Contacts of the helix formed by residues 175 - 192 (chain B) in PDB entry 1DIZ
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 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU* 6.2 0.2 - - + -
134B LEU* 6.0 0.9 - - + -
170B LYS* 5.0 0.2 - - + -
174B MET* 1.3 95.7 - - + +
176B LEU* 1.3 65.4 + - - +
177B LYS* 4.2 7.0 - - + +
178B ARG* 3.2 45.7 + - + +
179B ALA* 3.1 17.8 + - - +
18D A 3.9 28.7 - - - +
19D T 3.5 30.3 - - + +
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PRO* 3.9 33.4 - - + -
167B GLN* 4.8 7.2 - - + +
170B LYS* 4.2 29.5 - - + +
174B MET 3.7 0.4 + - - -
175B PRO* 1.3 69.8 - - - +
177B LYS* 1.3 69.5 + - + +
179B ALA* 3.3 3.7 + - - +
180B GLU* 2.9 48.2 + - - +
19D T 5.0 1.2 + - - -
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Residues in contact with LYS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PRO* 3.2 6.4 - - + +
176B LEU* 1.3 85.8 - - + +
178B ARG* 1.3 55.8 + - - +
180B GLU* 3.9 20.2 + - - +
181B ALA* 3.0 28.6 + - - +
214B GLY* 4.7 8.0 - - - -
11C C 6.5 0.7 - - - -
18D A 6.1 6.5 - - - -
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Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.6 26.6 + - + +
122B LEU* 4.8 6.6 - - + +
124B GLN* 2.7 52.6 + - - +
125B LEU* 3.7 33.3 - - - +
126B VAL* 5.2 3.8 - - - +
134B LEU* 5.8 3.3 - - + +
174B MET* 4.0 13.7 - - + -
175B PRO* 3.2 45.0 + - + +
176B LEU 3.2 0.4 - - - -
177B LYS* 1.3 76.8 - - - +
179B ALA* 1.3 65.1 + - - +
181B ALA* 3.1 16.2 + - - +
182B LEU* 3.2 16.3 + - - +
214B GLY* 6.1 0.2 - - - -
9C T 4.3 16.0 + - - -
10C G 5.0 4.4 + - - -
18D A 5.5 1.8 + - - -
19D T 6.0 0.2 - - - -
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PRO* 3.6 15.5 - - + +
169B LEU* 3.5 32.0 - - + +
170B LYS 4.0 3.1 - - - +
174B MET* 3.4 15.7 - - - -
175B PRO 3.1 7.8 + - - +
176B LEU* 3.7 9.0 - - - +
178B ARG* 1.3 81.4 - - - +
180B GLU* 1.3 60.7 + - - +
182B LEU* 3.2 14.5 + - - +
183B ILE* 3.3 18.4 + - - +
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Residues in contact with GLU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PRO* 4.1 25.3 - - + +
176B LEU* 2.9 42.1 + - - +
177B LYS* 4.0 22.6 + - - +
179B ALA* 1.3 74.6 - - - +
181B ALA* 1.3 65.1 + - - +
183B ILE* 3.3 9.6 + - + +
184B HIS* 3.0 22.9 + - - +
213B PRO* 5.2 3.7 - - + +
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Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.7 19.8 - - + +
177B LYS 3.0 15.1 + - - +
178B ARG* 3.1 13.9 + - - +
180B GLU* 1.3 78.7 - - - +
182B LEU* 1.3 55.8 + - - +
184B HIS* 3.4 5.2 + - - +
185B LEU* 3.0 28.4 + - - +
213B PRO* 3.5 28.2 - - - +
214B GLY* 3.7 13.2 - - - +
215B ILE* 5.7 0.7 - - - +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 4.8 1.6 - - - -
118B VAL* 3.9 29.6 - - + +
121B ILE* 3.4 39.9 - - + -
122B LEU* 3.9 22.9 - - + -
138B VAL* 4.6 9.9 - - + -
161B LEU* 4.7 15.7 - - + +
169B LEU* 4.6 13.2 - - + -
174B MET* 4.1 16.2 - - + -
178B ARG 3.2 11.3 + - - +
179B ALA 3.2 7.7 + - - +
181B ALA* 1.3 73.8 - - - +
183B ILE* 1.3 61.0 + - - +
185B LEU* 3.2 5.7 + - - +
186B ALA* 2.9 29.5 + - - +
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Residues in contact with ILE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU 3.7 19.3 - - - +
162B ALA* 3.9 20.0 - - - +
164B ALA 3.5 16.2 - - - +
166B PRO* 3.4 39.7 - - + -
169B LEU* 4.0 12.3 - - + -
179B ALA 3.3 15.1 + - - +
180B GLU* 3.6 11.0 - - + +
181B ALA 3.3 0.4 - - - -
182B LEU* 1.3 73.7 - - - +
184B HIS* 1.3 63.7 + - - +
186B ALA* 3.6 3.4 + - - +
187B ASN* 3.2 27.8 + - - +
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Residues in contact with HIS 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B GLU 3.0 16.0 + - - +
181B ALA 3.8 4.5 - - - +
183B ILE* 1.3 75.9 - - - +
185B LEU* 1.3 66.1 + - - +
187B ASN* 3.2 11.6 + - + +
188B ALA* 3.0 21.2 + - + +
212B PHE* 3.7 38.9 - + + -
213B PRO* 3.2 44.4 - - + +
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 3.7 25.4 - - + +
117B GLY* 3.7 14.1 - - - +
118B VAL* 3.6 32.1 - - + +
121B ILE* 4.4 7.9 - - + -
181B ALA 3.0 17.9 + - - +
182B LEU* 3.5 5.4 - - - +
184B HIS* 1.3 80.9 - - - +
186B ALA* 1.3 61.7 + - - +
188B ALA* 3.1 7.9 + - - +
189B ALA* 3.1 20.8 + - - +
194B LEU* 3.9 29.6 - - + +
209B LEU* 5.2 0.4 - - + -
212B PHE* 4.6 5.6 - - + -
215B ILE* 4.3 22.4 - - + -
223B PHE* 5.9 0.4 - - + -
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Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PHE* 3.6 16.7 - - + -
158B PRO* 3.3 23.4 - - - +
161B LEU* 3.7 10.5 - - + -
162B ALA* 3.5 15.7 - - - +
182B LEU 2.9 16.7 + - - +
183B ILE 3.8 3.1 - - - +
184B HIS 3.3 0.2 - - - -
185B LEU* 1.3 75.8 - - - +
187B ASN* 1.3 64.6 + - - +
189B ALA* 3.2 5.4 + - - +
190B LEU* 3.1 26.7 + - - +
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Residues in contact with ASN 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ALA* 3.2 27.1 + - - +
183B ILE* 3.2 19.6 + - - +
184B HIS* 3.2 16.2 + - + +
185B LEU 3.2 0.4 - - - -
186B ALA* 1.3 75.7 - - - +
188B ALA* 1.3 66.0 + - - +
190B LEU* 3.3 12.4 + - - +
191B GLU* 3.1 37.6 + - - +
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Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B HIS* 3.0 15.1 + - + +
185B LEU* 3.1 9.8 + - - +
187B ASN* 1.3 75.4 - - - +
189B ALA* 1.3 53.7 + - - +
191B GLU* 3.2 2.4 + - - -
192B GLY 2.8 31.4 + - - -
193B THR* 2.8 27.7 + - + -
194B LEU* 4.0 9.2 - - + -
212B PHE* 3.7 31.4 - - + -
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PRO* 3.9 5.2 - - - +
200A GLY 3.7 10.6 + - - -
114B PHE* 4.0 16.2 - - + -
158B PRO* 3.8 24.9 - - + -
185B LEU 3.1 12.2 + - - +
186B ALA 3.4 9.2 - - - +
188B ALA* 1.3 78.4 - - - +
190B LEU* 1.3 62.0 + - - +
192B GLY* 3.5 7.9 + - - -
194B LEU* 4.2 14.1 - - + +
196B MET* 5.3 6.8 - - - +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PRO* 3.6 3.5 - - - +
200A GLY* 3.6 18.4 + - - +
201A ASP* 2.9 38.3 + - + +
158B PRO* 3.8 7.2 - - + -
159B GLN* 3.2 45.8 - - + +
162B ALA* 3.7 29.6 - - + -
186B ALA 3.1 9.3 + - - +
187B ASN* 3.6 16.2 - - - +
188B ALA 3.2 0.2 - - - -
189B ALA* 1.3 78.6 - - - +
191B GLU* 1.3 63.1 + - + +
192B GLY 3.6 0.2 + - - -
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A PRO* 4.6 2.9 - - - +
199A PRO* 4.3 1.8 - - - -
201A ASP* 5.9 0.4 - - + -
204A GLN* 3.4 40.4 + - + +
205A ALA* 3.7 21.8 - - - +
208A THR* 4.9 7.5 + - - +
187B ASN* 3.1 26.1 + - - +
188B ALA* 5.3 0.9 - - - -
190B LEU* 1.3 77.6 - - + +
192B GLY* 1.3 59.5 + - - +
193B THR* 3.7 20.1 + - - +
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Residues in contact with GLY 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLY 4.6 6.9 - - - +
193A THR 5.0 1.9 - - - +
195A PRO* 3.6 30.1 - - - +
199A PRO* 3.9 16.2 - - - -
188B ALA 2.8 5.6 + - - -
189B ALA* 3.5 4.2 + - - -
190B LEU 3.3 3.2 - - - -
191B GLU* 1.3 79.5 - - - +
193B THR* 1.3 57.7 + - - +
194B LEU 3.1 15.6 + - - +
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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
------------------------------------------------------------
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