Contacts of the helix formed by residues 161 - 182 (chain B) in PDB entry 2O9D
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 161 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B PRO* 3.7 30.2 + - + +
159B ALA 3.4 16.4 - - - -
160B GLY* 1.3 78.9 - - - +
162B ALA* 1.3 63.1 + - - +
163B PRO* 3.4 1.3 - - - -
164B ILE* 3.2 37.6 + - + +
165B ALA* 3.2 12.0 + - + +
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Residues in contact with ALA 162 (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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152B ALA* 3.6 31.0 + - - +
153B THR* 3.9 21.1 - - + -
158B PRO 5.1 1.0 + - - -
160B GLY 4.6 2.0 - - - +
161B PHE* 1.3 77.3 - - - +
163B PRO* 1.4 62.9 - - + +
165B ALA* 3.3 1.1 + - - +
166B ILE* 2.8 42.5 + - + +
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Residues in contact with PRO 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.6 18.9 - - - +
51B ALA* 3.9 29.6 - - + +
52B PHE* 3.6 42.4 - - + +
160B GLY 3.4 15.3 - - - +
161B PHE 3.5 0.9 - - - -
162B ALA* 1.4 91.7 - - + +
164B ILE* 1.3 52.7 + - - +
166B ILE* 4.7 2.7 - - + -
167B GLY* 2.8 30.8 + - - -
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.0 13.7 - - + -
52B PHE* 3.9 27.8 - - + -
161B PHE* 3.2 35.9 + - + +
163B PRO* 1.3 74.1 - - - +
165B ALA* 1.3 68.4 + - - +
168B LEU* 3.0 48.8 + - + +
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 3.8 10.9 - - + +
152B ALA* 3.8 23.6 - - + -
161B PHE* 3.2 9.9 + - + +
162B ALA* 3.7 6.7 - - - +
164B ILE* 1.3 80.4 - - - +
166B ILE* 1.3 59.2 + - - +
168B LEU* 4.1 2.4 - - - +
169B ALA* 3.2 27.0 + - - +
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Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.8 18.7 - - + +
51B ALA* 5.9 3.4 - - + -
60B GLY 5.9 2.5 - - - +
145B PHE* 3.5 19.5 - - + -
148B VAL* 4.6 4.7 - - + -
149B ILE* 3.9 52.9 - - + +
152B ALA* 4.3 7.2 - - + -
153B THR* 4.0 23.3 - - + -
162B ALA* 2.8 27.6 + - + +
163B PRO* 4.3 2.9 - - + +
165B ALA* 1.3 75.7 - - - +
167B GLY* 1.3 64.7 + - - +
169B ALA* 3.4 8.0 + - - -
170B LEU* 3.4 8.3 + - - +
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Residues in contact with GLY 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLY* 3.1 41.4 - - - -
47B VAL* 3.8 12.5 - - - +
48B LEU* 3.9 4.5 - - - -
163B PRO 2.8 22.1 + - - -
166B ILE* 1.3 74.2 - - - +
168B LEU* 1.3 56.8 + - - +
170B LEU* 3.0 16.6 + - - +
171B THR 3.3 0.7 + - - -
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Residues in contact with LEU 168 (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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41B LEU* 5.1 7.9 - - + -
44B GLY 5.7 0.2 - - - -
45B LEU* 5.0 9.4 - - + -
48B LEU* 4.4 17.0 - - + +
164B ILE* 3.0 37.7 + - + +
165B ALA* 4.4 2.5 - - - +
167B GLY* 1.3 71.9 - - - +
169B ALA* 1.3 59.8 + - - +
171B THR* 3.4 20.2 - - + +
172B LEU* 3.1 25.6 + - - +
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Residues in contact with ALA 169 (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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145B PHE* 4.0 16.8 - - + -
148B VAL* 4.2 20.9 - - + -
165B ALA 3.2 19.9 + - - +
166B ILE 3.7 5.8 - - - +
167B GLY 3.3 0.6 - - - -
168B LEU* 1.3 72.8 - - - +
170B LEU* 1.3 60.0 + - - +
172B LEU* 3.4 13.3 + - + +
173B ILE* 2.9 37.1 + - + +
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Residues in contact with LEU 170 (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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15B LEU* 4.5 8.3 - - + -
40B ALA 4.7 0.2 - - - -
43B PHE* 3.6 38.1 - - + +
44B GLY* 3.9 3.8 - - - -
47B VAL* 3.9 17.0 - - + -
63B ASN* 6.2 0.2 - - - +
145B PHE* 4.0 23.1 - - + -
166B ILE 3.4 7.3 + - - +
167B GLY 3.0 11.5 + - - +
169B ALA* 1.3 75.2 - - - +
171B THR* 1.3 67.7 + - - +
173B ILE* 3.3 5.0 + - + +
174B HIS* 2.9 48.1 + - + +
185B VAL* 3.6 31.4 - - + -
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Residues in contact with THR 171 (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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37B ALA 5.5 0.2 - - - +
40B ALA* 3.3 28.2 + - + +
41B LEU* 3.9 21.6 + - + +
44B GLY* 3.2 21.4 - - - -
167B GLY 3.3 3.4 + - - -
168B LEU* 3.4 23.1 - - + +
170B LEU* 1.3 80.4 - - - +
172B LEU* 1.3 62.7 + - - +
174B HIS 3.2 0.2 + - - -
175B LEU* 2.9 41.7 + - + +
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Residues in contact with LEU 172 (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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168B LEU 3.1 14.3 + - - +
169B ALA* 3.6 15.0 - - + +
170B LEU 3.2 0.2 - - - -
171B THR* 1.3 74.6 - - - +
173B ILE* 1.3 67.9 + - + +
175B LEU* 3.0 28.6 + - + +
176B ILE* 3.2 37.1 + - + +
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Residues in contact with ILE 173 (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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141B LEU* 3.5 48.0 - - + +
144B GLY 5.3 0.7 - - - -
145B PHE* 3.6 33.9 - - + +
169B ALA* 2.9 23.9 + - + +
170B LEU* 3.6 7.9 - - + +
172B LEU* 1.3 80.1 - - + +
174B HIS* 1.3 57.1 + - - +
176B ILE* 3.3 10.6 + - - +
177B SER* 3.1 29.8 + - - -
183B CYS* 3.5 20.0 - - - -
185B VAL* 3.8 19.3 - - + -
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Residues in contact with HIS 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 5.6 0.5 - - - +
40B ALA* 3.3 23.8 - - + -
43B PHE* 3.4 56.2 - + + +
170B LEU* 2.9 48.9 + - + +
173B ILE* 1.3 69.8 - - - +
175B LEU* 1.3 64.1 + - - +
176B ILE 3.4 0.3 + - - -
178B ILE* 3.3 41.0 + - + +
179B PRO* 4.9 0.2 - - - +
182B ASN 4.4 1.8 - - - -
183B CYS* 3.3 47.5 + - + +
184B SER 5.1 2.9 + - - -
185B VAL* 4.9 1.3 - - + -
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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
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36B PHE* 5.1 2.2 - - - -
37B ALA* 3.9 26.5 - - + +
40B ALA* 3.8 16.4 - - + -
171B THR* 2.9 31.7 + - + +
172B LEU* 3.0 19.0 + - + +
174B HIS* 1.3 76.2 - - - +
176B ILE* 1.3 60.2 - - + +
178B ILE 5.1 0.2 - - - -
179B PRO* 5.0 4.9 - - - +
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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
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137B VAL* 4.5 9.4 - - + -
141B LEU* 3.7 33.9 - - + -
172B LEU* 3.2 42.3 + - + +
173B ILE* 3.6 4.5 - - - +
175B LEU* 1.3 78.7 - - + +
177B SER* 1.3 62.1 + - - +
178B ILE 3.7 0.7 - - - -
179B PRO* 3.8 11.2 - - - +
180B VAL* 4.7 6.1 - - - +
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Residues in contact with SER 177 (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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137B VAL* 3.8 20.0 - - - -
138B GLU* 4.4 2.7 + - - -
141B LEU* 3.5 24.0 - - - +
173B ILE 3.1 12.9 + - - -
176B ILE* 1.3 77.3 - - - +
178B ILE* 1.3 65.8 + - - +
179B PRO* 3.3 2.7 - - - -
180B VAL* 2.9 16.2 + - - -
181B THR* 3.1 13.4 + - - -
183B CYS* 3.2 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
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36B PHE* 3.6 62.8 - - + +
39B VAL* 3.8 23.1 - - + -
126B PRO* 3.3 6.8 - - - +
174B HIS* 3.3 29.3 + - + +
177B SER* 1.3 76.4 + - - +
179B PRO* 1.4 65.3 - - + +
180B VAL 2.9 2.3 + - - -
182B ASN* 2.9 53.4 + - - +
183B CYS* 4.0 7.0 - - + -
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Residues in contact with PRO 179 (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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36B PHE* 4.3 20.2 - - + -
126B PRO* 4.1 8.7 - - + -
127B GLY* 2.9 29.1 + - - +
129B TYR* 3.4 18.2 - - + +
174B HIS 4.9 0.9 - - - +
175B LEU 5.0 4.3 - - - +
176B ILE 3.8 13.0 - - - +
177B SER 3.5 4.3 - - - -
178B ILE* 1.4 95.1 - - + +
180B VAL* 1.3 59.7 + - + +
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Residues in contact with VAL 180 (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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125B SER* 2.8 26.8 + - - -
126B PRO* 4.1 1.1 - - - -
129B TYR* 3.8 37.4 - - + +
133B SER* 3.5 22.4 - - - +
134B ALA* 3.9 6.4 - - - +
137B VAL* 3.5 33.9 - - + -
176B ILE 4.7 5.4 - - - +
177B SER* 2.9 17.0 + - - +
178B ILE 2.9 1.6 + - - -
179B PRO* 1.3 81.4 - - + +
181B THR* 1.3 59.6 + - - +
182B ASN 3.9 0.2 - - - -
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Residues in contact with THR 181 (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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119B ASN* 3.1 22.7 - - - +
120B GLY 3.2 16.4 + - - +
126B PRO* 3.9 4.3 - - - -
134B ALA* 3.3 44.0 - - + +
137B VAL* 4.6 2.8 - - + +
138B GLU* 2.6 25.0 + - + -
177B SER* 3.1 6.0 + - - -
180B VAL* 1.3 77.4 - - + +
182B ASN* 1.3 66.7 + - - +
183B CYS* 3.1 8.8 + - - -
208B PHE* 3.7 20.4 - - + -
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Residues in contact with ASN 182 (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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36B PHE* 5.3 2.8 - - - -
43B PHE* 5.6 1.0 - - - -
117B ALA* 3.3 28.6 + - - +
118B SER 2.8 26.0 + - - +
119B ASN* 3.7 4.7 - - - +
126B PRO* 3.1 23.7 - - + +
174B HIS* 4.4 2.8 - - - -
178B ILE* 2.9 37.2 + - - +
181B THR* 1.3 76.5 - - - +
183B CYS* 1.3 71.6 + - - +
189B ARG* 3.6 6.8 + - - +
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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
------------------------------------------------------------
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