MSE 3.1 43.0 - - + +
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Residues in contact with ASP 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLN 2.7 20.1 + - - +
164B THR* 3.7 6.3 - - - +
166B LEU* 1.3 75.8 - - - +
168B MSE 1.3 65.1 + - - +
170B ALA* 3.9 5.4 - - - +
171B ARG* 2.9 56.7 + - - +
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Residues in contact with MSE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 3.8 25.4 - - + -
164B THR* 3.0 25.7 + - + +
165B LEU* 3.6 7.6 - - - +
166B LEU 3.2 0.2 - - - -
167B ASP* 1.3 79.2 - - - +
169B ILE* 1.3 57.1 + - - +
171B ARG* 3.2 24.5 + - - +
172B GLU* 2.9 30.7 + - - +
178B VAL* 3.7 13.8 - - + +
179B ASP* 3.3 52.3 - - + +
182B ALA* 4.6 4.9 - - + -
183B ILE* 4.1 20.2 - - + -
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Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU 3.1 18.0 + - - +
166B LEU* 3.8 7.0 - - - +
168B MSE 1.3 73.9 - - - +
170B ALA* 1.3 64.1 + - - +
172B GLU* 3.2 7.7 + - - +
173B ARG* 3.0 40.3 + - - +
183B ILE* 4.4 16.8 - - + -
205B PHE* 3.8 33.2 - - + -
209B PHE* 3.8 30.1 - - + -
212B MSE 4.9 2.9 - - + -
247B ARG* 4.0 22.7 + - - +
251B CYS* 6.2 0.4 - - + -
252B LEU* 4.4 11.0 - - + -
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B LEU 3.0 18.4 + - - +
167B ASP* 4.0 7.2 - - - +
169B ILE* 1.3 80.8 - - - +
171B ARG* 1.3 59.4 + - + +
173B ARG* 3.6 12.4 + - - +
174B LYS* 3.2 30.5 + - + +
212B MSE 4.9 13.2 - - + -
216B PHE* 5.9 0.3 - - - -
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Residues in contact with ARG 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ASP* 2.9 43.6 + - - +
168B MSE 3.7 28.7 - - - +
170B ALA* 1.3 74.1 - - + +
172B GLU* 1.3 65.9 + - - +
173B ARG 3.0 1.6 - - - -
174B LYS* 3.1 18.9 + - + -
175B GLY 3.2 0.3 + - - -
176B GLU* 2.8 76.5 + - + +
177B VAL 5.0 3.0 + - - -
178B VAL* 4.1 17.4 - - + +
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Residues in contact with GLU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B MSE 2.9 16.8 + - - +
169B ILE* 3.8 5.6 - - - +
171B ARG* 1.3 77.9 - - - +
173B ARG* 1.3 63.1 + - - +
175B GLY* 3.2 11.6 + - - -
176B GLU 3.3 20.8 - - - +
177B VAL* 5.3 0.7 - - - -
178B VAL* 3.6 23.5 + - + +
180B ARG* 2.9 55.1 + - - +
183B ILE* 6.2 0.4 - - - -
243B GLU* 4.8 1.4 - - - +
247B ARG* 3.2 22.4 + - - +
251B CYS* 4.7 2.3 - - - -
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ILE* 3.0 26.8 + - - +
170B ALA* 3.6 12.3 - - - +
171B ARG 3.0 0.6 - - - -
172B GLU* 1.3 80.6 - - - +
174B LYS* 1.3 58.4 + - - +
175B GLY 3.3 0.7 + - - -
209B PHE* 3.8 12.1 - - - -
212B MSE 3.6 21.4 - - - -
213B SER* 2.9 36.7 + - - +
216B PHE* 3.5 43.1 - - + +
217B PHE* 3.9 7.4 - - - -
240B ARG* 4.0 10.4 + - - +
243B GLU* 3.9 14.5 - - - +
244B GLU* 2.6 42.2 + - - +
247B ARG* 3.8 14.5 - - - +
260B ILE* 4.4 0.4 - - - +
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Residues in contact with LYS 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ALA* 3.2 21.8 - - + +
171B ARG* 3.1 14.2 + - + +
173B ARG* 1.3 79.3 - - + +
175B GLY* 1.3 56.0 + - - +
176B GLU* 3.7 14.2 - - + +
216B PHE* 5.4 9.9 - - + -
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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) + - + + + + + -
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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