Contacts of the helix formed by residues 177 - 190 (chain B) in PDB entry 2CMG
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 GLU 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ILE 4.3 7.4 - - - +
8B THR* 5.7 1.4 - - - -
172B LYS* 4.0 20.6 + - + +
173B HIS 2.9 17.1 + - - +
176B LEU* 1.3 88.5 - - + +
178B HIS* 1.3 65.2 + - - +
179B VAL* 3.1 4.7 - - + +
180B SER* 3.0 25.3 + - - +
181B MET* 3.0 9.5 + - - +
207B ASN* 3.4 33.6 + - - +
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Residues in contact with HIS 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 PRO 2.9 23.6 + - - +
175B LEU 4.0 7.4 + - - +
176B LEU 3.9 1.5 - - - -
177B GLU* 1.3 74.9 - - - +
179B VAL* 1.3 80.8 + - + +
181B MET* 4.3 0.7 - - - -
182B GLN* 2.7 34.6 + - - +
252B LEU* 3.6 19.5 - - + -
255B VAL* 3.7 26.9 - - + +
256B PHE* 3.1 17.8 - - + -
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Residues in contact with VAL 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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177B GLU* 3.0 1.7 + - - -
178B HIS* 1.3 109.4 - - + +
180B SER* 1.3 63.8 + - - +
182B GLN* 3.0 11.8 + - - +
183B ASN* 3.0 22.6 + - + +
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Residues in contact with SER 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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148B GLU* 4.0 12.5 + - - +
171B ALA* 5.7 0.2 - - - +
172B LYS* 3.1 25.7 + - - +
177B GLU* 3.0 29.6 + - - +
179B VAL* 1.3 80.9 - - - +
181B MET* 1.3 58.8 + - - +
183B ASN* 3.4 8.1 + - - +
184B ALA* 3.0 25.6 + - - +
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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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171B ALA* 3.4 26.2 - - + -
172B LYS* 3.2 27.7 - - - +
174B PRO* 3.8 22.4 - - + -
177B GLU 3.0 12.1 + - - +
178B HIS 3.7 6.3 - - - +
180B SER* 1.3 73.6 - - - +
182B GLN* 1.3 61.6 + - - +
184B ALA* 4.0 5.4 - - - -
185B LEU* 3.0 39.1 + - + +
197B PRO* 3.8 19.3 - - + -
198B PHE 5.1 0.7 - - - +
209B GLY* 4.1 1.3 - - - -
210B TYR 3.8 24.2 - - - +
211B ILE* 4.1 3.6 - - - -
256B PHE* 3.8 20.2 - - + -
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Residues in contact with GLN 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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178B HIS* 2.7 19.7 + - - +
179B VAL* 3.2 13.3 - - - +
181B MET* 1.3 78.6 - - - +
183B ASN* 1.3 56.2 + - - +
185B LEU* 3.2 6.3 + - - +
186B LYS* 2.9 35.0 + - - +
255B VAL* 3.0 39.0 + - - +
256B PHE* 3.8 11.0 - - + -
259B ASN* 3.2 29.3 + - - +
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Residues in contact with ASN 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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148B GLU* 5.5 4.6 + - - -
179B VAL* 3.0 12.4 + - + +
180B SER* 3.7 10.9 + - - +
182B GLN* 1.3 74.2 - - - +
184B ALA* 1.3 65.1 + - - +
186B LYS* 3.8 13.4 - - - +
187B ASN* 3.2 41.3 + - - -
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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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148B GLU* 4.7 13.7 + - + +
154B ILE* 5.5 0.2 - - - +
171B ALA* 4.0 26.5 - - + -
180B SER 3.0 13.3 + - - +
181B MET* 3.4 13.7 - - - +
183B ASN* 1.3 79.8 - - - +
185B LEU* 1.3 63.2 + - - +
187B ASN* 3.4 7.5 + - - +
188B MET* 3.2 27.0 + - + +
211B ILE* 4.4 6.3 - - + -
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Residues in contact with LEU 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 MET* 3.0 32.7 + - + +
182B GLN 3.6 3.8 - - - +
184B ALA* 1.3 74.1 - - - +
186B LYS* 1.3 60.1 + - - +
188B MET* 3.2 4.4 + - - +
189B GLY* 2.8 28.8 + - - -
195B ALA* 4.0 16.9 - - + +
197B PRO* 3.9 38.8 - - + -
211B ILE* 4.1 26.5 - - + -
256B PHE* 4.2 20.6 - - + -
259B ASN* 3.6 23.5 - - + +
260B ILE* 4.3 9.2 - - + -
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Residues in contact with LYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B GLN* 2.9 23.5 + - - +
183B ASN* 3.8 15.0 - - - +
184B ALA 3.3 0.2 - - - -
185B LEU* 1.3 78.0 - - - +
187B ASN* 1.3 70.8 + - - +
189B GLY* 3.3 7.0 + - - -
190B GLY* 3.4 8.0 + - - -
259B ASN* 4.2 22.1 + - - +
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Residues in contact with ASN 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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149B PRO 4.7 4.9 - - - +
150B ASP* 5.0 0.9 - - - -
151B ILE* 3.5 31.6 + - + +
154B ILE* 3.4 27.7 - - + +
183B ASN* 3.2 32.3 + - - +
184B ALA* 3.7 8.2 - - - +
186B LYS* 1.3 80.9 - - - +
188B MET* 1.3 63.5 + - - +
190B GLY* 3.0 17.0 + - - -
191B VAL* 4.3 4.9 + - - +
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Residues in contact with MET 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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149B PRO* 5.7 1.3 - - + -
154B ILE* 4.4 12.8 - - + +
167B PHE* 3.5 27.1 - - + +
169B SER* 3.5 24.7 - - - +
184B ALA 3.2 13.3 + - - +
185B LEU* 3.5 8.5 - - - +
187B ASN* 1.3 78.2 - - - +
189B GLY* 1.3 63.3 + - - +
190B GLY 3.4 0.3 + - - -
191B VAL* 3.4 3.9 + - - +
192B PHE* 3.3 47.3 + - + +
195B ALA* 4.1 15.9 - - + -
211B ILE* 3.5 23.1 - - + +
213B ALA* 3.1 27.1 - - + -
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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 LEU 2.8 18.5 + - - -
186B LYS* 3.3 3.1 + - - -
187B ASN 3.2 0.6 + - - -
188B MET* 1.3 73.2 - - - +
190B GLY* 1.3 52.6 + - - +
191B VAL* 2.7 12.8 + - - -
192B PHE 3.1 8.1 + - - +
195B ALA* 4.4 5.8 - - - +
259B ASN 5.5 1.6 - - - -
261B LYS* 2.6 45.2 + - - -
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Residues in contact with GLY 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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186B LYS 3.4 7.7 + - - -
187B ASN 3.0 12.6 + - - -
189B GLY* 1.3 73.6 - - - +
191B VAL* 1.3 65.9 + - - +
261B LYS* 4.9 0.9 - - - -
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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