Contacts of the helix formed by residues 171 - 188 (chain B) in PDB entry 4DTZ
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 HIS 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLU* 4.7 4.8 + - - -
160B TYR* 2.8 36.0 + + - -
161B ARG 5.0 0.9 - - - -
162B PHE* 3.8 33.2 - + + +
164B SER* 5.7 0.4 + - - -
167B ARG* 3.6 30.7 - - - +
170B PRO* 1.3 76.6 - - - +
172B PRO* 1.3 76.1 - - + +
173B PHE* 2.9 41.3 + - + +
174B ILE* 2.8 23.1 + - + +
175B THR 3.1 7.3 + - - -
215B LEU* 4.0 13.5 - - + -
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Residues in contact with PRO 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ARG* 4.7 6.3 - - - +
170B PRO 3.8 5.2 - - - +
171B HIS* 1.3 95.8 - - + +
173B PHE* 1.3 65.5 + - - +
175B THR* 3.3 7.5 + - - +
176B SER* 3.0 27.7 + - - -
211B VAL* 4.2 11.0 - - + -
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PHE* 5.7 0.2 - + - -
162B PHE* 3.9 15.7 - + + -
171B HIS* 2.9 24.5 + - + +
172B PRO* 1.3 79.5 - - - +
174B ILE* 1.3 64.3 + - + +
176B SER* 3.6 1.7 - - - -
177B MET* 2.8 49.8 + - + +
211B VAL* 4.1 10.4 - - + +
212B MET* 3.6 39.4 - - + +
215B LEU* 3.7 25.4 - - + -
216B VAL* 3.7 24.2 - - + -
259B ILE* 4.5 9.2 - - + -
262B LEU* 3.8 33.4 - - + -
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Residues in contact with ILE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 3.7 39.7 - - + -
162B PHE* 3.7 45.5 - - + -
164B SER* 3.8 14.8 - - - +
170B PRO* 3.6 22.9 - - + -
171B HIS* 2.8 17.8 + - + +
173B PHE* 1.3 81.2 - - + +
175B THR* 1.3 65.8 + - - +
177B MET* 3.2 3.8 + - + +
178B VAL* 2.8 35.4 + - + +
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Residues in contact with THR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLN* 5.8 0.5 - - - +
170B PRO* 3.8 24.8 + - - +
171B HIS 3.1 11.0 + - - -
172B PRO* 3.7 10.5 - - - +
173B PHE 3.3 0.2 - - - -
174B ILE* 1.3 78.4 - - - +
176B SER* 1.3 57.1 + - - +
178B VAL* 3.9 5.1 - - - +
179B ARG* 3.0 57.2 + - + +
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PRO 3.0 16.1 + - - -
173B PHE 3.6 3.6 - - - -
175B THR* 1.3 77.3 - - - +
177B MET* 1.3 57.0 + - - +
179B ARG* 3.3 5.3 + - - +
180B ALA* 2.8 30.9 + - - +
208B ASP* 2.7 47.3 + - - +
211B VAL* 3.5 26.2 - - - +
212B MET* 4.5 2.9 - - - -
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Residues in contact with MET 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 4.9 1.3 - - + -
150B LEU* 3.8 28.5 - - + -
173B PHE* 2.8 35.6 + - + +
174B ILE* 3.7 5.6 - - - +
176B SER* 1.3 72.5 - - - +
178B VAL* 1.3 64.8 + - + +
180B ALA* 3.3 2.2 + - - +
181B LEU* 2.9 30.7 + - + +
212B MET* 3.7 23.7 - - - +
259B ILE 4.6 0.9 - - - +
262B LEU* 3.7 12.1 - - - +
263B ALA* 3.5 38.8 - - + -
266B HIS* 3.9 21.1 - - + +
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 5.3 1.6 - - + -
174B ILE* 2.8 37.9 + - + +
175B THR* 4.0 5.4 - - - +
177B MET* 1.3 81.0 - - + +
179B ARG* 1.3 58.1 + - - +
181B LEU* 3.4 10.3 + - + +
182B ASP* 3.0 39.5 + - - +
266B HIS* 4.8 13.9 - - + +
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Residues in contact with ARG 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B THR* 3.0 40.5 + - - +
176B SER* 3.7 8.3 + - - +
178B VAL* 1.3 77.9 - - - +
180B ALA* 1.3 58.4 + - - +
182B ASP* 3.2 10.0 + - + +
183B GLU* 3.0 29.7 + - + +
204B GLN* 3.4 33.9 + - + +
207B GLU* 4.5 4.6 + - - -
208B ASP* 2.7 41.8 + - - +
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 3.6 18.0 - - + -
176B SER 2.8 19.2 + - - +
177B MET 3.7 4.5 - - - +
179B ARG* 1.3 73.8 - - - +
181B LEU* 1.3 65.2 + - - +
183B GLU 3.4 0.5 + - - -
184B ALA* 3.0 24.1 + - - +
205B PHE* 3.6 23.8 - - + -
208B ASP* 4.2 7.7 + - + -
209B ILE* 5.5 0.7 - - + +
212B MET* 3.8 23.3 - - + -
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 4.2 10.1 - - + -
81B PHE* 3.7 23.7 - - + -
177B MET* 2.9 28.1 + - + +
178B VAL* 3.5 11.9 - - + +
180B ALA* 1.3 74.0 - - - +
182B ASP* 1.3 66.9 + - - +
184B ALA* 3.3 3.7 + - - +
185B MET* 3.1 28.6 + - + +
263B ALA* 3.9 22.9 - - + +
266B HIS* 4.2 12.1 - - + -
267B GLU* 4.1 16.8 - - - +
436B THR* 6.3 1.8 - - - -
437B LEU* 4.0 35.0 - - + +
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Residues in contact with ASP 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B VAL* 3.0 32.6 + - - +
179B ARG* 3.6 10.5 - - + +
180B ALA 3.2 0.6 - - - -
181B LEU* 1.3 78.6 - - - +
183B GLU* 1.3 51.9 + - - +
185B MET* 3.2 5.5 + - - +
186B ASN* 2.8 50.8 + - - +
436B THR* 4.3 22.9 - - - +
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ARG* 3.0 16.5 + - + +
180B ALA 3.7 0.2 - - - +
181B LEU 3.2 0.2 - - - -
182B ASP* 1.3 72.3 - - - +
184B ALA* 1.3 66.9 + - - +
186B ASN* 3.1 5.9 + - - +
187B LYS* 2.8 44.7 + - - +
190B ARG* 2.7 45.7 + - - -
201B ASN* 3.4 25.7 + - - +
202B LYS* 4.5 3.5 + - - +
205B PHE* 3.4 40.6 - - + +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA* 4.8 1.6 - - - +
77B PHE* 3.7 42.3 - - + +
78B VAL* 4.1 17.5 - - + +
81B PHE* 4.5 2.0 - - + -
180B ALA 3.0 17.6 + - - +
181B LEU 3.7 4.7 - - - +
182B ASP 3.3 0.2 - - - -
183B GLU* 1.3 79.4 - - - +
185B MET* 1.3 62.3 + - + +
187B LYS* 3.7 13.8 + - - +
188B LEU* 3.6 14.0 - - - +
205B PHE* 4.7 3.5 - - + -
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Residues in contact with MET 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO* 6.2 3.8 - - + -
74B ALA* 4.0 18.6 - - + -
78B VAL* 5.6 1.8 - - - -
181B LEU* 3.1 17.7 + - + +
182B ASP* 3.7 6.5 - - - +
184B ALA* 1.3 79.8 - - - +
186B ASN* 1.3 69.0 + - - +
188B LEU* 3.3 43.8 - - + +
189B ARG* 4.1 8.4 + - - +
436B THR* 3.6 23.1 - - - +
437B LEU* 3.7 46.2 - - + +
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Residues in contact with ASN 186 (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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182B ASP* 2.8 33.8 + - - +
183B GLU* 3.7 5.8 + - - +
185B MET* 1.3 78.3 - - - +
187B LYS* 1.3 59.0 + - - +
188B LEU 3.1 0.2 - - - -
189B ARG* 2.8 37.5 + - - +
190B ARG* 3.5 30.4 - - + +
201B ASN* 5.7 2.2 - - - +
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Residues in contact with LYS 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 3.6 39.8 - - + +
80B ASP* 4.0 13.1 + - - -
183B GLU* 2.8 43.9 + - - +
184B ALA* 3.7 8.7 - - - +
186B ASN* 1.3 76.2 - - - +
188B LEU* 1.3 62.2 + - - +
189B ARG 3.2 1.2 + - - -
190B ARG* 3.3 31.7 + - - +
193B PRO* 5.4 5.7 - - + +
202B LYS* 6.2 3.1 - - - -
205B PHE* 3.7 31.4 - - - -
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Residues in contact with LEU 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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17B LEU* 4.6 16.5 - - - +
20B LEU* 5.9 2.4 - - - +
73B GLN* 3.2 33.9 - - + +
74B ALA* 3.7 12.8 - - + +
77B PHE* 3.5 27.4 - - + -
184B ALA 3.6 6.3 - - - +
185B MET* 3.3 48.7 - - + +
186B ASN 3.1 0.4 - - - -
187B LYS* 1.3 78.1 - - - +
189B ARG* 1.3 61.6 + - + +
190B ARG 3.3 1.2 + - - -
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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
------------------------------------------------------------
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