Contacts of the helix formed by residues 174 - 190 (chain B) in PDB entry 3AEV
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 ASN 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B GLY 3.4 16.6 - - - +
117B GLU* 3.8 8.4 + - - +
118B TYR* 5.0 0.2 - - - -
173B GLY* 1.3 74.0 - - - -
175B PRO* 1.4 76.4 - - + +
176B ILE* 3.0 18.8 - - - +
177B GLN* 2.9 50.3 + - - +
178B ILE* 2.8 20.0 + - - +
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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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165A GLU* 3.8 28.0 - - + +
169A ASN* 5.2 2.2 - - - +
116B GLY 4.3 0.9 - - - +
118B TYR* 4.0 24.4 - - + -
174B ASN* 1.4 89.4 - - + +
176B ILE* 1.3 59.0 + - + +
178B ILE* 3.3 11.2 + - + +
179B GLU* 2.8 31.0 + - - +
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Residues in contact with ILE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ASN* 3.0 11.7 - - - +
175B PRO* 1.3 79.2 - - + +
177B GLN* 1.3 66.0 + - + +
179B GLU* 3.2 7.2 + - - +
180B ILE* 3.1 39.3 + - + +
204B ARG* 4.6 11.2 + - - +
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Residues in contact with GLN 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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111B ARG* 3.3 20.1 + - - +
117B GLU* 3.6 3.2 + - - +
158B SER* 3.3 28.4 - - - +
159B GLY* 3.6 20.5 + - - +
160B ALA* 4.1 12.8 - - + -
173B GLY* 3.4 0.9 - - - -
174B ASN* 2.9 51.8 + - - +
176B ILE* 1.3 73.2 - - + +
178B ILE* 1.3 62.9 + - - +
180B ILE* 3.3 3.0 + - - -
181B ALA* 3.1 23.9 + - - +
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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
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118B TYR* 3.4 29.6 - - + +
120B GLU* 3.9 34.5 - - + +
171B ILE* 3.8 29.4 - - + +
173B GLY 3.2 30.1 - - - +
174B ASN 2.8 20.3 + - - +
175B PRO* 3.7 8.7 - - + +
177B GLN* 1.3 71.6 - - - +
179B GLU* 1.3 58.7 + - - +
181B ALA* 3.3 1.2 + - - +
182B LYS* 2.8 37.6 + - + +
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Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PRO 2.8 21.3 + - - +
176B ILE* 3.2 5.3 + - - +
178B ILE* 1.3 74.4 - - - +
180B ILE* 1.3 63.0 + - + +
182B LYS* 3.8 12.5 - - + +
183B THR* 2.8 35.2 + - - -
200B TYR* 4.2 5.4 + - - -
204B ARG* 5.0 9.7 + - - +
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Residues in contact with ILE 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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157B MET 4.7 5.6 - - - +
158B SER* 3.8 27.6 - - - +
176B ILE* 3.1 32.2 + - + +
177B GLN 3.9 4.9 - - - +
178B ILE 3.3 0.2 - - - -
179B GLU* 1.3 75.6 - - - +
181B ALA* 1.3 65.7 + - - +
183B THR* 3.3 1.7 + - - -
184B ALA* 3.1 21.8 + - - +
200B TYR* 3.9 10.4 - - + -
201B LEU* 3.7 24.9 - - + -
204B ARG* 3.9 50.3 - - + +
205B LYS* 5.6 0.7 - - - +
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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
----------------------------------------------------------
154B ILE* 3.8 22.2 - - + -
158B SER* 3.8 17.0 - - - +
160B ALA* 4.2 10.8 - - + -
162B VAL* 4.5 3.1 - - + -
171B ILE* 4.3 12.1 - - + -
177B GLN 3.1 15.6 + - - +
178B ILE 4.1 2.0 - - - +
180B ILE* 1.3 77.9 - - - +
182B LYS* 1.3 64.0 + - - +
184B ALA* 3.2 2.9 + - - +
185B ILE* 2.8 33.3 + - + +
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU* 4.0 15.5 + - + +
122B ILE* 3.6 35.7 - - + -
171B ILE* 4.0 12.3 - - + +
178B ILE* 2.8 23.6 + - + +
179B GLU* 3.8 12.8 - - + +
181B ALA* 1.3 77.2 - - - +
183B THR* 1.3 64.7 - - - +
185B ILE* 3.2 4.3 + - - +
186B GLU* 2.9 51.2 + - + +
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Residues in contact with THR 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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179B GLU* 2.8 37.7 + - - -
180B ILE 3.8 0.2 - - - -
182B LYS* 1.3 76.8 - - - +
184B ALA* 1.3 58.0 + - - +
186B GLU* 3.1 15.0 + - - +
187B LYS* 2.8 46.0 + - + +
200B TYR* 3.2 36.2 + - + +
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Residues in contact with ALA 184 (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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154B ILE* 4.4 12.3 - - + -
180B ILE 3.1 8.0 + - - +
181B ALA 3.7 6.7 - - - +
183B THR* 1.3 75.8 - - - +
185B ILE* 1.3 64.6 + - - +
187B LYS* 3.2 7.6 + - - +
188B LEU* 3.1 26.9 + - - +
197B VAL* 3.7 18.4 - - + +
200B TYR* 4.1 6.2 - - + -
201B LEU* 3.7 31.9 - - + -
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Residues in contact with ILE 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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122B ILE* 5.5 6.1 - - + -
124B LEU* 4.9 4.0 - - + -
127B ILE* 5.5 1.8 - - + -
143B ILE* 3.9 30.3 - - + +
154B ILE* 4.4 11.4 - - + -
162B VAL* 4.4 11.2 - - + -
169B VAL* 3.8 43.3 - - + -
171B ILE* 4.1 19.1 - - + -
181B ALA* 2.8 29.8 + - + +
182B LYS* 3.6 4.0 - - - +
184B ALA* 1.3 75.0 - - - +
186B GLU* 1.3 64.6 + - + +
188B LEU* 3.1 10.2 + - - +
189B ALA* 2.9 21.1 + - + +
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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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122B ILE* 5.6 2.3 - - + +
127B ILE* 3.7 33.1 - - + +
182B LYS* 2.9 47.6 + - + +
183B THR* 3.5 16.6 + - + +
185B ILE* 1.3 77.0 - - + +
187B LYS* 1.3 64.7 + - + +
189B ALA* 3.1 2.6 + - - +
190B ARG* 2.9 37.7 + - - +
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Residues in contact with LYS 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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183B THR* 2.8 34.1 + - + +
184B ALA* 3.2 7.4 + - - +
186B GLU* 1.3 72.7 - - + +
188B LEU* 1.3 61.0 + - - +
190B ARG* 3.4 6.0 + - - +
191B GLY 3.2 6.1 + - - -
192B SER* 3.0 43.8 + - - +
196B SER* 5.2 6.4 + - - +
197B VAL* 3.7 17.9 - - + -
200B TYR* 4.0 43.0 - - + +
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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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139B VAL* 4.7 4.2 - - - +
142B ARG* 3.3 55.1 + - + +
143B ILE* 4.2 17.5 - - + -
150B THR* 3.8 26.0 - - + -
154B ILE* 3.9 15.5 - - + -
184B ALA 3.1 17.6 + - - +
185B ILE* 3.1 8.1 + - - +
187B LYS* 1.3 75.1 - - - +
189B ALA* 1.3 62.6 + - - +
191B GLY* 3.4 3.1 + - - -
192B SER 4.0 2.2 - - - +
194B HIS* 4.2 26.2 - - + +
197B VAL* 3.7 24.9 - - + -
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Residues in contact with ALA 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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124B LEU* 5.0 6.3 - - + -
127B ILE* 3.7 28.9 - - + -
128B ILE* 4.6 14.0 - - + +
139B VAL* 4.1 35.4 - - + +
143B ILE* 5.3 0.4 - - + +
185B ILE* 2.9 12.6 + - + +
186B GLU* 3.1 8.3 + - - +
188B LEU* 1.3 78.5 - - - +
190B ARG* 1.3 57.9 + - - +
191B GLY 3.1 5.2 + - - -
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Residues in contact with ARG 190 (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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127B ILE* 3.7 25.8 - - + +
128B ILE 5.6 4.3 - - - +
186B GLU* 2.9 25.1 + - - +
187B LYS* 3.4 6.2 + - - +
189B ALA* 1.3 74.6 - - - +
191B GLY* 1.3 57.8 + - - +
192B SER* 3.7 2.5 - - - +
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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