Contacts of the helix formed by residues 173 - 189 (chain B) in PDB entry 3N4E
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 ASP 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B VAL* 1.3 88.3 - - + +
174B ILE* 1.3 59.3 + - - +
175B PRO* 3.8 10.8 - - - +
176B GLY* 3.2 27.4 + - - -
177B ASP* 2.9 42.5 + - - +
180B LYS* 5.4 4.7 + - - -
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Residues in contact with ILE 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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171B ASP* 3.9 35.8 + - + +
172B VAL 4.0 0.4 - - - -
173B ASP* 1.3 73.5 - - - +
175B PRO* 1.4 74.4 - - + +
177B ASP* 3.2 7.5 + - - +
178B ILE* 3.0 41.7 + - + +
202B TYR* 3.9 20.6 - - + -
206B GLY* 3.9 20.9 - - - +
209B ARG* 4.1 25.8 - - - +
210B VAL* 3.9 11.2 - - + -
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Residues in contact with PRO 175 (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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173B ASP* 3.7 9.6 - - - +
174B ILE* 1.4 96.9 - - + +
176B GLY* 1.3 55.3 + - - +
178B ILE* 3.4 9.6 + - + +
179B ALA* 3.0 28.6 + - - +
182B ARG* 5.6 0.2 + - - -
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Residues in contact with GLY 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 5.3 1.0 - - - +
173B ASP* 3.2 30.9 + - - -
174B ILE 3.2 0.2 - - - -
175B PRO* 1.3 75.2 - - - +
177B ASP* 1.3 61.0 + - - +
179B ALA* 3.4 7.0 + - - +
180B LYS* 3.0 37.7 + - - +
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Residues in contact with ASP 177 (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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136B ALA* 5.5 0.2 - - - -
163B TRP* 2.8 47.3 + - + +
173B ASP* 2.9 38.9 + - - +
174B ILE* 3.7 4.0 - - - +
176B GLY* 1.3 73.3 - - - +
178B ILE* 1.3 59.5 + - + +
180B LYS* 3.4 8.2 + - - +
181B ALA* 3.1 26.0 + - - +
196B PHE* 4.0 6.5 - - + -
202B TYR* 2.6 40.3 + - - +
210B VAL* 5.4 1.3 - - + -
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Residues in contact with ILE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 3.0 39.0 + - + +
175B PRO* 3.7 7.9 - - + +
177B ASP* 1.3 73.7 - - - +
179B ALA* 1.3 60.0 + - - +
181B ALA* 3.2 8.3 + - - +
182B ARG* 2.9 51.4 + - - +
196B PHE* 5.8 0.2 - - - -
209B ARG* 4.6 8.1 - - + +
210B VAL* 4.5 21.1 - - + -
213B ALA* 3.8 33.7 - - + -
214B LEU* 6.1 1.6 - - + -
217B LEU* 4.3 6.4 - - + +
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Residues in contact with ALA 179 (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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140B VAL* 4.6 15.6 - - + +
175B PRO 3.0 17.7 + - - +
176B GLY* 3.6 8.5 - - - +
177B ASP 3.3 0.2 - - - -
178B ILE* 1.3 77.8 - - - +
180B LYS* 1.3 60.0 + - - +
182B ARG* 3.4 19.2 + - - +
183B ALA* 3.1 24.1 + - - +
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Residues in contact with LYS 180 (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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135B ASN 2.8 24.1 + - - +
136B ALA* 3.4 15.0 + - - +
138B ARG 2.8 31.2 + - - -
139B SER* 4.2 5.8 - - - +
140B VAL* 4.3 17.0 - - + +
143B VAL* 3.9 21.2 - - + +
161B ILE* 4.8 1.3 - - - -
163B TRP* 3.8 23.1 - - + +
173B ASP* 5.4 4.6 + - - -
176B GLY* 3.0 22.7 + - - +
177B ASP* 3.6 9.7 + - - +
178B ILE 3.3 0.4 - - - -
179B ALA* 1.3 76.2 - - - +
181B ALA* 1.3 61.3 + - - +
183B ALA* 3.4 5.3 + - - +
184B VAL* 3.1 29.3 + - - +
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Residues in contact with ALA 181 (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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161B ILE* 4.2 5.1 - - - +
163B TRP* 4.7 0.2 - - - -
177B ASP 3.1 13.4 + - - +
178B ILE* 3.2 8.7 + - - +
180B LYS* 1.3 72.5 - - - +
182B ARG* 1.3 64.1 + - - +
185B ARG* 3.1 16.5 + - - +
196B PHE* 4.0 8.5 - - + -
214B LEU* 3.8 27.4 - - + -
217B LEU* 3.9 7.9 - - + -
219B TYR* 2.8 32.3 + - + +
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Residues in contact with ARG 182 (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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175B PRO 5.6 0.4 + - - -
178B ILE* 2.9 37.4 + - - +
179B ALA* 3.6 24.4 - - - +
180B LYS 3.3 0.2 - - - -
181B ALA* 1.3 77.2 - - - +
183B ALA* 1.3 57.6 + - - +
185B ARG* 3.2 4.9 + - - +
186B GLU* 2.9 38.8 + - + +
217B LEU* 3.7 28.9 - - + +
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Residues in contact with ALA 183 (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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140B VAL* 3.7 25.8 - - + -
143B VAL* 6.4 0.2 - - + -
144B VAL* 3.8 16.4 - - + +
179B ALA 3.1 17.0 + - - +
180B LYS* 3.9 4.3 - - - +
182B ARG* 1.3 78.1 - - - +
184B VAL* 1.3 57.8 + - - +
186B GLU* 3.9 8.0 - - - +
187B LEU* 3.0 26.7 + - - +
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL* 3.6 26.5 - - + -
144B VAL* 4.8 6.3 - - + -
147B VAL* 3.9 24.9 - - + -
159B VAL* 5.0 0.4 - - + -
161B ILE* 4.0 13.7 - - + -
180B LYS 3.1 16.8 + - - +
182B ARG 3.2 0.2 - - - -
183B ALA* 1.3 74.9 - - - +
185B ARG* 1.3 60.5 - - - +
187B LEU* 3.3 4.9 + - - +
188B LEU* 2.9 50.1 + - + +
194B ILE* 4.3 9.2 - - + -
219B TYR* 3.9 15.0 - - - +
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Residues in contact with ARG 185 (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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181B ALA 3.1 14.6 + - - +
182B ARG 3.5 7.6 - - - +
184B VAL* 1.3 73.2 - - - +
186B GLU* 1.3 71.3 + - - +
188B LEU 3.2 1.0 + - - -
189B GLY* 2.9 51.8 + - - +
190B PRO* 3.5 24.3 + - - -
192B ALA 2.8 28.5 + - - +
194B ILE* 3.5 31.5 - - + +
217B LEU* 2.7 39.7 + - + +
218B GLY* 3.1 29.6 + - - -
219B TYR* 3.9 6.4 + - + +
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Residues in contact with GLU 186 (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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182B ARG* 2.9 32.2 + - + +
183B ALA* 3.9 8.1 - - - +
185B ARG* 1.3 79.2 - - - +
187B LEU* 1.3 62.7 + - - +
189B GLY* 3.8 6.4 + - - -
217B LEU* 6.1 0.7 - - - +
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Residues in contact with LEU 187 (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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144B VAL* 3.7 38.1 - - + +
147B VAL* 3.7 32.1 - - + -
148B ALA* 3.9 21.3 - - + +
183B ALA 3.0 17.6 + - - +
184B VAL* 3.6 5.6 - - - +
185B ARG 3.2 0.4 - - - -
186B GLU* 1.3 79.4 - - - +
188B LEU* 1.3 67.5 + - + +
189B GLY 3.5 0.3 + - - -
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Residues in contact with LEU 188 (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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147B VAL* 4.0 9.0 - - + -
151B VAL* 3.9 33.2 - - + -
159B VAL* 3.9 29.6 - - + -
184B VAL* 2.9 37.6 + - + +
185B ARG 3.2 0.9 + - - +
187B LEU* 1.3 84.8 - - + +
189B GLY* 1.3 61.8 + - - +
192B ALA* 3.5 25.3 + - + +
193B VAL 5.3 0.2 - - - +
194B ILE* 3.9 17.5 - - + -
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Residues in contact with GLY 189 (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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185B ARG* 2.9 40.8 + - - +
186B GLU* 3.8 5.4 + - - -
187B LEU 3.4 4.0 + - - -
188B LEU* 1.3 81.3 - - - +
190B PRO* 1.3 64.1 - - - +
191B ASP 3.2 4.1 + - - -
192B ALA* 3.5 2.3 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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