Contacts of the helix formed by residues 151 - 171 in PDB entry 2IIL
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 ASN 151
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72 ARG 5.4 1.8 - - - -
74 VAL* 4.5 2.4 - - - +
148 TRP* 5.6 7.2 - - + -
149 ARG* 3.1 37.2 + - - +
150 PRO* 1.3 75.2 - - - +
152 ASN* 1.3 70.8 + - - +
153 ARG* 3.2 26.1 - - - +
154 HIS* 2.9 37.3 + - - -
155 ALA* 3.3 17.7 + - - +
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Residues in contact with ASN 152
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72 ARG* 4.7 24.3 + - + +
77 ILE* 5.3 7.2 - - + +
151 ASN* 1.3 83.2 + - - +
153 ARG* 1.3 59.7 + - - +
155 ALA* 3.3 10.4 + - - +
156 TYR* 2.8 34.6 + - - +
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Residues in contact with ARG 153
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148 TRP* 6.1 2.0 - - - -
151 ASN* 3.2 22.1 + - - +
152 ASN* 1.3 84.4 + - - +
154 HIS* 1.3 77.7 + - - +
156 TYR* 3.2 11.0 + - + +
157 VAL* 3.0 41.2 + - + +
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Residues in contact with HIS 154
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74 VAL* 5.6 0.9 - - + -
133 LEU* 5.0 4.4 - - - +
140 GLN* 6.2 0.7 - - - -
148 TRP* 2.9 35.9 + + - -
150 PRO* 3.6 18.6 - - + -
151 ASN* 2.9 42.1 + - - +
153 ARG* 1.3 94.3 + - + +
155 ALA* 1.3 57.0 + - - +
157 VAL* 3.2 13.2 + - - +
158 GLY* 2.9 25.8 + - - -
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Residues in contact with ALA 155
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73 ASN 5.1 0.4 - - - -
74 VAL* 4.1 25.9 - - + +
77 ILE* 3.5 36.9 - - + +
133 LEU* 4.5 2.9 - - - +
151 ASN 3.3 10.0 + - - +
152 ASN* 3.3 11.8 + - - +
154 HIS* 1.3 76.8 - - - +
156 TYR* 1.3 55.1 - - - +
158 GLY* 3.4 2.7 + - - +
159 ILE* 2.9 33.6 + - - +
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Residues in contact with TYR 156
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77 ILE* 4.4 1.3 - - - +
152 ASN 2.8 16.3 + - - +
153 ARG* 3.3 14.6 - - + +
155 ALA* 1.3 70.3 - - - +
157 VAL* 1.3 69.2 + - + +
159 ILE* 3.0 39.6 - - + +
160 ALA* 3.0 21.6 + - + +
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Residues in contact with VAL 157
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153 ARG* 3.0 34.9 + - + +
154 HIS* 3.2 13.0 + - - +
156 TYR* 1.3 78.0 - - + +
158 GLY* 1.3 53.3 + - - +
160 ALA* 3.2 8.0 + - - +
161 VAL* 2.8 50.5 + - + +
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Residues in contact with GLY 158
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133 LEU* 3.2 40.2 - - - -
154 HIS 2.9 10.3 + - - -
155 ALA 3.6 1.6 - - - -
157 VAL* 1.3 76.1 - - - +
159 ILE* 1.3 60.6 + - - +
161 VAL* 3.3 8.5 + - - +
162 ILE* 3.0 28.6 + - - +
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Residues in contact with ILE 159
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77 ILE* 3.3 44.6 - - + +
78 LEU* 4.3 8.3 - - + -
80 VAL* 5.9 4.5 - - + -
81 ASN* 4.0 19.9 + - + +
133 LEU* 4.0 0.2 - - - +
155 ALA 2.9 14.0 + - - +
156 TYR* 3.0 48.9 - - + +
158 GLY* 1.3 70.6 - - - +
160 ALA* 1.3 61.6 + - - +
162 ILE* 3.1 18.9 + - - +
163 TRP* 3.2 23.4 + - + +
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Residues in contact with ALA 160
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156 TYR* 3.0 34.3 + - + +
157 VAL* 3.4 7.0 - - - +
159 ILE* 1.3 74.6 - - + +
161 VAL* 1.3 61.2 + - + +
163 TRP* 3.2 12.9 + - - +
164 VAL* 3.0 30.5 + - + +
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Residues in contact with VAL 161
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133 LEU* 6.4 0.7 - - + -
157 VAL* 2.8 37.2 + - + +
158 GLY* 3.4 11.4 - - - +
160 ALA* 1.3 68.6 - - - +
162 ILE* 1.3 70.1 + - + +
164 VAL* 3.2 9.2 + - + +
165 LEU* 3.0 48.4 + - + +
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Residues in contact with ILE 162
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78 LEU* 4.2 3.4 - - + -
81 ASN* 3.5 8.5 - - - +
126 VAL* 3.0 44.4 - - + +
129 PHE* 3.1 39.5 - - + +
130 SER* 3.5 19.3 - - - +
133 LEU* 4.0 12.3 - - + -
158 GLY* 3.0 29.3 + - - +
159 ILE* 3.1 11.9 + - - +
161 VAL* 1.3 81.9 - - + +
163 TRP* 1.3 51.6 + - - +
165 LEU* 3.5 1.6 + - + +
166 ALA* 2.8 36.0 + - - +
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Residues in contact with TRP 163
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81 ASN* 2.8 23.1 + - - -
84 PHE* 3.4 41.3 - + - -
85 SER* 3.9 18.2 - - - -
88 LEU* 4.8 9.0 - - + -
122 VAL* 4.5 24.7 - - + -
126 VAL* 4.8 4.0 - - + -
159 ILE* 3.2 27.6 + - + +
160 ALA* 3.2 11.5 + - - +
162 ILE* 1.3 74.9 - - + +
164 VAL* 1.3 54.9 + - + +
166 ALA* 3.5 3.8 - - - +
167 VAL* 2.8 41.1 + - + +
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Residues in contact with VAL 164
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160 ALA* 3.0 20.6 + - + +
161 VAL* 3.2 10.9 + - - +
163 TRP* 1.3 73.8 - - + +
165 LEU* 1.3 68.1 + - + +
167 VAL* 3.2 12.9 - - + +
168 ALA* 3.1 27.1 + - + +
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Residues in contact with LEU 165
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129 PHE* 3.3 57.1 - - + -
132 VAL* 6.5 0.9 - - + -
161 VAL* 3.0 40.2 + - + +
162 ILE* 5.9 0.2 - - + -
164 VAL* 1.3 82.4 - - + +
166 ALA* 1.3 64.3 + - - +
168 ALA* 3.4 11.5 + - + +
169 SER* 3.3 16.8 + - - -
218 LEU* 5.9 8.5 - - + +
219 GLN* 5.3 1.0 - - - +
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Residues in contact with ALA 166
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122 VAL* 4.2 6.1 - - + -
125 THR* 3.3 28.6 - - + +
126 VAL* 3.5 24.7 - - + +
129 PHE* 3.7 1.4 - - - -
162 ILE 2.8 20.5 + - - +
163 TRP* 3.5 5.2 - - - +
165 LEU* 1.3 73.6 - - - +
167 VAL* 1.3 60.4 + - - +
169 SER* 3.2 6.2 + - - -
170 SER* 2.9 31.0 + - - -
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Residues in contact with VAL 167
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118 PHE* 4.8 9.9 - - + -
122 VAL* 4.9 4.4 - - + +
163 TRP* 2.8 23.5 + - + +
164 VAL* 3.2 25.4 - - + +
166 ALA* 1.3 69.3 - - - +
168 ALA* 1.3 60.5 + - - +
170 SER* 4.3 4.7 - - - +
171 LEU* 2.8 58.7 + - + +
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Residues in contact with ALA 168
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164 VAL* 3.1 16.2 + - + +
165 LEU* 3.4 17.3 - - + +
167 VAL* 1.3 75.6 - - - +
169 SER* 1.3 56.3 + - - +
172 PRO* 3.1 26.9 - - - +
211 TYR* 3.2 4.7 + - - -
214 LEU* 6.0 2.6 - - - +
218 LEU* 5.4 12.1 - - + -
219 GLN* 4.4 2.0 - - - +
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Residues in contact with SER 169
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121 CYS* 3.1 20.2 - - - -
125 THR* 3.8 15.3 + - - -
165 LEU 3.3 3.3 + - - -
166 ALA 3.2 10.0 + - - -
167 VAL 3.1 0.2 - - - -
168 ALA* 1.3 78.0 - - - +
170 SER* 1.3 60.2 + - - +
171 LEU 3.4 0.2 - - - -
173 PHE* 3.0 17.2 - - - -
211 TYR* 2.6 18.9 + - - -
215 LEU* 4.3 1.2 - - - +
219 GLN* 2.8 43.9 + - - +
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Residues in contact with SER 170
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118 PHE* 3.1 45.6 - - - -
121 CYS* 3.2 15.2 - - - -
122 VAL* 2.9 33.5 + - - -
166 ALA 2.9 15.9 + - - -
167 VAL* 4.4 1.1 - - - -
169 SER* 1.3 72.5 - - - +
171 LEU* 1.3 63.9 + - - +
173 PHE* 3.4 13.5 - - - -
174 LEU* 3.6 4.3 - - - +
179 MET* 3.8 1.7 - - - +
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Residues in contact with LEU 171
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118 PHE* 3.4 11.0 - - + -
167 VAL* 2.8 42.2 + - + +
170 SER* 1.3 71.3 - - - +
172 PRO* 1.3 75.0 - - + +
174 LEU* 3.1 43.6 + - + +
175 ILE* 4.2 1.1 + - + +
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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