Contacts of the helix formed by residues 167 - 181 (chain B) in PDB entry 2BEW
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 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B PHE* 3.4 15.0 - - - -
23B LEU* 3.7 11.7 - - - +
165B PRO 3.6 1.2 - - - -
166B ARG* 1.3 89.5 + - - +
168B PRO* 1.3 67.7 - - - +
169B PHE* 4.4 0.3 - - - +
170B GLN* 3.1 25.3 + - - +
171B ALA* 2.8 30.5 + - - +
193B LEU* 4.8 0.7 - - - -
199B GLU* 3.1 19.2 + - - -
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Residues in contact with PRO 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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6B PHE* 3.7 13.5 - - + -
21B MET 3.5 20.0 - - - +
22B ASN 3.8 8.5 - - - +
23B LEU* 3.5 13.5 - - + +
26B SER* 3.3 17.7 + - - +
167B SER* 1.3 85.6 - - - +
169B PHE* 1.3 65.6 + - - +
171B ALA 3.2 0.3 + - - -
172B LYS* 3.1 21.0 + - - +
197B ALA* 3.2 32.3 - - + +
198B ALA* 4.1 1.6 - - - -
199B GLU* 3.4 10.1 - - + +
201B VAL* 3.8 13.5 - - + -
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Residues in contact with PHE 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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15B TYR* 4.0 21.5 - + - -
167B SER* 4.4 0.9 - - - +
168B PRO* 1.3 74.4 - - - +
170B GLN* 1.3 82.1 + - + +
173B GLY 3.4 6.8 + - - -
199B GLU* 2.8 28.7 + - - +
200B GLU 4.0 11.0 - - - +
201B VAL* 3.7 5.5 - - - +
202B PRO* 3.6 31.9 - - + -
206B TYR* 2.7 49.0 + + - -
208B ILE* 3.8 14.2 - - + +
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Residues in contact with GLN 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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165B PRO* 3.9 3.4 - - + -
166B ARG* 3.7 36.6 - - + +
167B SER* 3.1 27.7 + - - +
168B PRO 3.2 0.4 - - - -
169B PHE* 1.3 95.3 - - + +
171B ALA* 1.3 64.6 + - - +
174B LEU* 2.9 33.0 + - + +
208B ILE* 3.7 10.9 - - - +
214B GLU* 3.3 18.2 + - - -
255B ARG* 3.0 39.0 + - - +
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Residues in contact with ALA 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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23B LEU* 3.9 15.5 - - + -
26B SER* 3.7 15.9 - - - +
27B VAL* 4.7 5.6 - - + -
165B PRO* 3.5 27.8 - - + +
167B SER 2.8 21.9 + - - +
168B PRO 3.2 0.2 + - - -
170B GLN* 1.3 74.5 - - - +
172B LYS* 1.3 58.0 + - - +
175B LEU* 2.9 33.7 + - - +
187B PHE* 3.4 5.6 - - + -
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Residues in contact with LYS 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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26B SER* 3.6 15.6 + - - +
29B SER* 2.8 34.2 + - - +
30B ALA* 4.0 17.9 - - + +
33B ASN* 2.8 27.9 + - - -
168B PRO 3.1 12.6 + - - +
171B ALA* 1.3 76.4 - - - +
173B GLY* 1.3 60.0 + - - +
175B LEU* 3.9 0.9 - - - +
176B LEU* 3.0 42.3 + - + +
201B VAL* 3.7 11.0 - - + -
202B PRO 2.9 19.3 + - - -
203B ILE 3.0 11.1 + - - -
204B GLU 3.5 8.2 + - - -
206B TYR* 3.5 25.1 - - + +
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Residues in contact with GLY 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 PHE 3.4 8.3 + - - -
171B ALA 3.4 0.2 - - - -
172B LYS* 1.3 80.5 - - - +
174B LEU* 1.3 60.6 + - - +
176B LEU* 3.7 0.5 + - - +
177B SER* 3.2 16.1 + - - -
206B TYR* 3.6 31.1 - - - -
207B ASN* 3.8 2.3 - - - -
208B ILE* 3.2 29.3 + - - -
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Residues in contact with LEU 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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163B VAL* 3.9 15.7 - - + -
164B ILE 4.2 3.4 - - - +
165B PRO* 3.8 27.4 - - + -
170B GLN* 2.9 33.3 + - - +
173B GLY* 1.3 75.3 - - - +
175B LEU* 1.3 59.2 + - - +
177B SER* 3.3 2.8 + - - -
178B CYS* 2.9 31.2 + - - -
187B PHE* 3.8 13.9 - - + -
208B ILE* 3.7 36.3 - - + +
209B PRO 3.9 9.6 - - - +
210B LEU* 4.0 13.1 - - + +
255B ARG* 4.3 16.8 - - + -
256B THR* 5.1 0.9 - - - +
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Residues in contact with LEU 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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27B VAL* 3.9 30.3 - - + +
30B ALA* 3.8 19.1 - - + -
31B LEU* 4.3 5.8 - - + -
94B ILE* 5.4 0.2 - - + -
131B THR* 4.2 14.4 - - + -
133B ARG* 4.2 17.7 - - - -
171B ALA 2.9 20.2 + - - +
172B LYS 3.9 2.7 - - - +
174B LEU* 1.3 73.6 - - - +
176B LEU* 1.3 67.5 + - - +
178B CYS* 3.2 1.6 + - + -
179B ILE* 2.9 50.7 + - + +
187B PHE* 3.6 36.5 - - + -
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Residues in contact with LEU 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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30B ALA* 3.6 16.4 - - + +
33B ASN* 4.2 4.9 - - + +
34B SER* 3.2 31.4 - - - +
37B LYS* 4.7 3.4 - - - -
172B LYS* 3.0 36.1 + - + +
173B GLY 4.0 0.2 - - - +
175B LEU* 1.3 76.5 - - - +
177B SER* 1.3 62.6 + - - +
179B ILE* 3.3 3.4 + - + +
180B GLU* 3.0 44.9 + - - +
205B PRO* 3.9 13.5 - - + -
206B TYR 3.3 39.5 - - - +
207B ASN* 3.7 7.6 - - - +
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Residues in contact with SER 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 GLY 3.2 4.9 + - - -
174B LEU 3.6 7.6 - - - -
175B LEU 3.2 0.2 - - - -
176B LEU* 1.3 75.2 - - - +
178B CYS* 1.3 59.1 + - - +
180B GLU* 3.8 2.3 - - - +
181B ASP* 2.9 31.8 + - - +
207B ASN* 3.3 26.7 + - - +
208B ILE 2.6 29.2 + - - -
209B PRO* 4.5 1.8 - - - +
210B LEU* 3.7 17.4 - - - +
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Residues in contact with CYS 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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131B THR* 3.2 14.7 + - + -
163B VAL* 3.8 36.1 - - - -
174B LEU 2.9 18.2 + - - +
175B LEU* 3.2 10.7 + - + +
177B SER* 1.3 76.3 - - - +
179B ILE* 1.3 61.4 + - - +
180B GLU 3.3 0.5 + - - -
181B ASP* 3.3 6.3 + - - +
185B CYS* 3.9 29.8 - - + -
186B ILE 5.0 0.2 - - - -
187B PHE* 4.0 13.5 - - + -
210B LEU* 4.2 3.8 - - - -
1343B K 2.8 24.9 - - - -
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Residues in contact with ILE 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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30B ALA 4.6 2.9 - - - +
31B LEU* 4.2 8.7 - - + -
34B SER* 3.4 31.2 - - - +
38B ASP* 5.6 1.3 - - - +
92B THR* 3.8 32.0 + - + +
94B ILE* 3.9 24.0 - - + -
129B SER* 4.9 6.4 - - - +
131B THR* 3.4 14.4 + - + +
175B LEU* 2.9 46.0 + - + +
176B LEU* 3.3 6.0 + - - +
178B CYS* 1.3 76.4 - - - +
180B GLU* 1.3 66.0 + - + +
181B ASP 3.8 1.4 + - - +
1343B K 3.9 5.7 - - - -
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Residues in contact with GLU 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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34B SER* 5.3 0.2 + - - -
37B LYS* 3.1 36.8 - - - +
176B LEU* 3.0 28.6 + - - +
177B SER* 4.2 2.9 - - - +
179B ILE* 1.3 83.1 - - + +
181B ASP* 1.3 65.4 + - - +
182B LYS* 3.7 17.5 + - - +
205B PRO* 5.6 0.5 - - - +
207B ASN* 2.9 27.1 + - - +
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Residues in contact with ASP 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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370A GLU* 5.2 0.5 - - - +
128B GLY 3.1 4.7 - - - +
129B SER* 4.8 1.0 - - - -
161B LYS* 2.9 26.8 + - - +
177B SER 2.9 18.1 + - - +
178B CYS 3.3 7.8 + - - +
179B ILE 4.1 1.2 - - - +
180B GLU* 1.3 80.4 - - - +
182B LYS* 1.3 62.3 + - - +
183B ASN* 2.9 38.2 + - - +
185B CYS* 4.1 7.4 - - - -
210B LEU* 3.8 14.8 - - + +
1343B K 2.9 20.1 - - - -
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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