Contacts of the helix formed by residues 158 - 172 (chain A) in PDB entry 1DZI
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 PRO 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A TYR* 1.3 110.1 - - + +
159A TRP* 1.3 66.8 + - - +
160A ASP* 4.3 9.0 - - + +
161A ALA* 3.1 28.4 + - + +
162A VAL* 3.5 7.3 + - - +
282A VAL* 5.3 1.5 - - + +
285A TYR* 3.2 43.7 - - + -
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Residues in contact with TRP 159 (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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150A CYS* 4.0 9.2 - - - -
151A ASP 3.4 25.4 - - - -
152A GLU* 4.0 13.0 - - + -
156A ILE* 4.0 5.8 - - + -
157A TYR* 4.2 4.6 - - - +
158A PRO* 1.3 72.5 - - - +
160A ASP* 1.3 59.1 + - - +
162A VAL* 2.8 49.7 + - + +
163A LYS* 2.8 58.7 + - + +
166A LEU* 5.2 0.4 - - + -
186A GLN* 3.9 29.4 - - - -
213A THR* 3.4 16.1 + - + -
214A SER* 3.9 6.5 - - - -
215A GLN* 3.7 46.8 - - + +
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Residues in contact with ASP 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 3.1 9.0 - - + +
159A TRP* 1.3 78.7 - - - +
161A ALA* 1.3 55.4 + - - +
163A LYS* 3.4 19.4 + - - +
164A ASN* 3.0 29.8 + - - +
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 3.1 29.1 + - + +
160A ASP* 1.3 78.6 - - - +
162A VAL* 1.3 62.7 + - + +
164A ASN* 3.6 6.7 + - - +
165A PHE 3.2 16.8 + - - -
282A VAL* 6.0 0.7 - - + -
285A TYR* 4.0 20.9 - - + +
315A VAL* 3.6 20.3 - - + +
316A SER* 4.0 11.3 - - - +
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Residues in contact with VAL 162 (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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150A CYS* 3.4 33.0 - - - -
151A ASP 5.4 0.4 - - - +
156A ILE* 4.0 15.5 - - + -
158A PRO 3.8 12.3 - - - +
159A TRP* 2.8 36.7 + - + +
161A ALA* 1.3 75.1 - - + +
163A LYS* 1.3 65.4 + - - +
165A PHE* 3.2 4.0 + - - +
166A LEU* 3.0 32.5 + - + +
252A VAL* 4.7 6.1 - - + -
282A VAL* 4.5 20.4 - - + -
315A VAL* 4.4 7.2 - - + -
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Residues in contact with LYS 163 (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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159A TRP* 2.8 45.0 + - + +
160A ASP* 3.8 20.8 + - - +
162A VAL* 1.3 72.0 - - - +
164A ASN* 1.3 58.5 + - - +
166A LEU* 3.3 9.9 + - - +
167A GLU* 2.8 41.5 + - - +
210A THR* 4.4 6.3 - - - +
211A SER* 4.5 15.9 + - - +
212A GLN 5.4 0.6 - - - -
213A THR* 3.1 33.8 + - + +
214A SER* 5.0 1.2 - - - +
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Residues in contact with ASN 164 (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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160A ASP 3.0 17.0 + - - +
161A ALA* 3.7 8.3 - - - +
162A VAL 3.2 0.2 - - - -
163A LYS* 1.3 76.5 - - - +
165A PHE* 1.3 59.2 + - - +
167A GLU* 3.5 8.6 - - - +
168A LYS* 2.8 62.7 + - - +
315A VAL 5.2 3.1 - - - +
316A SER* 5.8 2.3 - - - -
318A GLU* 2.9 26.2 + - - +
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Residues in contact with PHE 165 (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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148A VAL* 5.5 0.7 - - + -
161A ALA 3.2 3.0 + - - -
162A VAL* 3.4 5.6 - - - +
164A ASN* 1.3 79.8 + - - +
166A LEU* 1.3 72.3 + - + +
168A LYS* 3.1 4.9 + - - +
169A PHE* 2.7 51.7 + + + +
250A VAL* 4.3 10.5 - - + -
252A VAL* 3.7 25.8 - - + -
280A ILE* 3.6 24.2 - - + -
313A PHE* 3.6 27.1 - + - -
315A VAL* 3.4 44.4 - - + +
317A ASP 6.1 0.4 - - - -
318A GLU* 6.5 0.4 - - - -
321A LEU* 3.9 24.7 - - + -
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Residues in contact with LEU 166 (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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148A VAL* 3.9 30.1 - - + -
150A CYS* 4.3 17.3 - - + -
159A TRP* 5.2 0.4 - - + -
162A VAL* 3.0 28.5 + - + +
163A LYS* 3.7 6.1 - - - +
165A PHE* 1.3 90.2 - - + +
167A GLU* 1.3 63.8 + - - +
169A PHE* 3.3 5.7 + - + +
170A VAL* 3.1 30.6 + - + +
184A LEU* 4.6 16.4 - - + -
186A GLN* 4.8 1.3 - - - +
210A THR* 3.7 15.0 - - + +
213A THR* 4.2 25.4 - - + -
252A VAL* 4.7 1.3 - - + -
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Residues in contact with GLU 167 (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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163A LYS* 2.8 23.9 + - - +
164A ASN* 3.5 9.8 - - - +
166A LEU* 1.3 79.5 - - - +
168A LYS* 1.3 68.6 + - + +
171A GLN* 3.2 21.9 + - + +
207A ILE* 3.5 32.0 - - + +
210A THR* 3.4 12.7 - - + +
211A SER* 4.0 28.5 - - - -
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Residues in contact with LYS 168 (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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164A ASN* 2.8 53.9 + - - +
165A PHE* 3.7 4.3 - - - +
167A GLU* 1.3 78.4 - - + +
169A PHE* 1.3 66.5 + - - +
171A GLN* 3.4 13.2 + - + +
172A GLY* 3.4 14.0 + - - -
318A GLU* 3.7 28.0 - - + +
321A LEU* 3.8 21.1 - - + +
322A LEU* 6.1 0.5 - - - +
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Residues in contact with PHE 169 (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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146A VAL* 3.8 24.0 - - + -
148A VAL* 3.8 29.4 - - + -
165A PHE* 2.7 40.1 + + + +
166A LEU* 3.6 7.0 - - - +
168A LYS* 1.3 73.4 - - - +
170A VAL* 1.3 71.8 + - + +
172A GLY* 3.2 11.8 + - - -
173A LEU* 3.5 42.5 + - + +
182A VAL* 4.7 3.6 - - + -
248A VAL* 6.3 0.2 - - + -
250A VAL* 4.0 14.6 - - + -
278A PHE* 6.5 0.2 - + - -
321A LEU* 3.9 24.7 - - + +
325A ALA* 4.0 20.0 - - + -
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Residues in contact with VAL 170 (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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166A LEU* 3.1 14.6 + - + +
169A PHE* 1.3 86.5 - - + +
171A GLN* 1.3 62.7 + - - +
173A LEU* 3.1 22.1 + - - +
175A ILE* 4.0 7.1 - - + +
182A VAL* 4.6 10.3 - - + -
195A PHE* 5.5 1.1 - - + -
203A LYS* 3.3 12.9 - - + -
206A MET* 3.6 42.8 - - + -
207A ILE* 3.4 28.5 - - + -
210A THR* 4.2 11.0 - - - +
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Residues in contact with GLN 171 (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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167A GLU* 3.2 16.9 + - + +
168A LYS* 3.6 20.2 - - + +
169A PHE 3.2 0.6 - - - -
170A VAL* 1.3 78.0 - - - +
172A GLY* 1.3 55.9 + - - +
203A LYS* 2.6 41.2 + - - +
207A ILE* 4.1 17.7 - - + +
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Residues in contact with GLY 172 (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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168A LYS 3.4 6.2 + - - -
169A PHE 3.2 8.1 + - - -
170A VAL 3.2 1.0 - - - -
171A GLN* 1.3 77.5 - - - +
173A LEU* 1.3 63.1 + - - +
174A ASP 4.2 0.3 + - - -
203A LYS* 4.6 0.2 - - - -
322A LEU* 5.3 12.8 - - - -
326A GLY* 3.6 19.7 - - - +
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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