Contacts of the helix formed by residues 177 - 190 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ILE 5.2 6.6 - - - +
172A LYS* 3.1 48.8 + - + +
173A HIS 3.0 19.8 + - - +
176A LEU* 1.3 90.1 - - + +
178A HIS* 1.3 64.0 + - - +
179A VAL* 3.2 3.6 - - - -
180A SER* 3.2 18.0 + - - -
181A MET* 3.3 10.4 + - - +
207A ASN* 3.9 12.6 + - - +
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Residues in contact with HIS 178 (chain A).
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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174A PRO* 3.3 24.6 + - - +
175A LEU 5.4 2.4 + - - -
176A LEU 3.9 2.4 + - - -
177A GLU* 1.3 73.5 + - - +
179A VAL* 1.3 88.0 + - + +
181A MET* 3.4 0.6 + - - -
182A GLN* 2.8 32.4 + - - +
252A LEU* 3.7 20.4 - - + -
255A VAL* 4.2 29.4 - - + +
256A PHE* 3.3 9.6 - - + -
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLU* 3.2 1.7 - - - -
178A HIS* 1.3 102.8 - - + +
180A SER* 1.3 66.5 + - - +
182A GLN* 2.9 25.2 + - - +
183A ASN* 2.9 14.7 + - + +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU* 4.2 12.6 + - - +
172A LYS* 3.1 35.1 + - - +
177A GLU* 3.2 21.1 + - - +
179A VAL* 1.3 79.2 - - - +
181A MET* 1.3 57.1 + - - +
183A ASN* 3.0 10.1 + - - +
184A ALA* 2.9 27.1 + - - +
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Residues in contact with MET 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ALA* 4.0 12.3 - - + -
172A LYS* 3.5 27.9 - - - +
174A PRO* 4.0 26.0 - - + -
177A GLU 3.3 5.5 + - - +
178A HIS 3.7 6.5 - - - +
179A VAL 3.3 0.2 - - - -
180A SER* 1.3 80.2 + - - +
182A GLN* 1.3 58.0 + - - +
184A ALA* 3.4 4.2 + - - -
185A LEU* 2.9 41.3 + - + +
197A PRO* 3.8 20.6 - - + -
198A PHE 5.0 2.0 - - - +
199A VAL* 5.8 0.4 - - + -
209A GLY* 4.5 0.2 - - - -
210A TYR 3.7 24.2 - - - +
211A ILE* 4.0 13.2 - - - -
256A PHE* 3.5 24.0 - - + -
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Residues in contact with GLN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A HIS* 2.8 24.0 + - - +
179A VAL* 2.9 15.6 + - - +
181A MET* 1.3 74.0 - - - +
183A ASN* 1.3 58.6 + - - +
185A LEU* 3.4 5.1 + - - +
186A LYS* 3.0 26.1 + - + +
255A VAL* 3.3 39.8 + - - +
256A PHE* 3.6 14.6 - - + -
259A ASN* 3.4 22.6 - - - +
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Residues in contact with ASN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU* 4.9 8.1 + - - -
179A VAL* 2.9 12.2 + - + +
180A SER* 3.4 9.6 + - - +
182A GLN* 1.3 74.8 - - - +
184A ALA* 1.3 58.7 + - - +
186A LYS* 2.7 39.8 + - - +
187A ASN* 2.8 40.2 + - - -
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU* 4.2 19.3 - - + +
171A ALA* 4.1 15.0 - - + -
180A SER 2.9 12.6 + - - +
181A MET* 3.6 7.4 - - - +
183A ASN* 1.3 77.1 - - - +
185A LEU* 1.3 60.4 + - - +
187A ASN* 3.5 9.9 + - - +
188A MET* 3.2 28.8 + - - +
211A ILE* 3.4 22.4 - - + -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A MET* 2.9 42.6 + - + +
182A GLN 3.7 4.5 - - - +
184A ALA* 1.3 74.1 - - - +
186A LYS* 1.3 59.9 + - - +
188A MET* 3.7 2.8 - - - +
189A GLY* 2.9 26.9 + - - -
195A ALA* 3.7 26.3 - - + +
197A PRO* 4.0 25.1 - - + -
211A ILE* 3.9 28.3 - - + -
256A PHE* 4.2 20.6 - - + -
259A ASN* 3.9 22.4 - - + +
260A ILE* 4.2 6.1 - - + -
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Residues in contact with LYS 186 (chain A).
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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182A GLN* 3.0 15.4 + - + +
183A ASN* 2.7 31.8 + - - +
185A LEU* 1.3 69.8 - - - +
187A ASN* 1.3 73.2 + - - +
189A GLY* 3.3 9.1 + - - -
190A GLY* 3.3 12.0 + - - -
259A ASN* 4.4 17.2 - - - +
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Residues in contact with ASN 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLU* 5.7 0.5 - - - +
149A PRO 5.0 3.7 - - - +
150A ASP* 5.5 1.0 - - - -
151A ILE* 4.0 27.5 + - + +
154A ILE* 3.6 28.0 - - + +
183A ASN* 2.8 45.6 + - - +
184A ALA* 3.9 7.3 - - - +
186A LYS* 1.3 85.4 - - - +
188A MET* 1.3 59.9 + - - +
189A GLY 3.6 0.2 + - - -
190A GLY* 4.0 5.4 + - - -
191A VAL* 4.1 15.6 - - - +
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Residues in contact with MET 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO* 5.3 3.6 - - + -
154A ILE* 4.4 15.5 - - + -
167A PHE* 3.2 35.9 - - + +
169A SER* 3.0 27.1 - - - +
184A ALA 3.2 20.6 + - - +
185A LEU 3.9 4.0 - - - +
186A LYS 3.2 0.2 - - - -
187A ASN* 1.3 77.2 - - - +
189A GLY* 1.3 58.4 + - - +
192A PHE* 3.0 57.0 + - + +
195A ALA* 4.1 14.4 - - + +
211A ILE* 4.1 17.9 - - + -
213A ALA* 3.9 13.2 - - + -
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Residues in contact with GLY 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU 2.9 16.6 + - - -
186A LYS* 3.3 2.6 + - - -
188A MET* 1.3 74.3 - - - +
190A GLY* 1.3 55.0 + - - +
191A VAL 2.7 16.6 + - - -
192A PHE 2.9 22.6 + - - +
195A ALA* 4.3 8.3 - - - -
259A ASN* 4.8 4.0 - - - -
261A LYS* 2.9 22.0 + - - -
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Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A LYS 3.3 12.7 + - - -
187A ASN 4.0 1.9 + - - -
188A MET 3.6 0.2 - - - -
189A GLY* 1.3 73.6 - - - +
191A VAL* 1.3 64.5 + - - +
261A LYS* 5.2 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