Contacts of the helix formed by residues 167 - 182 (chain B) in PDB entry 3EQR
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 GLN 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162B PRO* 3.4 33.0 - - + +
163B ASP 3.1 12.6 + - - +
164B VAL 3.5 3.7 - - - +
166B SER* 1.3 84.2 - - - +
168B PRO* 1.3 66.8 - - - +
169B GLU* 3.2 2.5 - - + +
170B ALA* 3.3 24.2 + - + +
171B MET* 3.3 17.3 + - - +
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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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164B VAL* 3.2 20.6 - - + +
165B LEU 4.1 5.4 - - - +
166B SER 3.8 7.6 - - - +
167B GLN* 1.3 86.2 - - - +
169B GLU* 1.3 60.5 + - + +
171B MET* 3.3 7.1 + - + +
172B ASP* 2.9 28.1 + - - +
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Residues in contact with GLU 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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167B GLN* 3.2 2.1 - - + -
168B PRO* 1.3 80.1 - - + +
170B ALA* 1.3 63.9 - - - +
172B ASP* 3.5 10.7 + - + +
173B ASP* 3.1 23.7 + - - +
176B ARG* 5.4 0.3 + - - -
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Residues in contact with ALA 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 PHE* 4.9 4.0 - - + +
160B LEU* 3.8 26.1 - - + +
162B PRO* 4.3 5.8 - - + +
167B GLN* 3.3 35.8 + - + +
169B GLU* 1.3 76.5 - - - +
171B MET* 1.3 58.5 + - - +
173B ASP* 3.5 7.6 + - - +
174B PHE* 3.1 26.9 + - - +
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Residues in contact with MET 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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160B LEU* 3.6 17.4 - - + +
162B PRO 5.0 0.7 - - - +
163B ASP* 4.7 1.8 - - - -
164B VAL* 3.8 47.6 - - + +
167B GLN 3.3 10.3 + - - +
168B PRO 3.5 8.7 - - - +
169B GLU 3.2 0.4 - - - -
170B ALA* 1.3 76.4 - - - +
172B ASP* 1.3 64.4 + - - +
174B PHE* 3.1 9.2 + - - +
175B ILE* 2.9 43.9 + - + +
201B MET* 3.3 39.5 - - - +
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Residues in contact with ASP 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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168B PRO 2.9 17.0 + - - +
169B GLU* 3.5 13.4 - - + +
171B MET* 1.3 75.7 - - - +
173B ASP* 1.3 56.6 + - - +
175B ILE* 3.6 6.8 + - - +
176B ARG* 2.4 66.0 + - - +
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Residues in contact with ASP 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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136B SER* 4.4 9.9 - - - -
137B PHE* 3.7 26.3 + - - +
169B GLU 3.1 17.6 + - - +
170B ALA* 3.7 7.9 - - - +
171B MET 3.2 0.2 - - - -
172B ASP* 1.3 75.2 - - - +
174B PHE* 1.3 63.1 + - - +
176B ARG* 3.5 13.2 + - - +
177B GLU* 3.2 24.2 + - - +
272B GLY 4.0 15.2 - - - +
275B ARG* 5.0 2.9 + - - -
290B ARG* 3.6 26.3 + - - +
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Residues in contact with PHE 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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137B PHE* 3.5 36.3 - + + -
160B LEU* 3.9 18.6 - - + -
170B ALA 3.1 13.5 + - - +
171B MET* 3.4 9.9 - - - +
173B ASP* 1.3 75.4 + - - +
175B ILE* 1.3 71.4 + - + +
177B GLU* 3.3 4.2 + - - +
178B VAL* 3.0 49.9 + - + +
195B VAL* 4.8 1.3 - - + -
196B VAL 4.5 1.1 - - - -
197B LEU* 4.3 8.1 - - + -
201B MET* 3.3 39.7 - - + -
202B LYS* 3.6 32.3 - - - -
203B MET* 3.7 16.1 - - + +
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Residues in contact with ILE 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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171B MET* 2.9 37.0 + - + +
172B ASP* 3.8 7.0 - - - +
174B PHE* 1.3 90.9 - - + +
176B ARG* 1.3 66.7 + - - +
178B VAL* 3.2 7.7 + - + +
179B ASN* 2.9 42.5 + - - +
197B LEU* 5.6 3.4 - - + -
201B MET* 5.0 4.5 - - + -
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Residues in contact with ARG 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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169B GLU 5.4 0.4 + - - -
172B ASP* 2.4 61.0 + - - +
173B ASP* 3.8 13.7 + - - +
174B PHE 3.4 0.2 - - - -
175B ILE* 1.3 78.2 - - - +
177B GLU* 1.3 56.8 + - - +
179B ASN* 3.4 6.0 + - - +
180B ALA* 2.9 31.4 + - + +
274B MET 5.3 3.1 - - - +
275B ARG* 3.6 52.8 - - - +
284B TYR* 5.4 1.1 - - - -
290B ARG* 5.4 4.0 - - - +
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Residues in contact with GLU 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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1B T74 3.3 16.1 - - - -
136B SER* 2.7 26.9 + - - -
137B PHE* 3.6 13.3 - - + -
158B LYS* 2.7 25.5 + - - -
173B ASP* 3.2 17.6 + - - +
174B PHE 3.7 3.6 - - - +
176B ARG* 1.3 73.1 - - - +
178B VAL* 1.3 65.4 + - - +
180B ALA* 3.4 4.9 + - - +
181B MET* 3.0 26.5 + - - +
203B MET* 4.0 11.4 - - + -
271B PHE* 3.9 22.4 + - + +
272B GLY* 3.4 18.2 + - - +
274B MET 6.0 0.2 - - - -
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Residues in contact with VAL 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 THR* 6.2 0.7 - - + -
174B PHE* 3.0 33.9 + - + +
175B ILE* 3.6 12.1 - - + +
177B GLU* 1.3 75.4 - - - +
179B ASN* 1.3 67.9 + - - +
181B MET 3.3 0.7 + - - -
182B HIS* 2.8 31.8 + - + +
192B LEU* 3.8 6.8 - - + +
195B VAL* 3.8 28.5 - - + -
203B MET* 3.7 32.3 - - + -
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Residues in contact with ASN 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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175B ILE* 2.9 40.0 + - - +
176B ARG* 3.8 5.8 - - - +
178B VAL* 1.3 81.9 - - - +
180B ALA* 1.3 66.0 + - - +
182B HIS* 3.5 20.2 + - - +
248B PHE* 4.8 4.0 - - - -
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Residues in contact with ALA 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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176B ARG 2.9 17.6 + - - +
177B GLU* 3.8 7.2 - - - +
178B VAL 3.3 0.2 - - - -
179B ASN* 1.3 78.9 - - - +
181B MET* 1.3 61.6 + - + +
182B HIS 4.5 0.9 - - - +
184B LEU* 3.4 20.1 - - - +
248B PHE* 3.6 31.1 - - + -
271B PHE 5.1 1.6 - - - +
274B MET* 3.9 34.4 - - + +
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Residues in contact with MET 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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1B T74 3.7 13.0 - - + -
177B GLU* 3.0 17.5 + - - +
178B VAL 4.0 2.7 - - - +
180B ALA* 1.3 76.0 - - + +
182B HIS* 1.3 67.4 + - - +
183B SER 3.1 1.0 + - - -
184B LEU* 2.9 28.1 + - + +
190B ILE 3.4 26.5 - - - +
192B LEU* 4.0 33.4 + - + +
203B MET* 3.6 24.0 - - - -
205B THR* 4.0 13.9 - - + -
271B PHE* 3.6 44.9 - - + -
274B MET* 4.9 0.2 - - + -
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Residues in contact with HIS 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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118B THR* 3.3 37.0 + - + +
178B VAL* 2.8 21.7 + - + +
179B ASN* 3.8 17.5 - - - +
180B ALA 3.5 3.3 - - - +
181B MET* 1.3 74.4 - - - +
183B SER* 1.3 80.0 + - - +
184B LEU* 3.2 6.9 + - - +
192B LEU* 4.1 10.3 - - + +
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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