Contacts of the helix formed by residues 161 - 182 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PRO* 3.7 38.3 + - + +
159A ALA 3.3 17.0 - - - -
160A GLY* 1.3 78.3 - - - +
162A ALA* 1.3 66.3 + - - +
163A PRO* 3.3 2.5 - - - -
164A ILE* 2.9 39.2 + - + +
165A ALA* 3.3 11.4 + - + +
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Residues in contact with ALA 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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152A ALA* 3.6 31.4 + - - +
153A THR* 3.7 24.5 - - + -
158A PRO 4.7 0.6 + - - -
160A GLY 3.4 1.7 - - - +
161A PHE* 1.3 76.8 - - - +
163A PRO* 1.4 69.8 - - + +
164A ILE 3.2 0.5 + - - -
165A ALA* 3.2 2.5 + - - +
166A ILE* 3.0 34.4 + - + +
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Residues in contact with PRO 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL 4.7 0.3 - - - +
48A LEU* 3.5 18.1 - - - +
51A ALA* 3.8 36.3 - - + +
52A PHE* 3.6 39.0 - - + -
160A GLY* 3.5 13.5 - - - +
161A PHE 3.4 4.5 - - - -
162A ALA* 1.4 92.3 - - + +
164A ILE* 1.3 55.2 + - - +
166A ILE* 4.8 3.8 - - + -
167A GLY 3.1 21.7 + - - -
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Residues in contact with ILE 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.9 14.8 - - + +
52A PHE* 3.9 26.9 - - + -
161A PHE* 2.9 36.0 + - + +
163A PRO* 1.3 74.1 - - - +
165A ALA* 1.3 65.3 + - - +
168A LEU* 3.0 49.9 + - + +
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Residues in contact with ALA 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* 3.9 10.5 - - + +
152A ALA* 3.9 24.2 - - + -
161A PHE* 3.3 7.5 + - + +
162A ALA* 3.2 7.7 + - - +
164A ILE* 1.3 80.0 - - - +
166A ILE* 1.3 56.9 + - - +
168A LEU* 3.9 3.3 - - - +
169A ALA* 2.9 28.4 + - - +
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Residues in contact with ILE 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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47A VAL* 3.6 21.5 - - + -
51A ALA* 5.9 3.1 - - + -
60A GLY 5.7 3.4 - - - +
145A PHE* 3.5 15.8 - - + -
148A VAL* 4.6 4.9 - - + +
149A ILE* 3.7 50.0 - - + +
152A ALA* 4.7 3.1 - - + -
153A THR* 4.2 11.7 - - + -
162A ALA* 3.0 37.3 + - + +
163A PRO* 4.4 4.0 - - + +
165A ALA* 1.3 73.4 - - - +
167A GLY* 1.3 66.3 + - - +
169A ALA* 3.3 7.9 + - - +
170A LEU* 3.1 18.4 + - - +
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Residues in contact with GLY 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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44A GLY* 2.9 44.3 - - - -
47A VAL* 4.0 7.7 - - - +
48A LEU* 3.8 9.6 - - - -
163A PRO 3.1 17.8 + - - -
164A ILE 4.1 0.2 - - - -
166A ILE* 1.3 76.5 - - - +
168A LEU* 1.3 58.3 + - - +
170A LEU* 3.2 12.7 + - - +
171A THR 3.2 1.0 + - - -
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Residues in contact with LEU 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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41A LEU* 5.3 6.5 - - + -
44A GLY 5.8 0.2 - - - -
45A LEU* 5.1 11.0 - - + -
48A LEU* 4.5 14.8 - - + +
164A ILE* 3.0 40.6 + - + +
165A ALA* 4.2 3.6 - - - +
167A GLY* 1.3 73.6 - - - +
169A ALA* 1.3 58.5 + - - +
170A LEU 3.1 1.8 - - - -
171A THR* 3.1 15.1 + - + +
172A LEU* 2.9 29.2 + - - +
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Residues in contact with ALA 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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145A PHE* 4.1 15.0 - - + -
148A VAL* 4.1 23.3 - - + -
165A ALA 2.9 21.2 + - - +
166A ILE 3.3 7.2 + - - +
168A LEU* 1.3 74.8 - - - +
170A LEU* 1.3 57.3 + - - +
172A LEU* 3.4 12.7 - - + +
173A ILE* 2.8 37.8 + - + +
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Residues in contact with LEU 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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15A LEU* 4.4 11.0 - - + -
43A PHE* 3.8 21.5 - - + +
44A GLY* 4.2 2.2 - - - -
47A VAL* 3.5 29.8 - - + -
63A ASN* 6.0 0.9 - - - +
145A PHE* 4.0 19.5 - - + -
166A ILE 3.1 12.2 + - - +
167A GLY* 3.5 10.5 - - - +
168A LEU 3.1 0.8 - - - -
169A ALA* 1.3 73.8 - - - +
171A THR* 1.3 64.3 + - - +
173A ILE* 4.2 6.3 - - + -
174A HIS* 2.9 46.6 + - + +
185A VAL* 3.6 31.0 - - + -
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Residues in contact with THR 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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37A ALA 5.5 0.2 - - - +
40A ALA* 2.7 32.5 + - + +
41A LEU* 3.4 22.9 + - + +
44A GLY* 3.3 15.5 - - - -
167A GLY 3.2 5.7 + - - -
168A LEU* 3.1 18.7 + - + +
170A LEU* 1.3 73.2 - - - +
172A LEU* 1.3 66.9 + - - +
174A HIS* 3.0 5.5 + - - +
175A LEU* 2.8 38.4 + - + +
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Residues in contact with LEU 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 LEU 2.9 15.2 + - - +
169A ALA* 3.4 15.5 - - + +
171A THR* 1.3 71.6 - - - +
173A ILE* 1.3 68.3 + - + +
175A LEU* 2.8 30.0 + - + +
176A ILE* 3.0 38.3 + - + +
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Residues in contact with ILE 173 (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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141A LEU* 3.7 32.7 - - + +
145A PHE* 3.6 45.3 - - + +
169A ALA* 2.8 26.7 + - + +
170A LEU* 3.8 9.4 - - + +
172A LEU* 1.3 76.2 - - + +
174A HIS* 1.3 56.2 + - - +
176A ILE* 3.5 8.0 + - - -
177A SER* 2.9 30.8 + - - -
183A CYS* 3.5 20.9 - - - -
185A VAL* 3.7 23.6 - - + -
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Residues in contact with HIS 174 (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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36A PHE* 5.0 1.2 - - - +
40A ALA* 3.3 23.3 - - + -
43A PHE* 3.3 55.6 - + + +
170A LEU* 2.9 39.4 + - + +
171A THR 3.0 4.5 + - - +
173A ILE* 1.3 73.5 - - - +
175A LEU* 1.3 62.9 + - - +
176A ILE 3.1 2.5 - - - -
178A ILE* 3.3 42.9 + - + +
179A PRO* 4.9 0.2 - - - +
182A ASN 4.6 1.6 - - - -
183A CYS* 3.3 46.0 + - + +
184A SER 4.9 4.5 - - - -
189A ARG* 4.5 0.6 + - - -
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Residues in contact with LEU 175 (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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36A PHE* 5.2 2.9 - - - -
37A ALA* 4.0 33.7 - - + +
40A ALA* 4.0 8.7 - - + -
171A THR* 2.8 30.9 + - + +
172A LEU* 2.8 24.1 + - + +
174A HIS* 1.3 72.1 - - - +
176A ILE* 1.3 62.2 + - + +
179A PRO* 4.9 5.0 - - - +
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Residues in contact with ILE 176 (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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137A VAL* 4.4 10.3 - - + -
141A LEU* 3.9 36.1 - - + -
172A LEU* 3.0 44.6 + - + +
173A ILE* 3.8 3.6 - - - +
175A LEU* 1.3 82.0 - - + +
177A SER* 1.3 61.8 + - - +
178A ILE 3.8 0.9 - - - -
179A PRO* 3.7 11.0 - - - +
180A VAL* 4.6 6.3 - - + +
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Residues in contact with SER 177 (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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137A VAL* 4.0 21.5 - - - -
138A GLU* 4.8 2.1 + - - -
141A LEU* 3.6 21.8 - - - +
173A ILE* 2.9 15.8 + - - +
176A ILE* 1.3 77.9 - - - +
178A ILE* 1.3 68.3 + - - +
179A PRO 3.2 2.9 - - - -
180A VAL* 3.0 17.0 + - - -
181A THR* 3.1 12.7 + - - -
183A CYS* 3.2 23.7 + - - +
185A VAL* 5.7 0.2 - - - +
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Residues in contact with ILE 178 (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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36A PHE* 3.5 66.0 - - + +
39A VAL* 4.1 21.5 - - + -
126A PRO* 3.3 4.9 - - - +
174A HIS* 3.3 38.0 + - + +
177A SER* 1.3 74.8 + - - +
179A PRO* 1.3 68.6 - - + +
182A ASN* 2.8 54.4 + - - +
183A CYS* 4.0 0.2 - - - +
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Residues in contact with PRO 179 (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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36A PHE* 4.2 20.9 - - + -
126A PRO* 3.6 9.2 - - + +
127A GLY* 2.7 35.9 + - - +
129A TYR* 3.4 15.1 - - + +
174A HIS 4.9 1.1 - - - +
175A LEU 4.9 3.4 - - - +
176A ILE 3.7 14.8 - - - +
177A SER 3.4 4.3 - - - -
178A ILE* 1.3 92.6 - - + +
180A VAL* 1.3 61.6 + - + +
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Residues in contact with VAL 180 (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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120A GLY 3.8 0.2 - - - +
121A TYR* 4.9 0.3 - - - -
125A SER* 2.4 28.8 + - - -
126A PRO* 4.2 0.9 - - - -
129A TYR* 3.7 40.3 - - + +
133A SER* 3.9 19.5 - - - +
134A ALA* 4.1 5.6 - - - +
137A VAL* 3.8 32.8 - - + -
176A ILE* 4.6 5.8 - - + +
177A SER* 3.0 18.4 + - - +
179A PRO* 1.3 81.9 - - + +
181A THR* 1.3 60.1 + - - +
182A ASN 3.8 0.2 - - - -
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Residues in contact with THR 181 (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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119A ASN* 3.2 24.8 - - - +
120A GLY 3.3 16.4 + - - +
126A PRO* 4.2 2.9 - - - -
134A ALA* 3.4 37.2 - - + +
137A VAL* 4.4 3.7 - - + +
138A GLU* 2.6 36.9 + - + +
177A SER* 3.1 6.1 + - - -
180A VAL* 1.3 80.5 - - + +
182A ASN* 1.3 65.9 + - - +
183A CYS* 3.1 9.0 + - - -
208A PHE* 3.9 11.0 - - + -
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Residues in contact with ASN 182 (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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36A PHE* 5.1 2.4 - - - -
43A PHE* 5.8 0.2 - - - -
117A ALA* 3.6 22.7 - - - +
118A SER 3.0 26.6 + - - +
119A ASN* 3.4 5.8 - - - +
120A GLY 5.1 0.2 - - - +
126A PRO* 3.2 25.6 - - + +
174A HIS* 4.6 1.4 - - - -
178A ILE* 2.8 37.7 + - - +
181A THR* 1.3 77.1 - - - +
183A CYS* 1.3 70.5 + - - +
189A ARG* 3.6 7.4 + - - -
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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