Contacts of the helix formed by residues 182 - 195 (chain A) in PDB entry 3HNF
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 ASP 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A HIS* 2.6 24.5 + - - +
180A LYS 4.2 0.9 - - - -
181A GLU* 1.3 69.3 - - - +
183A ILE* 1.3 63.3 + - - +
184A ASP* 3.4 10.6 + - - +
185A ALA* 3.1 29.4 + - - +
186A ALA* 3.2 14.4 + - - +
479A LYS* 4.0 16.3 + - - +
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Residues in contact with ILE 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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123A ILE* 4.4 9.9 - - + -
127A ASN* 3.6 39.3 - - + +
130A ARG* 4.1 22.4 - - + +
131A LEU* 3.8 23.1 - - + -
176A VAL* 5.9 1.1 - - + -
180A LYS 4.0 15.5 - - - +
181A GLU* 3.4 9.3 + - - +
182A ASP* 1.3 70.9 + - - +
184A ASP* 1.3 51.1 + - - +
186A ALA* 2.7 27.9 + - + +
187A ILE* 2.7 44.0 + - + +
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Residues in contact with ASP 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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130A ARG* 2.6 29.4 + - - +
182A ASP* 3.4 8.2 + - - +
183A ILE* 1.3 74.9 - - - +
185A ALA* 1.3 57.6 + - - +
187A ILE* 3.2 5.1 + - - +
188A GLU* 3.0 30.9 + - - +
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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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179A HIS* 3.1 27.6 + - + +
182A ASP* 3.1 28.1 + - - +
184A ASP* 1.3 76.2 - - - +
186A ALA* 1.3 59.7 + - - +
188A GLU* 4.0 6.6 - - - +
189A THR* 3.0 32.6 + - - -
479A LYS* 4.2 1.6 - - - +
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Residues in contact with ALA 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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131A LEU* 5.0 2.5 - - + -
172A MET* 5.3 1.6 - - - -
175A SER* 3.6 15.6 - - - +
176A VAL* 4.3 20.6 - - + -
179A HIS* 3.7 17.9 - - + -
180A LYS 5.6 0.4 - - - +
182A ASP 3.2 13.2 + - - +
183A ILE* 2.7 23.7 + - + +
185A ALA* 1.3 71.8 - - - +
187A ILE* 1.3 52.4 + - + +
189A THR* 3.2 1.2 + - - -
190A TYR* 2.7 35.8 + - - +
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Residues in contact with ILE 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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130A ARG* 3.5 42.8 - - + +
131A LEU* 4.5 8.5 - - + -
134A ALA* 3.8 25.8 - - + -
172A MET* 4.7 2.7 - - + -
183A ILE* 2.7 44.4 + - + +
184A ASP* 3.2 4.0 + - - +
186A ALA* 1.3 73.2 - - - +
188A GLU* 1.3 57.9 + - - +
190A TYR* 4.0 7.6 - - + -
191A ASN* 3.0 38.3 + - - +
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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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184A ASP 3.0 17.7 + - - +
185A ALA* 4.2 5.9 - - - +
187A ILE* 1.3 76.7 - - - +
189A THR* 1.3 63.9 + - - +
191A ASN* 4.1 4.8 - - + +
192A LEU* 3.3 33.9 + - + +
472A VAL* 3.4 31.5 - - - +
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Residues in contact with THR 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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175A SER* 3.4 17.9 - - - +
178A ILE* 5.5 2.5 - - + -
179A HIS* 2.7 28.9 + - - +
185A ALA 3.0 13.8 + - - -
186A ALA 3.6 3.1 - - - -
188A GLU* 1.3 74.2 + - - +
190A TYR* 1.3 68.4 + - - +
192A LEU* 3.9 6.2 - - - +
193A LEU* 3.1 36.2 + - + +
198A PHE* 4.6 2.2 - - + -
200A HIS* 4.9 3.4 - - + +
472A VAL* 4.4 5.7 - - - +
476A ASN* 3.1 27.5 + - - +
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Residues in contact with TYR 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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134A ALA 3.6 18.8 - - - -
135A ILE* 3.5 11.9 - - + +
136A ILE* 2.9 23.9 + - - -
139A ARG* 3.7 11.4 + - - -
168A GLN* 2.6 41.8 + - - -
171A LEU* 4.1 4.7 - - + -
172A MET* 3.6 46.9 - - + -
175A SER* 3.2 10.0 + - - +
186A ALA 2.7 20.6 + - - +
187A ILE* 3.6 7.6 - - + +
188A GLU 3.3 0.4 - - - -
189A THR* 1.3 74.8 - - - +
191A ASN* 1.3 86.5 + - - +
193A LEU* 3.6 3.2 - - - +
194A SER* 2.9 32.9 + - - -
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Residues in contact with ASN 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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134A ALA 4.8 2.1 - - - +
139A ARG* 3.5 21.8 + - - +
187A ILE* 3.0 24.1 + - - +
188A GLU* 4.1 6.7 - - + +
189A THR 3.4 0.2 - - - -
190A TYR* 1.3 88.4 - - - +
192A LEU* 1.3 69.5 + - + +
194A SER* 3.0 8.1 + - - -
195A GLU* 3.0 34.8 + - - +
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Residues in contact with LEU 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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188A GLU* 3.3 31.0 + - + +
189A THR 3.9 1.3 - - - +
191A ASN* 1.3 81.3 - - + +
193A LEU* 1.3 63.0 + - - +
195A GLU 3.5 0.3 + - - -
196A ARG 3.2 2.8 + - - -
197A TRP* 3.1 48.9 + - + +
198A PHE* 3.7 22.9 - - + -
465A LYS* 5.2 7.0 - - - +
469A VAL* 4.5 20.0 - - + -
472A VAL* 3.8 37.5 - - + -
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Residues in contact with LEU 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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143A TYR* 5.0 2.4 + - - -
171A LEU* 3.8 32.2 - - + +
174A VAL* 4.6 10.8 - - + -
175A SER* 3.8 9.9 - - - +
189A THR* 3.1 34.6 + - + +
190A TYR 3.6 2.9 - - - +
192A LEU* 1.3 79.1 - - - +
194A SER* 1.3 55.5 + - - +
196A ARG* 2.7 28.6 + - - +
198A PHE* 3.7 36.2 - - + +
199A THR* 3.9 18.8 - - - +
200A HIS* 4.1 18.4 - - + +
205A LEU* 4.8 4.7 - - + -
611A LEU* 5.8 0.3 - - - +
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Residues in contact with SER 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 3.0 38.6 + - - +
142A SER* 4.0 15.4 + - - -
143A TYR* 5.0 4.6 + - - -
168A GLN* 3.4 28.2 + - - +
171A LEU* 4.5 11.4 - - - -
190A TYR* 2.9 24.8 + - - -
191A ASN* 3.0 9.0 + - - -
193A LEU* 1.3 75.8 - - - +
195A GLU* 1.3 56.2 + - - +
196A ARG* 3.2 4.3 + - - +
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Residues in contact with GLU 195 (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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139A ARG* 2.9 37.5 + - + +
191A ASN* 3.0 22.4 + - - +
192A LEU* 5.8 0.2 - - - +
194A SER* 1.3 74.3 - - - +
196A ARG* 1.3 72.5 + - - +
197A TRP* 3.1 30.8 + - + +
453A MET* 3.0 21.4 - - + +
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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