Contacts of the helix formed by residues 184 - 193 (chain A) in PDB entry 3UCG
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 THR 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A GLY 4.1 6.5 - - - +
183A ALA* 1.3 76.6 - - - +
185A ALA* 1.3 60.0 + - - +
186A GLU* 3.6 10.2 + - - +
187A GLU* 3.1 42.9 + - - +
188A LEU* 3.0 30.1 + - - +
203A ILE* 3.8 5.8 - - - -
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Residues in contact with ALA 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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184A THR* 1.3 70.5 - - - +
186A GLU* 1.3 61.1 + - - +
188A LEU* 3.8 1.2 - - - +
189A GLU* 2.9 32.1 + - - +
201A VAL* 4.0 36.4 - - + +
203A ILE* 3.7 9.9 - - + +
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Residues in contact with GLU 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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184A THR* 3.3 8.8 + - - +
185A ALA* 1.3 80.1 - - - +
187A GLU* 1.3 70.8 + - - +
189A GLU* 3.9 6.4 - - - +
190A ALA* 2.9 38.7 + - - +
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Residues in contact with GLU 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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182A GLY 3.8 1.0 - - - +
183A ALA* 3.6 0.2 - - - -
184A THR* 3.1 45.8 + - - +
186A GLU* 1.3 84.7 - - - +
188A LEU* 1.3 58.7 + - - +
190A ALA* 3.3 7.1 + - - +
191A HIS 3.0 23.6 + - - -
237A PHE* 3.5 22.3 - - + -
238A ARG* 3.1 37.2 + - + -
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Residues in contact with LEU 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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176A VAL* 4.5 13.9 - - + -
179A VAL* 4.7 10.5 - - + -
183A ALA* 4.8 1.6 - - + -
184A THR 3.0 16.5 + - - +
185A ALA 3.8 3.8 - - - +
187A GLU* 1.3 74.3 - - - +
189A GLU* 1.3 65.0 + - - +
191A HIS* 3.2 9.2 + - - -
192A PHE* 3.2 38.5 + - + -
201A VAL* 3.8 14.8 - - + -
203A ILE* 3.7 31.6 - - + -
216A ALA* 3.7 17.7 - - + -
218A ILE* 4.6 9.6 - - + -
237A PHE* 3.5 33.2 - - + -
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Residues in contact with GLU 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 ALA 2.9 22.0 + - - +
186A GLU* 3.9 6.0 - - - +
188A LEU* 1.3 72.7 - - - +
190A ALA* 1.3 61.2 + - - +
192A PHE* 3.1 3.2 + - - -
193A HIS* 2.6 67.8 + - - +
196A GLY 5.3 0.5 - - - +
197A SER* 5.9 0.3 - - - -
198A VAL* 4.0 33.0 + - + +
201A VAL* 4.4 12.4 - - + +
218A ILE* 5.6 0.4 - - - -
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Residues in contact with ALA 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 GLU* 2.9 30.1 + - - +
187A GLU* 3.6 7.9 - - - +
188A LEU 3.2 0.2 - - - -
189A GLU* 1.3 86.5 + - - +
191A HIS* 1.3 60.6 + - - +
193A HIS* 3.5 15.2 + - - +
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Residues in contact with HIS 191 (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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187A GLU 3.0 13.8 + - - +
188A LEU* 3.2 9.4 + - + +
190A ALA* 1.3 76.9 - - - +
192A PHE* 1.3 81.5 + + + +
193A HIS 3.8 0.2 + - - -
194A GLY 5.0 1.7 + - - -
232A LEU* 3.5 23.4 - - + +
235A SER* 2.8 28.9 + - - -
236A LEU 3.3 27.3 + - - -
237A PHE* 3.7 23.9 - + + -
242A ILE* 3.8 11.8 - - + +
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Residues in contact with PHE 192 (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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174A ILE* 3.4 28.5 - - + -
176A VAL* 3.9 9.9 - - + -
188A LEU* 3.2 22.9 + - + +
189A GLU 3.1 4.2 + - - +
191A HIS* 1.3 90.4 - + + +
193A HIS* 1.3 58.0 + - - +
194A GLY 3.3 2.5 - - - -
195A CYS* 2.9 28.7 + - - +
196A GLY 3.9 5.6 + - - +
198A VAL* 4.8 6.1 - - + -
218A ILE* 2.9 33.0 - - + -
220A PHE* 4.0 12.9 - + + -
229A SER* 4.0 14.4 - - - -
232A LEU* 3.5 30.5 - - + -
242A ILE* 3.8 13.7 - - + -
244A VAL* 3.8 20.2 - - + -
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Residues in contact with HIS 193 (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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189A GLU* 2.6 44.3 + - - +
190A ALA* 3.5 15.0 + - - +
191A HIS 3.5 0.4 - - - -
192A PHE* 1.3 77.3 - - - +
194A GLY* 1.3 64.2 + - - +
195A CYS 3.3 0.9 + - - -
196A GLY* 3.3 19.9 + - - +
197A SER* 6.2 2.0 - - - -
198A VAL* 5.2 0.4 - - - -
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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