Contacts of the helix formed by residues 177 - 188 (chain A) in PDB entry 3CUQ
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 ASN 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ALA* 5.5 0.2 - - - +
175A GLU* 3.3 29.3 + - - +
176A LEU* 1.3 73.0 - - - +
178A MET* 1.3 57.6 + - - +
179A ASP* 2.9 13.0 - - + +
180A HIS* 2.7 67.3 + - - +
181A THR* 3.4 4.7 + - - -
212A VAL* 4.8 6.8 - - - +
215A HIS* 4.6 20.0 - - - +
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Residues in contact with MET 178 (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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176A LEU* 2.7 10.8 + - + +
177A ASN* 1.3 71.9 - - - +
179A ASP* 1.3 65.9 + - - +
181A THR* 3.2 11.7 + - - +
182A VAL* 3.0 37.5 + - + +
208A ARG* 5.9 0.7 - - - +
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Residues in contact with ASP 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 ASN* 4.3 10.3 - - + -
178A MET* 1.3 86.5 - - - +
180A HIS* 1.3 58.7 + - - +
182A VAL* 4.6 0.9 - - - +
183A VAL* 3.3 29.5 + - - +
204A TRP* 3.0 22.7 - - + -
208A ARG* 2.7 47.2 + - - +
212A VAL* 3.8 16.5 - - + +
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Residues in contact with HIS 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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161A ILE* 5.3 2.1 - - + +
170A GLN* 4.3 10.4 + - - -
174A ALA* 5.0 11.1 - - + +
175A GLU 5.5 1.6 - - - +
177A ASN* 2.7 51.9 + - - +
179A ASP* 1.3 72.7 - - - +
181A THR* 1.3 64.7 + - - +
183A VAL* 3.5 1.0 + - - +
184A LEU* 3.1 50.2 + - + +
212A VAL* 4.1 9.2 - - + -
215A HIS* 4.4 18.0 - + + -
216A LEU* 3.7 25.7 - - + +
219A GLU* 5.9 0.2 - - - +
221A LEU* 3.9 17.4 - - + +
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Residues in contact with THR 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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161A ILE* 4.4 21.8 - - + +
162A PRO* 5.3 4.3 - - + -
176A LEU 5.3 1.0 + - - -
177A ASN 3.4 4.6 + - - -
178A MET* 3.2 14.2 + - - +
180A HIS* 1.3 81.5 + - - +
182A VAL* 1.3 65.9 + - + +
183A VAL 3.0 0.7 + - - -
184A LEU* 3.1 11.0 + - - +
185A GLN* 3.0 48.0 + - + +
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Residues in contact with VAL 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 MET* 3.0 25.3 + - + +
179A ASP* 4.2 3.8 - - - +
180A HIS 3.3 0.2 - - - -
181A THR* 1.3 79.1 - - + +
183A VAL* 1.3 61.0 + - - +
185A GLN* 3.2 23.0 + - - +
186A LEU* 3.1 19.2 + - - +
202A LEU* 3.3 44.2 - - + -
204A TRP* 4.2 12.8 - - + -
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Residues in contact with VAL 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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179A ASP 3.3 18.4 + - - +
180A HIS 4.1 2.9 - - - +
181A THR 3.1 0.6 - - - -
182A VAL* 1.3 74.1 - - + +
184A LEU* 1.3 70.1 + - - +
185A GLN 2.9 0.9 - - - -
186A LEU* 2.7 17.5 + - - +
187A ALA* 2.7 14.0 + - + +
193A VAL* 4.0 24.0 - - + -
198A ILE* 4.1 15.9 - - + -
202A LEU* 5.0 1.6 - - + -
204A TRP* 3.9 20.6 - - + -
209A ALA 6.0 0.4 - - - +
212A VAL* 3.9 18.2 - - + -
213A LEU* 4.8 2.7 - - + -
216A LEU* 4.2 22.7 - - + -
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Residues in contact with LEU 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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118A LEU* 4.1 22.7 - - + -
161A ILE* 3.7 32.1 - - + -
163A VAL* 4.3 3.4 - - - +
168A LEU* 4.5 12.8 - - + +
180A HIS* 3.1 44.5 + - + +
181A THR* 3.1 9.8 + - - +
183A VAL* 1.3 79.3 - - - +
185A GLN* 1.3 62.0 + - - +
187A ALA* 3.2 5.4 + - + +
188A GLU* 3.1 21.8 + - - +
216A LEU* 4.5 9.2 - - + -
221A LEU* 5.5 0.7 - - + -
236A LEU* 3.3 33.4 - - + -
239A LEU* 5.5 0.5 - - - +
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Residues in contact with GLN 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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161A ILE* 5.1 0.7 - - + -
162A PRO* 3.0 32.2 - - - +
163A VAL* 4.0 17.7 - - + +
164A GLY 5.5 0.9 - - - +
181A THR* 3.0 39.5 + - + +
182A VAL* 3.5 22.5 - - - +
183A VAL 2.9 3.2 + - - -
184A LEU* 1.3 75.9 - - + +
186A LEU* 1.3 63.3 + - - +
188A GLU* 3.6 12.8 + - - +
189A LYS* 4.5 2.3 + - - +
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Residues in contact with LEU 186 (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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182A VAL 3.1 11.7 + - - +
183A VAL* 2.7 10.9 + - - +
185A GLN* 1.3 76.2 - - - +
187A ALA* 1.3 63.2 + - - +
188A GLU 3.0 2.5 + - - -
189A LYS* 3.5 14.3 + - + +
190A ASN* 4.8 1.9 + - - +
192A TYR 4.5 1.2 - - - +
193A VAL* 3.5 21.8 - - + -
197A GLU* 3.3 40.6 - - + +
198A ILE* 3.9 20.9 - - + -
201A SER* 4.3 15.7 - - - +
202A LEU* 4.1 15.9 - - + -
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Residues in contact with ALA 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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183A VAL* 2.7 17.0 + - + +
184A LEU* 3.3 14.6 - - - +
186A LEU* 1.3 72.5 - - - +
188A GLU* 1.3 64.1 + - - +
189A LYS 2.9 2.3 + - - -
190A ASN 3.1 2.4 + - - -
191A GLY* 2.9 23.4 + - - -
192A TYR 3.5 15.4 - - - +
193A VAL* 4.1 8.9 - - + +
236A LEU* 3.5 32.1 - - + -
239A LEU* 4.0 6.1 - - + -
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Residues in contact with GLU 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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120A THR* 5.7 2.4 - - - +
163A VAL* 3.7 35.3 - - + +
164A GLY* 4.0 14.1 + - - -
165A GLY 4.8 1.0 + - - -
166A THR* 3.9 16.3 - - - +
168A LEU* 4.6 5.0 - - + +
184A LEU 3.1 7.9 + - - +
185A GLN 3.6 13.5 - - - +
186A LEU 3.0 0.8 - - - -
187A ALA* 1.3 79.4 - - - +
189A LYS* 1.3 69.3 + - - +
190A ASN 3.5 0.2 + - - -
191A GLY 4.2 3.2 + - - -
239A LEU* 4.2 24.3 - - + +
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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