Contacts of the helix formed by residues 163 - 178 (chain B) in PDB entry 3EBL
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 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ARG 3.9 0.7 - - - +
162B TYR* 1.3 114.0 - - + +
164B CYS* 1.3 69.5 + - - +
165B ALA 3.3 2.9 - - - -
166B TYR* 3.0 11.7 + - + +
167B ASP* 2.9 38.7 + - - +
258B TYR* 3.9 2.7 - - - +
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Residues in contact with CYS 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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155B ARG* 3.6 39.2 + - + +
160B HIS* 4.0 28.0 - - + +
161B ARG 3.1 20.6 + - - +
163B PRO* 1.3 80.2 - - - +
165B ALA* 1.3 63.2 + - - +
167B ASP* 3.2 8.2 + - - +
168B ASP* 2.9 29.0 + - - -
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Residues in contact with ALA 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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124B PHE* 4.6 2.5 - - + -
154B TYR* 3.8 29.3 - - + +
155B ARG 3.9 11.3 + - - +
160B HIS 5.7 0.2 + - - -
163B PRO 3.3 1.0 - - - -
164B CYS* 1.3 78.2 - - - +
166B TYR* 1.3 58.1 + - - +
168B ASP* 3.2 8.9 + - - +
169B GLY* 3.0 23.6 + - - -
203B ILE* 3.9 21.2 - - + +
258B TYR* 4.0 23.0 + - + +
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Residues in contact with TYR 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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124B PHE* 4.3 0.8 - + - -
162B TYR* 3.5 31.6 - + - -
163B PRO* 3.0 10.8 + - + +
165B ALA* 1.3 72.7 - - - +
167B ASP* 1.3 68.1 + - - +
169B GLY* 3.1 2.1 + - - +
170B TRP* 3.0 22.5 + - - +
202B ASN* 2.5 30.9 + - - -
203B ILE* 3.9 29.8 - - + -
206B HIS* 3.2 42.5 - + + -
207B VAL* 4.0 6.3 - - + +
210B ARG* 5.1 1.5 + - - -
258B TYR* 3.3 28.3 - + - -
269B ALA* 3.3 20.1 + - + +
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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
----------------------------------------------------------
155B ARG* 4.2 11.7 + - - +
163B PRO* 2.9 37.5 + - - +
164B CYS* 3.2 12.7 + - - +
166B TYR* 1.3 76.4 - - - +
168B ASP* 1.3 57.3 + - - +
170B TRP* 3.2 8.9 + - - +
171B THR* 2.9 32.7 + - - +
210B ARG* 4.4 12.0 + - - +
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Residues in contact with ASP 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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74B VAL* 3.8 15.0 - - - +
76B LEU* 3.6 31.4 - - + +
152B VAL* 4.3 3.3 - - + +
154B TYR* 4.0 9.3 - - + +
155B ARG* 2.8 59.0 + - - +
164B CYS 2.9 14.5 + - - +
165B ALA 3.5 7.4 - - - +
167B ASP* 1.3 76.5 - - - +
169B GLY* 1.3 58.4 + - - +
171B THR* 3.5 4.9 + - - -
172B ALA* 3.0 27.2 + - - +
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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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117B ILE* 5.5 0.2 - - - +
119B PHE* 3.4 33.0 - - - -
165B ALA 3.0 12.5 + - - -
166B TYR 3.1 3.5 + - - -
168B ASP* 1.3 75.8 - - - +
170B TRP* 1.3 58.3 + - - +
172B ALA* 3.3 2.8 + - - +
173B LEU* 3.0 27.7 + - - +
203B ILE* 4.6 0.2 - - - -
207B VAL* 3.6 16.3 - - - +
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Residues in contact with TRP 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 TYR 3.0 10.9 + - - +
167B ASP 3.6 7.4 - - - +
169B GLY* 1.3 74.0 - - - +
171B THR* 1.3 67.7 + - - +
173B LEU* 3.1 25.6 + - + +
174B LYS* 2.9 61.1 + - + +
207B VAL* 3.8 9.5 - - + +
210B ARG* 3.2 65.8 - - + +
211B ALA* 3.5 34.5 - - - -
214B GLU* 3.5 24.6 + - + -
216B VAL* 4.1 18.2 - - + -
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Residues in contact with THR 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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70B ILE* 4.4 10.3 - - + +
71B ASP* 4.1 27.8 + - + +
76B LEU* 3.8 20.6 - - + -
167B ASP* 2.9 18.5 + - - +
168B ASP* 3.6 9.9 + - - -
170B TRP* 1.3 78.6 - - - +
172B ALA* 1.3 57.7 + - - +
174B LYS* 3.7 6.3 + - - +
175B TRP* 2.9 27.9 + - + +
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Residues in contact with ALA 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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70B ILE* 3.7 19.7 - - + -
78B VAL* 4.8 1.6 - - + -
117B ILE* 4.5 6.1 - - + -
150B VAL* 5.5 2.0 - - + -
152B VAL* 3.5 32.5 - - + -
168B ASP 3.0 18.3 + - - +
169B GLY* 3.6 5.8 - - - +
170B TRP 3.1 0.2 - - - -
171B THR* 1.3 74.2 - - - +
173B LEU* 1.3 61.7 + - - +
175B TRP* 3.4 1.9 + - - +
176B VAL* 2.9 34.8 + - - +
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Residues in contact with LEU 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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117B ILE* 3.8 13.8 - - + +
169B GLY 3.0 14.2 + - - +
170B TRP* 3.1 33.8 + - + +
172B ALA* 1.3 75.2 - - - +
174B LYS* 1.3 53.5 + - + +
176B VAL* 3.0 4.5 + - - +
177B MET* 2.7 53.8 + - + +
192B VAL* 3.7 31.0 - - + -
194B LEU* 4.3 3.4 - - + -
207B VAL* 3.8 19.1 - - + -
211B ALA* 3.9 16.8 - - + -
216B VAL* 4.2 10.5 - - + -
218B VAL* 4.5 7.2 - - + -
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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 TRP* 2.9 64.1 + - + +
171B THR* 4.0 5.6 - - - +
173B LEU* 1.3 76.2 - - + +
175B TRP* 1.3 57.9 + - - +
177B MET* 3.1 11.2 + - + +
178B SER* 2.8 32.0 + - - -
216B VAL* 6.2 1.6 - - + -
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Residues in contact with TRP 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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68B HIS* 3.7 26.2 + + - -
70B ILE* 3.6 45.3 - - + +
78B VAL* 4.5 8.5 - - + -
80B ILE* 3.8 26.0 - - + -
104B LEU* 5.5 7.4 - - + -
150B VAL* 4.6 4.7 - - + -
171B THR* 2.9 20.9 + - + +
172B ALA 3.7 4.0 - - - +
173B LEU 3.2 0.2 - - - -
174B LYS* 1.3 76.6 - - - +
176B VAL* 1.3 91.4 + - + +
178B SER* 3.3 14.8 + - - -
179B GLN* 3.0 55.7 - - + +
182B MET* 4.1 18.6 - - + -
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Residues in contact with VAL 176 (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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115B VAL* 3.5 26.0 - - + -
117B ILE* 3.8 22.4 - - + -
150B VAL* 4.1 16.6 - - + -
172B ALA 2.9 21.3 + - - +
173B LEU 3.6 6.1 - - - +
175B TRP* 1.3 92.5 - - + +
177B MET* 1.3 64.0 + - - +
179B GLN* 3.2 18.9 + - - +
182B MET* 3.7 22.3 - - + +
190B ALA* 4.4 2.0 - - + +
192B VAL* 4.0 15.5 - - + -
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Residues in contact with MET 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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173B LEU* 2.7 29.5 + - + +
174B LYS* 3.3 13.0 - - + +
176B VAL* 1.3 72.5 - - - +
178B SER* 1.3 57.0 + - - +
179B GLN 3.1 6.4 + - - +
183B ARG* 3.3 21.1 + - - +
189B GLN* 6.5 0.2 - - - -
190B ALA* 4.3 15.9 - - - +
192B VAL* 3.8 28.3 - - + -
216B VAL* 3.4 29.6 - - + -
217B LYS* 3.4 27.6 - - + +
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Residues in contact with SER 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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174B LYS 2.8 16.8 + - - -
175B TRP* 3.3 16.1 + - - -
176B VAL 3.2 0.8 - - - -
177B MET* 1.3 71.8 - - - +
179B GLN* 1.3 71.0 + - - -
180B PRO* 3.7 7.5 - - - +
183B ARG* 4.4 7.1 + - - +
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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