Contacts of the helix formed by residues 153 - 172 (chain B) in PDB entry 6WCZ
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 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B SER* 3.3 7.1 + - - -
152B SER* 1.3 83.0 + - - +
154B PRO* 1.3 71.0 - - - +
155B GLU* 2.3 31.3 + - - -
156B VAL* 3.1 30.6 + - - +
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Residues in contact with PRO 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLU* 5.9 8.1 - - + -
13B LYS* 3.4 25.4 - - + +
152B SER 3.4 6.5 - - - +
153B SER* 1.3 88.7 - - - +
155B GLU* 1.3 60.5 + - + +
156B VAL 3.1 0.2 - - - -
157B GLU* 2.9 30.7 - - + +
158B GLU* 2.9 27.8 + - - +
185B CYS* 5.0 0.4 - - - -
187B TYR* 4.0 15.3 - - + +
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B SER* 2.3 32.5 + - - -
154B PRO* 1.3 75.5 - - + +
156B VAL* 1.3 73.8 + - + +
158B GLU* 3.2 24.7 + - + +
159B THR* 2.8 33.5 + - - +
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B SER* 3.4 16.4 - - - +
153B SER* 3.3 23.3 - - - +
154B PRO 3.1 0.2 - - - -
155B GLU* 1.3 94.2 - - - +
157B GLU* 1.3 57.0 + - - +
159B THR* 3.3 22.2 - - - -
160B ARG* 2.9 38.1 + - - +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LYS* 2.9 32.3 + - - +
149B GLU 3.8 20.6 - - - +
150B SER* 5.0 1.1 - - - -
151B SER* 3.9 18.8 - - - +
154B PRO* 2.9 25.4 - - - +
156B VAL* 1.3 77.3 - - - +
158B GLU* 1.3 55.0 + - - +
159B THR 3.1 0.9 - - - -
160B ARG* 3.3 12.8 + - - +
161B THR* 2.7 32.1 + - - -
184B LEU* 3.8 16.0 - - + +
185B CYS* 3.2 31.8 - - - +
187B TYR* 4.2 1.6 + - - -
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PRO* 2.9 22.1 + - - +
155B GLU* 3.4 29.2 - - + +
157B GLU* 1.3 77.9 - - - +
159B THR* 1.3 55.9 + - - +
161B THR* 3.3 8.8 + - - -
162B LEU* 2.9 41.0 + - + +
185B CYS* 3.7 23.6 - - + +
187B TYR* 4.8 4.2 - - - -
188B THR* 3.3 29.4 - - + +
190B THR* 5.9 0.2 - - - -
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Residues in contact with THR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLU* 2.8 18.2 + - - +
156B VAL* 3.3 13.7 + - - -
157B GLU 3.1 0.2 - - - -
158B GLU* 1.3 75.9 - - - +
160B ARG* 1.3 60.1 + - + +
162B LEU* 3.1 16.1 + - + +
163B ARG* 2.9 25.5 + - + +
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Residues in contact with ARG 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLU* 4.4 32.2 + - - +
150B SER 5.7 1.0 + - - -
151B SER* 4.6 4.6 - - - -
156B VAL* 2.9 47.3 + - - +
157B GLU* 3.3 14.8 + - + +
158B GLU 3.3 0.4 - - - -
159B THR* 1.3 75.2 - - + +
161B THR* 1.3 60.4 + - - +
163B ARG* 3.2 9.8 + - - +
164B VAL* 2.9 31.6 + - - +
184B LEU* 5.5 8.5 - - + -
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Residues in contact with THR 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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157B GLU 2.7 17.2 + - - -
158B GLU* 3.4 11.9 - - - -
159B THR 3.3 0.2 - - - -
160B ARG* 1.3 77.6 - - - +
162B LEU* 1.3 60.0 + - + +
164B VAL* 3.3 11.7 - - + +
165B LEU* 2.9 51.7 + - + +
183B VAL* 4.1 23.6 - - + -
184B LEU* 3.2 25.9 - - - +
185B CYS* 3.9 10.3 + - - +
191B MET* 5.4 3.4 - - + -
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLU* 2.9 29.0 + - + +
159B THR* 3.1 15.9 + - + +
161B THR* 1.3 78.6 - - + +
163B ARG* 1.3 59.7 + - - +
165B LEU* 3.6 9.2 + - + +
166B SER* 2.7 31.4 + - - -
190B THR* 4.6 18.2 - - - +
191B MET* 6.0 2.2 - - + +
194B THR* 5.5 7.0 - - + +
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Residues in contact with ARG 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 5.8 1.4 - - - +
132B VAL* 2.8 37.8 + - - +
133B PHE* 3.2 41.3 + - + +
147B ILE* 5.4 7.3 - - - +
159B THR* 2.9 12.8 + - + +
160B ARG* 3.2 11.8 + - - +
162B LEU* 1.3 75.9 - - - +
164B VAL* 1.3 73.0 + - - +
166B SER* 3.0 10.2 + - - -
167B MET* 2.9 60.5 + - - +
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 6.0 0.7 - - + -
145B CYS* 3.8 28.5 - - + -
147B ILE* 5.2 15.3 - - + +
160B ARG 2.9 16.3 + - - +
161B THR* 3.3 19.5 - - + +
163B ARG* 1.3 91.7 - - - +
165B LEU* 1.3 65.4 + - + +
167B MET* 3.0 7.4 + - + +
168B VAL* 2.8 35.6 + - + +
181B ILE* 5.8 2.2 - - + -
182B LYS* 4.8 15.7 - - - +
184B LEU* 5.4 5.8 - - + +
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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
----------------------------------------------------------
161B THR* 2.9 38.5 + - + +
162B LEU* 4.0 10.3 - - + +
164B VAL* 1.3 77.0 - - + +
166B SER* 1.3 60.7 + - - +
168B VAL* 3.8 16.1 - - + +
169B GLY* 2.9 25.8 + - - -
181B ILE* 5.5 2.9 - - + -
182B LYS 5.8 1.6 - - - +
183B VAL* 5.1 11.0 - - + -
191B MET* 4.4 22.9 - - + -
194B THR* 3.8 33.5 - - + +
221B TRP* 4.8 19.1 - - + -
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Residues in contact with SER 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 LEU 2.7 19.4 + - - -
163B ARG* 3.0 14.2 + - - -
165B LEU* 1.3 79.3 - - - +
167B MET* 1.3 55.1 + - - +
169B GLY* 5.0 0.2 - - - -
170B ASP* 2.9 44.6 + - - +
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Residues in contact with MET 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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80B LEU* 5.8 4.9 - - + -
132B VAL* 3.3 35.2 - - + +
133B PHE 4.2 10.3 - - - +
135B MET 4.9 8.7 - - - +
163B ARG* 2.9 43.2 + - - +
164B VAL* 3.0 8.9 + - + +
166B SER* 1.3 75.1 - - - +
168B VAL* 1.3 61.7 + - - +
170B ASP* 3.7 4.5 - - + +
171B TRP* 2.9 48.2 + - + +
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Residues in contact with VAL 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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143B LEU* 4.1 15.3 - - + -
145B CYS* 5.7 3.4 - - + -
164B VAL* 2.8 25.8 + - + +
165B LEU* 3.8 23.3 - - + +
167B MET* 1.3 73.6 - - - +
169B GLY* 1.3 60.9 + - - +
171B TRP* 2.7 23.1 + - + -
172B LEU* 2.9 33.5 + - + +
181B ILE* 3.9 43.1 - - + -
221B TRP* 5.4 3.8 - - + -
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Residues in contact with GLY 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 2.9 20.7 + - - -
166B SER* 5.0 0.4 - - - -
168B VAL* 1.3 78.7 - - - +
170B ASP* 1.3 64.1 + - - +
172B LEU* 4.0 18.4 - - - +
173B GLU* 3.8 13.3 - - - +
198B LEU* 4.6 11.6 - - - +
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Residues in contact with ASP 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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137B ALA* 4.2 9.2 - - - +
166B SER* 2.9 30.5 + - - +
167B MET* 4.1 6.9 - - + +
169B GLY* 1.3 78.2 - - - +
171B TRP* 1.3 61.2 + - - +
172B LEU 3.5 0.2 - - - -
173B GLU* 3.1 32.7 - - - +
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Residues in contact with TRP 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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78B VAL* 4.5 16.3 - - + +
132B VAL* 4.8 3.6 - - + -
135B MET* 3.6 39.7 - - + -
136B ALA 3.2 30.1 - - - -
137B ALA* 3.6 20.5 - - + +
138B GLU* 3.4 38.6 + - + +
140B CYS* 5.2 2.9 - - - -
143B LEU* 3.5 38.0 - - + +
167B MET* 2.9 36.6 + - + +
168B VAL* 2.7 14.8 + - + +
170B ASP* 1.3 78.2 - - - +
172B LEU* 1.3 56.1 + - - +
173B GLU* 2.8 17.6 + - - +
174B LYS* 4.3 2.8 + - - +
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 5.9 4.5 - - + -
168B VAL* 2.9 39.0 + - + +
169B GLY* 4.0 9.4 - - - +
170B ASP 3.5 0.8 - - - -
171B TRP* 1.3 79.7 - - + +
173B GLU* 1.3 56.9 + - + +
174B LYS* 3.0 12.4 + - - -
175B ARG* 3.3 3.5 + - - -
176B PRO* 3.3 28.1 - - + +
179B PHE* 6.1 7.4 - - + -
181B ILE* 6.3 0.2 - - + -
198B LEU* 3.8 44.2 - - + -
202B HIS* 4.1 19.5 + - + +
221B TRP* 4.9 9.6 - - + -
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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