Contacts of the helix formed by residues 178 - 192 (chain A) in PDB entry 3ADK
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 SER 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A GLY* 1.2 83.9 - - - +
179A VAL* 1.3 65.3 + - - +
180A ASP* 3.1 16.4 - - - -
181A ASP* 3.0 29.7 + - - +
182A VAL* 3.0 26.7 + - - +
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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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23A THR* 4.5 10.5 - - - +
24A GLN* 3.4 13.4 - - - +
27A LYS* 3.0 34.8 - - + -
178A SER* 1.3 71.1 - - - +
180A ASP* 1.4 61.2 + - - +
182A VAL* 3.3 3.0 + - - -
183A PHE* 2.7 36.4 + - - +
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Residues in contact with ASP 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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27A LYS* 3.2 27.2 + - - -
178A SER* 3.1 8.0 - - - -
179A VAL* 1.4 86.2 - - - +
181A ASP* 1.3 63.2 + - - +
183A PHE* 3.7 9.9 - - + +
184A SER* 2.9 27.1 + - - -
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Residues in contact with ASP 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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176A GLU 5.5 1.1 - - - +
177A GLY* 4.8 3.8 - - - -
178A SER* 3.0 29.9 + - - +
179A VAL 3.4 0.2 - - - -
180A ASP* 1.3 81.8 - - - +
182A VAL* 1.3 65.2 + - - +
184A SER* 3.5 19.7 + - - -
185A GLN* 3.2 17.8 - - - +
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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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24A GLN* 4.1 21.5 - - + +
118A VAL* 5.1 1.3 - - + -
173A VAL* 3.5 25.8 - - + -
174A ASN 3.7 15.5 - - - +
175A ALA* 3.7 26.2 - - + +
176A GLU 4.2 4.9 - - - +
177A GLY 4.6 0.7 - - - +
178A SER 3.0 18.8 + - - +
179A VAL* 3.3 6.7 + - - +
181A ASP* 1.3 78.8 - - - +
183A PHE* 1.3 62.7 + - - +
185A GLN* 3.3 15.4 - - - +
186A VAL* 2.8 19.6 - - - +
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Residues in contact with PHE 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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24A GLN* 3.4 22.2 - - - +
27A LYS* 3.7 55.2 - - + -
28A ILE* 4.2 3.4 - - - -
31A LYS* 4.1 18.2 - - + -
32A TYR* 4.7 3.1 - + - -
179A VAL 2.7 19.7 + - - +
180A ASP* 3.7 11.0 - - - +
182A VAL* 1.3 75.5 - - - +
184A SER* 1.3 71.8 + - - +
186A VAL* 3.2 16.1 + - + -
187A CYS* 3.1 41.3 + - - -
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Residues in contact with SER 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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180A ASP 2.9 20.1 + - - -
181A ASP* 3.5 18.5 + - - -
183A PHE* 1.3 82.1 - - - +
185A GLN* 1.3 58.3 + - - +
187A CYS* 2.9 25.6 - - - +
188A THR* 3.4 6.3 + - - -
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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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172A LYS 5.1 1.0 + - - -
173A VAL* 3.9 14.3 - - + +
174A ASN* 2.8 51.8 + - - +
176A GLU 5.5 1.0 - - - +
181A ASP 3.2 18.8 - - - +
182A VAL* 3.3 12.5 - - - +
184A SER* 1.3 73.6 + - - +
186A VAL* 1.3 56.6 + - - +
188A THR* 3.0 19.5 + - - -
189A HIS* 2.7 31.2 + - + -
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Residues in contact with VAL 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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24A GLN* 3.6 17.7 - - + +
28A ILE* 3.9 20.6 - - + -
116A LEU* 4.7 10.5 - - + +
118A VAL* 6.2 0.4 - - + -
173A VAL* 4.2 16.1 - - + +
182A VAL* 2.8 22.9 - - + +
183A PHE* 3.2 24.4 + - + -
185A GLN* 1.3 69.8 - - - +
187A CYS* 1.4 59.8 + - - +
189A HIS* 2.9 26.0 + - - +
190A LEU* 3.0 38.4 + - + +
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Residues in contact with CYS 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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31A LYS* 4.6 10.1 - - - +
32A TYR* 3.4 23.8 - - - +
183A PHE* 3.1 43.3 + - - -
184A SER* 2.9 13.5 - - - +
186A VAL* 1.4 72.0 - - - +
188A THR* 1.3 67.9 + - - +
190A LEU* 4.4 0.4 - - - -
191A ASP* 2.8 37.3 + - - +
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Residues in contact with THR 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 SER 3.4 9.4 + - - -
185A GLN* 3.0 19.8 + - - -
187A CYS* 1.3 81.2 - - - +
189A HIS* 1.3 67.8 + - + +
191A ASP* 4.1 6.4 + - - +
192A THR* 3.4 15.9 - - - +
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Residues in contact with HIS 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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114A LEU* 4.7 7.5 - - + +
116A LEU* 4.4 13.9 - - + -
171A ARG* 3.0 46.0 - - + +
172A LYS 3.7 21.1 + - - -
173A VAL* 4.0 15.2 - - + +
185A GLN* 2.7 33.1 + - + -
186A VAL* 2.9 7.3 + - - +
188A THR* 1.3 84.5 - - + +
190A LEU* 1.4 64.3 + - - +
191A ASP 3.2 0.9 - - - -
192A THR* 3.3 17.8 + - - +
193A LEU* 4.1 13.3 + - - +
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Residues in contact with LEU 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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11A ILE* 4.0 26.0 - - + -
28A ILE* 3.6 25.1 - - + -
32A TYR* 3.7 38.8 - - + +
34A TYR* 4.7 5.0 + - + +
114A LEU* 4.2 15.5 - - + -
116A LEU* 4.7 6.1 - - + -
186A VAL* 3.0 40.9 + - + +
187A CYS 3.1 0.4 + - - -
189A HIS* 1.4 76.2 - - - +
191A ASP* 1.3 61.3 + - - +
193A LEU* 2.9 40.6 + - + +
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Residues in contact with ASP 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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31A LYS* 4.5 7.2 + - - -
32A TYR* 3.3 27.0 + - - -
187A CYS* 2.8 25.0 - - - +
188A THR* 4.1 7.5 - - - +
190A LEU* 1.3 72.7 - - - +
192A THR* 1.3 55.5 + - - +
193A LEU 3.0 14.6 + - - +
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Residues in contact with THR 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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171A ARG* 5.8 3.0 + - - +
188A THR 3.4 16.6 - - - +
189A HIS* 3.3 19.7 - - - +
191A ASP* 1.3 70.7 - - + +
193A LEU* 1.3 64.6 + - - +
194A LYS 3.3 8.3 + - - +
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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