Contacts of the helix formed by residues 182 - 192 (chain A) in PDB entry 1Z16
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 PHE 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ILE* 3.9 40.2 - - + -
179A GLU* 3.2 43.1 - - + -
180A LYS 4.2 0.7 - - - -
181A ASP* 1.3 76.5 - - - +
183A SER* 1.3 63.8 + - - +
184A THR* 3.2 3.4 - - - -
185A LEU* 3.0 15.3 + - + +
186A VAL* 2.9 27.1 + - + +
205A GLU* 4.1 24.7 - - + -
208A GLN* 3.5 30.5 - - + -
209A ILE* 3.9 24.7 - - + -
212A GLN* 2.8 22.7 + - - +
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Residues in contact with SER 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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181A ASP* 2.9 27.3 + - - -
182A PHE* 1.3 76.9 - - - +
184A THR* 1.3 65.7 + - - +
186A VAL* 2.9 26.5 - - - +
187A ALA* 3.0 13.5 + - - +
212A GLN* 3.8 2.5 + - - -
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Residues in contact with THR 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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181A ASP 5.4 0.4 + - - -
182A PHE* 3.2 1.0 - - - -
183A SER* 1.3 83.4 + - - +
185A LEU* 1.3 64.8 + - - +
187A ALA* 3.3 6.5 + - - +
188A ARG* 3.0 24.2 + - + +
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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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144A VAL* 4.1 33.4 - - + -
171A PHE* 4.3 20.4 - - + -
173A ASP* 6.0 2.7 - - + +
175A ILE* 4.4 13.9 - - + -
182A PHE* 3.0 19.0 + - + +
184A THR* 1.3 79.8 - - - +
186A VAL* 1.3 63.8 + - + +
188A ARG* 3.0 9.7 + - + +
189A LEU* 2.9 35.8 + - + +
197A VAL* 6.5 0.4 - - + -
209A ILE* 4.0 39.7 - - + -
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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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182A PHE* 2.9 19.5 + - + +
183A SER* 2.9 29.6 - - - +
185A LEU* 1.3 75.8 - - + +
187A ALA* 1.3 56.7 + - - +
189A LEU* 3.2 13.9 + - + +
190A LYS* 2.9 28.9 + - - +
209A ILE* 4.6 5.4 - - + +
212A GLN* 4.0 14.4 - - + +
213A ALA* 3.7 38.6 - - + +
216A ALA* 4.9 6.5 - - + -
218A LEU* 4.1 11.8 - - + +
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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 SER 3.0 19.9 + - - +
184A THR* 3.6 7.9 - - + +
185A LEU 3.1 0.2 - - - -
186A VAL* 1.3 77.1 - - - +
188A ARG* 1.3 57.9 + - - +
190A LYS* 3.2 8.1 + - - +
191A LYS* 2.8 31.5 + - - +
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Residues in contact with ARG 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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171A PHE* 3.5 60.4 - - + +
172A PHE 5.3 1.0 + - - -
173A ASP* 3.7 23.8 + - - +
184A THR* 3.0 16.9 + - + +
185A LEU* 3.0 12.3 + - - +
187A ALA* 1.3 78.7 - - - +
189A LEU* 1.3 56.9 + - - +
191A LYS* 3.9 8.8 - - + +
192A GLU* 2.9 41.9 + - - +
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Residues in contact with LEU 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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142A ALA* 4.1 0.7 - - + -
144A VAL* 5.6 0.9 - - + -
171A PHE* 3.8 25.6 - - + -
185A LEU* 2.9 32.0 + - + +
186A VAL* 3.5 15.7 - - + +
188A ARG* 1.3 76.7 - - - +
190A LYS* 1.3 58.3 + - - +
193A ASN* 3.1 6.9 + - - -
194A ILE* 3.0 44.9 + - + +
197A VAL* 3.8 32.3 - - + -
209A ILE* 5.5 1.1 - - + -
213A ALA* 5.1 0.2 - - + -
218A LEU* 3.6 24.7 - - + -
220A THR* 5.0 1.6 - - - +
222A PHE* 4.2 15.7 - - + -
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Residues in contact with LYS 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 VAL 2.9 15.5 + - - +
187A ALA* 3.6 7.9 - - - +
188A ARG 3.2 0.2 - - - -
189A LEU* 1.3 75.0 - - - +
191A LYS* 1.3 65.7 + - - +
193A ASN* 3.1 13.4 + - - +
216A ALA* 3.2 34.4 + - - +
217A GLY 5.8 0.4 - - - -
218A LEU* 4.2 20.2 - - + +
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Residues in contact with LYS 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 ALA 2.8 18.5 + - - +
188A ARG* 3.9 8.5 - - + +
190A LYS* 1.3 79.3 - - - +
192A GLU* 1.3 76.9 + - - +
193A ASN* 3.4 2.4 + - - +
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Residues in contact with GLU 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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140A ARG* 2.8 46.2 + - - +
170A VAL* 3.4 29.8 - - + +
171A PHE* 4.5 8.1 - - + -
188A ARG* 2.9 26.5 + - - +
191A LYS* 1.3 95.2 + - - +
193A ASN* 1.3 65.2 + - - +
194A ILE* 3.3 16.8 + - + +
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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