Contacts of the helix formed by residues 156 - 175 (chain E) in PDB entry 1S9D
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 GLU 156 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ASP* 6.1 1.6 - - - +
52A ASN* 6.3 1.1 - - + -
67A ASP* 3.7 8.3 - - - +
154E PRO* 3.4 14.8 - - - +
155E GLY* 1.3 81.5 + - - +
157E ALA* 1.3 65.7 + - - +
158E GLN* 4.4 9.9 - - + +
159E LYS* 3.1 44.3 + - + +
160E ILE* 3.0 22.5 + - - +
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Residues in contact with ALA 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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51A PHE* 3.8 20.8 - - + -
67A ASP* 3.0 38.9 + - - +
70A GLY 4.0 12.1 - - - +
403A AFB 4.1 1.3 - - + -
155E GLY 3.8 1.8 + - - -
156E GLU* 1.3 71.2 - - - +
158E GLN* 1.3 63.2 + - - +
160E ILE* 3.8 0.4 - - - +
161E ASP* 2.8 26.9 + - - +
190E TYR* 3.5 18.8 + - - +
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Residues in contact with GLN 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP* 5.0 6.8 + - - +
67A ASP* 4.8 0.6 + - - -
69A GLY* 3.2 32.5 - - - +
70A GLY* 4.2 1.8 - - - +
116E GLY 4.5 0.8 + - - -
118E ARG* 3.2 46.9 - - - +
156E GLU* 3.2 9.4 - - + +
157E ALA* 1.3 78.8 - - - +
159E LYS* 1.3 93.7 + - + +
161E ASP* 3.6 4.0 - - - +
162E ARG* 2.4 68.4 + - - +
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Residues in contact with LYS 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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113E ASP* 5.3 11.7 + - - +
116E GLY* 3.6 26.9 - - - +
117E GLU* 5.4 6.6 + - - -
154E PRO* 3.8 26.2 - - + +
156E GLU* 3.1 43.2 + - + +
158E GLN* 1.3 108.1 - - + +
160E ILE* 1.3 65.9 + - - +
162E ARG* 3.3 8.1 + - - +
163E MET* 3.0 29.5 + - - +
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Residues in contact with ILE 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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50A GLY 4.0 13.2 - - - +
51A PHE* 3.6 46.0 - - + -
153E LEU* 3.9 17.7 - - + -
154E PRO 3.3 28.5 - - - +
155E GLY 4.0 7.0 - - - -
156E GLU 3.0 13.6 + - - +
157E ALA 3.8 2.9 - - - +
159E LYS* 1.3 73.4 - - - +
161E ASP* 1.3 59.7 + - - +
163E MET* 3.2 7.1 + - - +
164E MET* 2.8 37.4 + - + +
190E TYR* 4.0 9.4 - - + -
193E ILE* 3.9 21.8 - - + -
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Residues in contact with ASP 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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70A GLY* 3.9 7.3 - - - -
71A GLN* 3.2 42.9 + - - +
74A ILE* 3.7 11.4 - - - +
157E ALA 2.8 18.7 + - - +
158E GLN 3.6 6.2 - - - +
160E ILE* 1.3 79.4 - - - +
162E ARG* 1.3 64.3 + - - +
164E MET* 3.2 0.5 + - - +
165E GLU* 3.0 20.1 + - - +
186E TYR* 2.5 34.2 + - - -
190E TYR* 3.7 15.9 - - + -
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Residues in contact with ARG 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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115E LEU 5.6 0.9 - - - -
116E GLY* 3.1 27.9 + - - -
117E GLU 4.2 1.2 + - - -
118E ARG* 3.7 27.4 - - - +
123E LEU* 3.1 35.2 - - + +
126E LEU* 4.4 12.6 - - + -
127E HIS* 5.9 3.6 - - - +
158E GLN* 2.4 45.4 + - - +
159E LYS* 3.3 10.9 + - - +
161E ASP* 1.3 83.0 + - - +
163E MET* 1.3 62.4 + - + +
165E GLU* 3.4 8.0 + - - +
166E ALA* 3.0 23.6 + - - +
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Residues in contact with MET 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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112E GLY 3.4 25.6 - - - +
115E LEU* 3.7 15.3 - - + +
116E GLY* 3.5 21.3 - - - +
126E LEU* 4.2 23.1 - - + -
147E PHE* 3.9 11.7 - - + -
151E PHE* 3.7 23.6 - - + -
153E LEU* 3.9 6.1 - - + -
154E PRO* 3.7 22.7 - - + -
159E LYS* 3.0 19.5 + - - +
160E ILE* 3.7 4.0 - - - +
162E ARG* 1.3 80.1 - - + +
164E MET* 1.3 67.3 + - + +
166E ALA* 3.6 2.2 + - - +
167E PHE* 3.1 27.0 + - - +
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Residues in contact with MET 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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144E LEU* 3.7 31.6 - - + -
147E PHE* 4.2 14.1 - - + -
148E LEU* 4.6 2.5 - - + -
153E LEU* 4.5 12.1 - - + -
160E ILE* 2.8 27.3 + - + +
161E ASP 3.8 3.8 - - - +
163E MET* 1.3 82.2 - - + +
165E GLU* 1.3 61.4 - - - +
167E PHE* 3.4 4.8 + - + +
168E ALA* 2.9 29.3 + - - +
186E TYR* 4.0 15.2 - - + +
189E SER* 3.9 17.0 - - - -
190E TYR* 4.2 12.8 - - + +
193E ILE* 3.7 31.2 - - + -
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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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71A GLN* 2.7 33.9 + - - +
73A LYS* 4.7 3.6 + - - -
161E ASP 3.0 14.2 + - - +
162E ARG* 3.8 7.8 - - - +
164E MET* 1.3 74.9 - - - +
166E ALA* 1.3 65.7 + - - +
168E ALA* 3.3 3.1 + - - +
169E GLN* 3.2 36.2 + - + +
183E ASP* 4.4 12.2 - - - +
186E TYR* 3.5 30.6 - - + -
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Residues in contact with ALA 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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126E LEU* 4.2 14.4 - - + -
127E HIS* 3.9 32.5 + - + +
130E VAL* 3.7 26.5 - - + +
162E ARG 3.0 18.0 + - - +
163E MET 3.9 3.6 - - - +
165E GLU* 1.3 81.0 - - - +
167E PHE* 1.3 61.8 + - - +
169E GLN* 3.3 13.2 + - - +
170E ARG 3.6 6.2 + - - -
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Residues in contact with PHE 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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130E VAL* 4.0 11.1 - - - +
135E PHE* 3.6 36.6 - + - -
140E LEU* 3.8 12.1 - - + -
143E ALA* 3.9 24.9 - - + -
144E LEU* 3.6 36.8 - - + -
147E PHE* 3.7 22.0 - + + -
163E MET 3.1 19.9 + - - +
164E MET* 3.6 6.7 - - + +
166E ALA* 1.3 72.2 - - - +
168E ALA* 1.3 62.1 + - - +
170E ARG* 3.2 5.5 + - - +
171E TYR* 2.8 39.9 + + + +
189E SER* 3.4 26.5 - - - -
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Residues in contact with ALA 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 MET 2.9 17.0 + - - +
165E GLU 3.4 7.0 - - - +
166E ALA 3.2 0.2 - - - -
167E PHE* 1.3 79.0 - - + +
169E GLN* 1.3 61.7 + - - +
171E TYR* 3.2 1.2 + - - +
172E CYS* 3.0 29.1 + - - -
182E THR* 4.0 7.4 - - - +
185E CYS* 3.8 15.0 - - - -
186E TYR* 3.5 37.0 - - + +
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Residues in contact with GLN 169 (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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127E HIS* 3.9 31.7 + - - -
165E GLU* 3.2 30.3 + - + +
166E ALA 3.3 7.1 + - - +
168E ALA* 1.3 74.2 - - - +
170E ARG* 1.3 57.6 + - - +
172E CYS* 3.5 2.8 + - - +
173E LEU* 3.1 26.7 + - - +
182E THR* 4.4 23.5 - - + +
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Residues in contact with ARG 170 (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 VAL* 3.4 31.6 - - + +
131E ASP* 2.9 44.3 + - - +
132E LEU 4.7 0.2 - - - -
133E HIS 3.0 23.0 + - - -
134E GLU* 3.6 17.4 + - - -
135E PHE* 3.8 20.0 - - + -
166E ALA 3.6 1.4 + - - +
167E PHE 3.2 3.5 + - - +
169E GLN* 1.3 76.6 - - - +
171E TYR* 1.3 61.0 + - - +
173E LEU* 3.7 21.1 - - - +
174E CME 2.9 72.5 + - - +
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Residues in contact with TYR 171 (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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135E PHE* 4.0 10.0 - - + -
138E LEU 2.7 29.5 + - - -
139E ASN* 3.6 22.0 - - - -
140E LEU* 3.7 16.8 + - + -
143E ALA* 3.7 21.8 - - + -
167E PHE* 2.8 29.2 + + + +
168E ALA 3.7 4.3 - - - +
170E ARG* 1.3 70.6 - - - +
172E CYS* 1.4 59.3 + - - +
174E CME 3.2 1.9 + - - -
175E ASN* 2.9 52.8 + - + +
178E VAL* 4.0 16.3 - - + +
179E PHE* 3.6 24.6 - + - -
185E CYS* 3.8 21.1 - - - -
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Residues in contact with CYS 172 (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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168E ALA 3.0 14.3 + - - +
169E GLN 3.9 3.8 - - - +
171E TYR* 1.4 73.1 - - - +
173E LEU* 1.3 64.4 + - - +
175E ASN 3.2 7.1 - - - +
176E PRO* 3.1 27.8 - - + +
179E PHE* 4.4 17.0 - - - +
181E SER 4.2 4.7 - - - -
182E THR* 4.0 28.3 - - + -
185E CYS* 3.4 33.9 - - - -
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Residues in contact with LEU 173 (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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131E ASP* 5.9 1.1 - - - +
169E GLN 3.1 17.6 + - - +
170E ARG* 3.7 33.2 - - - +
172E CYS* 1.3 79.3 - - - +
174E CME 1.4 76.5 + - + +
176E PRO* 3.6 12.2 - - - +
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Residues in contact with CME 174 (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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134E GLU* 4.1 13.9 - - - -
135E PHE* 3.7 17.5 - - + -
136E THR* 3.3 49.5 + - - +
170E ARG* 2.9 72.3 + - - +
171E TYR 3.6 4.3 - - - +
173E LEU* 1.4 92.4 + - + +
175E ASN* 1.3 67.0 + - - +
176E PRO* 3.4 7.2 - - - +
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Residues in contact with ASN 175 (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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135E PHE 2.8 30.1 + - - -
136E THR* 4.4 0.9 - - - +
137E ASP* 3.0 25.3 + - - -
138E LEU 4.0 1.9 + - - +
171E TYR* 2.9 48.0 + - + +
172E CYS* 3.2 10.7 - - - +
174E CME 1.3 80.2 + - - +
176E PRO* 1.3 68.7 - - - +
177E GLY 3.5 0.2 + - - -
178E VAL* 3.4 31.3 + - + +
179E PHE 4.8 1.0 + - - -
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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