Contacts of the helix formed by residues 172 - 189 (chain B) in PDB entry 1W98
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 LEU 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 3.7 19.5 - - + -
169B VAL* 2.9 21.9 + - + +
171B THR* 1.3 78.3 + - - +
173B LEU* 1.3 63.8 + - - +
174B GLN 3.4 1.6 - - - -
175B LEU* 3.3 33.1 + - + -
176B ILE* 3.2 44.0 + - + +
214B MET* 4.0 11.9 - - + -
217B MET* 6.0 2.5 - - + -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 3.8 35.4 - - + -
129B MET* 3.9 30.3 - - + +
130B ARG* 5.0 1.3 - - - +
133B LEU* 3.5 22.6 - - + +
158B PHE* 4.4 14.8 - - + -
162B MET* 4.1 9.9 - - + -
168B VAL* 3.8 24.0 - - + -
169B VAL 4.1 1.6 - - - +
170B LYS* 3.3 18.5 + - + +
172B LEU* 1.3 79.1 - - - +
174B GLN* 1.3 56.9 + - - +
176B ILE* 3.3 7.7 + - + +
177B GLY 2.9 26.0 + - - -
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Residues in contact with GLN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.0 11.4 - - + +
136B TRP* 3.5 37.2 + - + -
170B LYS 4.7 1.4 + - - -
171B THR 4.8 4.2 + - - +
172B LEU 3.4 0.8 - - - -
173B LEU* 1.3 77.4 - - - +
175B LEU* 1.3 57.3 + - - +
178B ILE* 3.0 30.1 + - - +
202B THR* 3.7 22.2 + - + +
205B ALA* 3.2 27.5 - - - +
206B CYS* 4.0 10.1 - - - -
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B THR 5.3 1.7 + - - +
172B LEU* 3.3 24.1 + - + +
173B LEU 3.3 0.4 - - - -
174B GLN* 1.3 78.9 - - - +
176B ILE* 1.3 60.0 + - - +
178B ILE* 3.7 1.4 - - - +
179B SER* 2.6 37.6 + - - +
206B CYS* 3.8 27.9 - - + -
210B GLU* 3.7 54.1 - - + +
211B ILE* 3.9 4.7 - - + +
214B MET* 3.7 27.6 - - + -
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Residues in contact with ILE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PHE* 3.7 24.7 - - + -
161B TYR* 3.7 29.8 - - + -
162B MET* 4.0 13.2 - - - -
168B VAL* 3.7 30.5 - - + -
172B LEU* 3.2 26.2 + - + +
173B LEU* 3.8 7.2 - - + +
175B LEU* 1.3 75.7 - - - +
177B GLY* 1.3 52.6 + - - +
180B SER* 2.7 38.6 + - - +
214B MET* 3.7 28.7 - - + -
218B ILE* 3.4 6.1 - - + +
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Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.1 19.0 - - - +
137B LEU* 3.6 17.7 - - - +
158B PHE* 4.6 3.1 - - - -
173B LEU 2.9 16.5 + - - -
174B GLN 4.0 0.2 - - - -
176B ILE* 1.3 73.4 - - - +
178B ILE* 1.3 60.4 + - - +
179B SER 3.1 1.3 + - - -
180B SER* 3.3 7.5 + - - -
181B LEU* 3.0 27.2 + - - +
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Residues in contact with ILE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TRP* 3.9 17.6 - - + -
137B LEU* 4.0 6.8 - - + +
140B VAL* 4.3 2.0 - - + -
174B GLN 3.0 24.2 + - - +
175B LEU* 3.7 9.0 - - - +
177B GLY* 1.3 70.6 - - - -
179B SER* 1.3 59.3 + - - +
181B LEU* 3.5 18.6 + - + +
182B PHE* 2.9 27.4 + - - +
198B PHE* 3.6 39.9 - - + +
201B VAL* 3.8 22.7 - - + -
202B THR* 4.0 13.0 - - + -
206B CYS* 4.4 0.9 - - - -
211B ILE* 3.7 26.2 - - + -
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 2.6 25.3 + - - +
178B ILE* 1.3 73.1 - - - +
180B SER* 1.3 65.2 + - - +
181B LEU 3.3 0.2 - - - -
182B PHE* 3.3 8.4 + - - +
183B ILE* 3.1 28.6 + - - +
211B ILE* 3.6 22.2 - - - +
214B MET* 3.5 30.9 - - - +
215B GLU* 4.2 9.0 - - - +
218B ILE* 3.9 7.9 - - - -
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 5.7 0.2 - - - -
154B ALA* 3.6 25.8 - - - -
157B PHE* 3.7 18.0 + - - +
158B PHE* 3.7 17.0 + - - +
161B TYR* 5.6 0.2 - - - +
176B ILE* 2.7 24.7 + - - +
177B GLY* 3.6 7.0 - - - -
179B SER* 1.3 72.7 - - - +
181B LEU* 1.3 63.4 + - - +
183B ILE* 3.5 10.7 + - - -
184B ALA* 3.1 24.1 + - - +
218B ILE* 3.5 11.1 - - - +
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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
----------------------------------------------------------
137B LEU* 3.8 22.0 - - + +
140B VAL* 3.5 31.2 - - + -
141B CYS* 3.7 30.1 - - - -
146B LEU* 4.2 5.8 - - + -
150B THR* 3.8 16.2 - - - +
151B PHE* 4.6 0.4 - - - -
154B ALA* 3.7 19.6 - - + +
177B GLY 3.0 14.2 + - - +
178B ILE* 3.5 11.7 - - + +
180B SER* 1.3 76.8 - - - +
182B PHE* 1.3 56.5 + - - +
184B ALA* 3.2 2.1 + - - +
185B ALA* 2.8 29.5 + - - +
198B PHE* 3.7 15.9 - - + -
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Residues in contact with PHE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 3.3 35.7 - - - -
178B ILE 2.9 20.2 + - - +
179B SER 3.3 5.8 + - - +
181B LEU* 1.3 73.7 - - - +
183B ILE* 1.3 62.5 + - - +
185B ALA* 3.9 0.5 - - - +
186B LYS* 3.0 50.7 + - + +
193B PRO 4.5 2.9 - - - -
195B LEU* 3.7 36.8 - - + -
198B PHE* 3.6 33.3 - + + -
211B ILE* 3.4 23.6 - - + -
212B LEU* 4.0 10.5 - - + -
215B GLU* 3.6 19.7 - - + -
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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
----------------------------------------------------------
49A ILE* 4.3 5.2 - - + +
157B PHE* 3.6 20.4 - - + -
179B SER 3.1 19.0 + - - +
180B SER* 3.8 6.1 - - - +
181B LEU 3.4 0.2 - - - -
182B PHE* 1.3 74.8 - - - +
184B ALA* 1.3 56.7 + - - +
186B LYS* 3.4 10.2 + - - +
187B LEU* 3.0 36.2 + - + +
215B GLU* 3.6 32.1 - - + +
218B ILE* 3.6 31.4 - - + -
219B MET* 3.7 35.4 - - + -
226B LEU* 4.2 4.5 - - + -
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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
----------------------------------------------------------
150B THR* 3.5 27.8 - - - +
153B LEU* 3.6 22.3 - - + +
154B ALA* 3.8 4.7 - - + +
157B PHE* 4.0 8.7 - - + -
180B SER 3.1 18.2 + - - +
181B LEU 3.5 4.7 - - - +
183B ILE* 1.3 76.3 - - - +
185B ALA* 1.3 58.2 + - - +
187B LEU* 3.4 3.0 + - - +
188B GLU* 2.9 33.4 + - - +
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Residues in contact with ALA 185 (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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146B LEU* 4.6 4.3 - - + -
150B THR* 3.9 12.5 + - - +
181B LEU 2.8 17.2 + - - +
182B PHE 3.9 1.1 - - - +
184B ALA* 1.3 74.8 - - - +
186B LYS* 1.3 64.3 + - - +
189B GLU* 3.0 30.1 + - + +
192B PRO* 3.4 22.8 - - + +
193B PRO* 4.3 5.2 - - + -
198B PHE* 3.6 25.1 - - + -
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Residues in contact with LYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 2.7 35.3 + - + +
44A VAL 2.7 22.7 + - - +
46A SER* 3.1 40.8 - - - +
49A ILE* 3.8 10.4 - - + +
50A ARG* 4.1 7.1 + - - -
182B PHE* 3.0 45.2 + - + +
183B ILE* 3.7 3.4 - - - +
184B ALA 3.4 0.2 - - - -
185B ALA* 1.3 78.3 - - + +
187B LEU* 1.3 60.8 + - - +
189B GLU 4.4 4.2 - - - +
192B PRO* 4.0 16.9 - - + +
215B GLU* 2.6 31.9 + - - -
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.6 24.0 - - + -
50A ARG* 2.9 57.1 + - + +
53A SER* 4.2 7.9 - - - +
150A ARG* 4.4 2.9 + - - -
153B LEU* 4.5 8.3 - - + -
157B PHE* 3.6 32.3 - - + -
183B ILE* 3.0 21.1 + - + +
184B ALA* 3.4 8.3 - - - +
186B LYS* 1.3 75.7 - - - +
188B GLU* 1.3 61.9 + - - +
226B LEU* 3.7 19.5 - - + +
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ARG* 3.0 29.0 + - - +
151A ALA* 6.1 0.7 - - - +
157A ARG* 2.6 59.2 + - - +
159A TYR* 5.3 0.7 - - - -
149B GLU* 3.4 33.2 - - + +
150B THR* 3.5 26.5 - - + -
153B LEU* 4.0 11.9 - - + +
184B ALA 2.9 17.7 + - - +
185B ALA 3.3 0.2 + - - -
187B LEU* 1.3 79.6 - - - +
189B GLU* 1.3 56.9 + - - +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 4.0 5.7 + - - -
157A ARG* 4.5 0.9 - - - +
160A TPO 3.9 6.4 + - - -
145B LYS 5.0 0.9 - - - +
146B LEU* 3.4 25.6 - - + +
147B HIS* 2.8 42.4 + - - -
150B THR* 2.6 33.5 - - + +
185B ALA* 3.0 22.4 + - + +
186B LYS 4.4 2.9 - - - +
188B GLU* 1.3 77.4 - - - +
190B ILE* 1.3 67.4 + - - +
191B TYR 4.2 3.6 - - - +
192B PRO* 3.8 22.9 - - + +
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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