Contacts of the helix formed by residues 149 - 168 (chain E) in PDB entry 3IFS
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 THR 149 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E ILE* 4.1 6.3 - - + -
144E SER* 3.9 9.8 + - - -
146E SER* 3.6 9.4 + - - -
147E GLY 3.7 0.6 - - - -
148E THR* 1.3 76.4 + - - +
150E THR* 1.3 67.8 + - - +
151E GLU* 3.8 15.3 - - - +
152E PRO* 3.2 19.7 - - + +
153E ALA* 3.1 19.4 + - - +
426E LYS* 5.5 8.6 + - - +
312F HIS* 3.9 20.2 - - + -
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Residues in contact with THR 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ILE* 5.4 1.3 - - + -
148E THR 2.9 7.5 + - - -
149E THR* 1.3 73.5 - - - +
151E GLU* 1.3 72.5 + - + +
153E ALA* 3.8 2.9 - - - +
154E LEU* 3.0 29.4 + - + +
429E MSE 3.4 31.6 - - + +
430E PHE* 3.6 16.3 - - - -
433E LEU* 5.0 7.1 - - + +
351F LEU* 4.8 15.4 - - + +
354F LEU* 5.6 2.5 - - + -
362F VAL* 4.2 24.9 - - + -
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Residues in contact with GLU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E ILE* 3.5 6.6 - - + +
118E GLY* 3.2 21.7 - - - +
120E ASN 3.8 10.8 - - - +
121E ILE* 3.5 23.3 - - + +
149E THR* 3.8 11.8 - - - +
150E THR* 1.3 81.0 - - - +
152E PRO* 1.3 60.9 - - + +
154E LEU* 3.9 5.3 - - - +
155E ALA* 3.1 28.9 + - - +
425E TYR* 4.3 6.2 + - - -
429E MSE 5.5 4.1 - - - +
308F SER* 2.7 35.8 + - - +
312F HIS* 2.9 30.5 + - - -
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Residues in contact with PRO 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E VAL* 3.4 16.6 - - + +
81E GLY* 4.1 19.1 - - - -
82E ILE* 3.7 21.1 - - + +
118E GLY* 3.6 9.0 - - - +
142E VAL* 5.0 3.1 - - + +
143E ILE 4.7 7.0 - - - +
144E SER* 4.9 9.9 - - - -
149E THR* 3.2 27.6 - - + +
151E GLU* 1.3 95.8 - - + +
153E ALA* 1.3 58.9 + - - +
156E PHE* 2.9 31.9 + - - +
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Residues in contact with ALA 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E GLY 3.6 23.8 - - - +
148E THR 4.2 4.5 - - - +
149E THR 3.1 21.7 + - - +
150E THR* 3.8 3.6 - - - +
152E PRO* 1.3 76.8 - - - +
154E LEU* 1.3 57.7 + - - +
156E PHE* 3.7 6.8 - - - +
157E ARG* 3.1 31.0 + - - +
349F ASP* 4.1 9.4 - - + +
351F LEU* 3.8 17.3 - - + -
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Residues in contact with LEU 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ILE* 4.2 24.2 - - + -
126E MSE 5.6 3.1 - - + -
150E THR* 3.0 21.3 + - + +
151E GLU* 3.9 4.5 - - - +
153E ALA* 1.3 76.4 - - - +
155E ALA* 1.3 65.2 + - - +
157E ARG* 3.3 7.7 + - - +
158E ILE* 3.2 38.9 + - + +
341F ILE* 3.7 40.2 - - + -
351F LEU* 3.9 16.3 - - + +
354F LEU* 5.3 3.6 - - + -
359F VAL* 4.5 10.3 - - + -
362F VAL* 4.3 22.2 - - + -
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Residues in contact with ALA 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E VAL* 4.2 6.7 - - + -
117E VAL* 4.2 13.2 - - + -
118E GLY* 3.4 38.1 - - - +
120E ASN 5.8 0.2 - - - +
126E MSE 4.5 12.5 - - - -
151E GLU 3.1 8.2 + - - +
152E PRO 4.1 1.8 - - - +
154E LEU* 1.3 73.8 - - - +
156E PHE* 1.3 62.5 + - - +
158E ILE* 3.3 3.5 + - - -
159E PHE* 2.9 38.9 + - + +
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Residues in contact with PHE 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E VAL* 4.0 10.5 - - + +
140E ILE* 4.1 20.6 - - + -
142E VAL* 3.6 42.6 - - + -
152E PRO 2.9 19.7 + - - +
153E ALA* 3.7 6.5 - - - +
154E LEU 3.2 0.2 - - - -
155E ALA* 1.3 78.8 - - - +
157E ARG* 1.3 65.6 + - + +
159E PHE* 5.1 0.2 - - - -
160E ARG* 2.9 66.3 + - + +
176E ILE* 4.1 17.9 - - + -
187E LEU* 4.5 9.4 - - + -
190E LEU* 3.7 21.1 - - + -
196E TYR* 4.3 6.3 - + - -
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Residues in contact with ARG 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E ALA 3.1 14.1 + - - +
154E LEU* 3.6 9.0 - - + +
155E ALA 3.3 0.4 - - - -
156E PHE* 1.3 81.5 - - + +
158E ILE* 1.3 64.8 + - + +
160E ARG* 4.1 7.3 + - - +
161E LYS* 3.2 23.6 + - - +
341F ILE* 4.7 9.7 - - + +
342F GLU 2.9 29.2 + - - -
343F SER* 3.8 1.0 - - - +
344F GLU* 3.6 35.1 + - - +
347F ASP* 2.9 12.5 + - - +
349F ASP* 2.7 43.6 + - - +
351F LEU* 3.8 18.0 + - + +
352F ASN* 2.8 38.1 + - - +
355F ALA* 5.7 0.2 - - - +
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Residues in contact with ILE 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E MSE 4.1 16.6 - - - -
130E MSE 3.5 31.9 - - + -
154E LEU* 3.2 22.1 + - + +
155E ALA 3.7 5.6 - - - +
156E PHE 3.3 0.2 - - - -
157E ARG* 1.3 83.2 - - + +
159E PHE* 1.3 67.9 - - + +
161E LYS* 3.5 5.5 + - - +
162E LEU* 3.2 24.2 + - + +
339F LEU* 4.3 8.5 - - + -
340F THR 5.7 5.6 - - - +
341F ILE* 5.6 5.6 - - + -
359F VAL* 3.8 29.2 - - + -
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Residues in contact with PHE 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E LEU* 3.4 28.9 - - + -
80E VAL* 5.3 2.0 - - + -
117E VAL* 3.6 25.8 - - + -
126E MSE 3.7 34.8 - - + -
129E LEU* 3.9 14.8 - - + -
130E MSE 3.9 17.7 - - + -
133E LEU* 3.6 23.3 - - + -
138E PHE* 4.5 3.5 - + + -
140E ILE* 3.6 11.3 - - + +
155E ALA 2.9 30.7 + - - +
156E PHE* 4.6 1.3 - - - +
158E ILE* 1.3 83.0 - - + +
160E ARG* 1.3 60.4 + - - +
161E LYS 3.2 1.6 - - - -
162E LEU* 3.3 15.1 + - + +
163E LEU* 2.9 28.1 + - - +
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Residues in contact with ARG 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E ILE* 3.9 10.6 - - - +
156E PHE* 2.9 49.7 + - + +
157E ARG* 4.1 8.5 + - - +
159E PHE* 1.3 76.2 - - - +
161E LYS* 1.3 59.7 + - - +
163E LEU* 3.3 3.6 + - - +
164E GLU* 2.9 60.1 + - - +
169E LYS* 4.8 4.8 - - - +
176E ILE* 4.1 10.5 - - + -
190E LEU* 4.3 23.3 - - - +
194E GLU* 4.7 9.3 + - - -
196E TYR* 3.1 22.1 + - - -
344F GLU* 3.4 31.3 + - - +
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Residues in contact with LYS 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E ARG 3.2 17.5 + - - +
158E ILE* 3.8 5.8 - - - +
159E PHE 3.2 0.2 - - - -
160E ARG* 1.3 80.6 - - - +
162E LEU* 1.3 61.3 + - - +
164E GLU* 3.3 15.0 + - + +
165E GLU* 2.9 61.3 + - + +
342F GLU* 3.2 45.3 + - + +
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Residues in contact with LEU 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E MSE 3.6 44.4 - - + -
133E LEU* 4.6 7.0 - - + -
138E PHE* 4.5 8.3 - - + -
158E ILE* 3.2 15.5 + - + +
159E PHE* 3.3 28.5 + - + +
161E LYS* 1.3 75.7 - - - +
163E LEU* 1.3 61.9 + - - +
165E GLU* 3.4 19.5 + - - +
166E LYS* 3.1 23.4 + - - +
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Residues in contact with LEU 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E PHE* 3.6 38.4 - - + +
140E ILE* 4.0 10.8 - - + -
159E PHE 2.9 13.6 + - - +
160E ARG 3.5 7.0 - - - +
161E LYS 3.2 0.2 - - - -
162E LEU* 1.3 78.0 - - - +
164E GLU* 1.3 57.9 + - - +
166E LYS* 3.2 2.1 + - - -
167E TYR* 3.0 61.3 + - + +
172E ALA* 3.7 20.9 - - + +
175E ARG* 4.2 8.5 - - + +
176E ILE* 3.4 38.1 - - + -
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Residues in contact with GLU 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E ARG* 2.9 58.6 + - + +
161E LYS* 3.7 13.5 - - + +
163E LEU* 1.3 75.8 - - + +
165E GLU* 1.3 59.1 + - + +
168E GLY* 2.8 32.0 + - - -
169E LYS* 3.5 35.9 - - + +
172E ALA* 4.0 21.3 - - + -
176E ILE* 5.4 0.8 - - + +
194E GLU* 5.2 0.3 - - - +
196E TYR* 4.6 2.3 + - - -
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Residues in contact with GLU 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E LYS* 2.9 53.1 + - + +
162E LEU* 3.7 24.0 - - - +
163E LEU 3.2 0.2 - - - -
164E GLU* 1.3 77.8 - - + +
166E LYS* 1.3 63.0 + - - +
168E GLY 4.6 0.9 + - - -
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Residues in contact with LYS 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E LEU 5.2 0.6 + - - -
135E GLY* 4.8 8.7 - - - +
136E LYS 3.1 35.6 + - - +
137E ASP* 4.3 3.5 + - - -
138E PHE* 4.0 15.0 - - + -
162E LEU 3.1 16.7 + - - +
163E LEU* 3.2 4.0 + - - +
165E GLU* 1.3 79.4 - - - +
167E TYR* 1.3 97.6 + - + +
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Residues in contact with TYR 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ASP* 2.6 50.2 + - - +
138E PHE* 3.1 7.4 + + - -
163E LEU* 3.0 45.1 + - + +
166E LYS* 1.3 103.6 - - + +
168E GLY* 1.3 64.2 + - - +
171E GLU* 3.5 38.2 + - + +
172E ALA 4.1 2.9 - - - +
175E ARG* 3.5 25.9 + - - -
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Residues in contact with GLY 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E GLU 2.8 25.2 + - - -
165E GLU 4.5 1.2 + - - -
166E LYS 3.8 0.6 - - - -
167E TYR* 1.3 73.2 - - - +
169E LYS* 1.3 65.0 + - - -
170E GLU 3.5 2.4 + - - -
171E GLU 4.3 0.2 - - - -
172E ALA* 3.0 25.1 + - - +
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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
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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