Contacts of the helix formed by residues 154 - 163 (chain E) in PDB entry 1UW9
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 GLY 154 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151E HYP 4.6 4.6 - - - -
153E HIS* 1.3 75.5 - - - +
155E ILE* 1.3 59.4 + - - -
156E GLN 3.4 2.5 - - - -
157E VAL 3.3 1.6 + - - -
158E GLU* 2.9 32.3 + - - +
324E ASP* 2.9 20.6 + - - -
372E PRO* 3.8 12.5 - - - +
373E GLY 3.2 15.0 - - - -
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Residues in contact with ILE 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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154E GLY* 1.3 71.0 - - - -
156E GLN* 1.3 65.2 + - - +
158E GLU* 3.3 8.2 + - - +
159E ARG* 3.0 29.4 + - + +
350E ARG* 3.8 30.5 - - + +
373E GLY* 3.1 20.9 + - - +
374E VAL 3.6 22.7 - - - +
375E MET* 3.6 34.5 - - + +
376E PRO* 4.6 0.4 - - + -
397E ASP* 3.8 31.6 - - + +
114F LYS* 6.0 0.7 - - - -
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Residues in contact with GLN 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B SER* 3.8 23.7 - - - -
182B ALA 5.3 1.4 - - - +
211B PHE 4.5 9.4 + - - +
154E GLY 3.4 0.4 - - - -
155E ILE* 1.3 80.8 - - - +
157E VAL* 1.3 79.4 + - - +
159E ARG* 3.4 2.6 + - - +
160E ASP* 2.9 41.8 + - - +
114F LYS* 3.3 16.4 - - + +
115F GLN* 3.0 32.7 - - - +
116F VAL* 4.2 15.7 - - + +
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Residues in contact with VAL 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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182B ALA* 5.8 4.3 - - + -
216B ASP* 3.4 39.7 - - + +
220B PHE* 5.2 3.6 - - + -
153E HIS* 3.7 37.9 - - + +
154E GLY 3.3 2.0 + - - +
156E GLN* 1.3 93.8 - - + +
158E GLU* 1.3 58.7 + - - +
160E ASP* 3.1 7.8 + - - +
161E LYS* 2.9 40.5 + - + +
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Residues in contact with GLU 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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153E HIS* 5.3 0.4 - - + -
154E GLY 2.9 18.0 + - - +
155E ILE* 3.5 5.9 - - - +
156E GLN 3.2 0.2 - - - -
157E VAL* 1.3 78.6 - - - +
159E ARG* 1.3 63.0 + - - +
162E LEU* 3.0 32.8 + - + +
169E LEU* 3.8 12.3 - - + +
199E PHE* 3.9 8.5 - - - -
290E PHE* 3.4 35.1 - - + -
324E ASP* 3.9 10.2 - - + +
325E HIS* 2.4 45.2 + - - -
375E MET* 3.7 18.9 - - + +
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Residues in contact with ARG 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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155E ILE* 3.0 27.4 + - + +
156E GLN 3.7 3.8 - - - +
158E GLU* 1.3 75.6 - - + +
160E ASP* 1.3 58.0 + - - +
162E LEU* 4.7 4.9 - - - -
163E ASN* 2.8 26.5 + - - -
164E LYS* 2.8 51.7 + - - +
165E TYR* 3.6 27.1 + - + +
166E GLY 4.7 2.9 - - - -
167E ARG* 2.9 21.4 + - - +
168E GLY* 4.5 0.6 - - - -
169E LEU* 4.2 18.7 - - + +
375E MET* 4.7 9.6 - - + +
396E ASP* 2.8 33.3 + - - +
397E ASP* 2.9 24.2 + - - +
398E ALA 4.8 0.4 - - - +
116F VAL* 4.4 13.0 - - + -
117F GLN 4.9 2.9 - - - -
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Residues in contact with ASP 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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181B SER* 4.4 6.1 + - - -
183B LYS* 3.6 33.9 + - + +
220B PHE* 3.6 30.2 - - + -
156E GLN* 2.9 38.3 + - - +
157E VAL* 3.1 7.7 + - - +
159E ARG* 1.3 76.4 - - - +
161E LYS* 1.3 59.9 - - - +
163E ASN* 3.5 8.0 + - - +
165E TYR* 2.8 26.0 + - - -
71F ARG* 4.6 2.1 + - - -
115F GLN 4.8 1.6 - - - +
116F VAL* 3.8 7.8 - - - +
117F GLN 5.0 1.4 + - - -
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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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215B ARG* 5.0 2.6 + - - +
216B ASP* 3.0 37.5 + - - +
219B LEU* 4.6 16.5 - - - +
220B PHE* 3.7 17.5 - - + -
153E HIS* 3.2 21.0 - - - -
157E VAL* 2.9 24.8 + - + +
160E ASP* 1.3 76.2 - - - +
162E LEU* 1.3 61.5 + - - +
288E GLY* 4.0 14.6 + - - -
290E PHE* 3.8 18.2 - - + -
66F LEU* 3.8 37.1 - - + +
68F TYR* 4.4 4.3 - - - -
71F ARG* 2.8 31.9 + - - +
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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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158E GLU* 3.0 36.4 + - + +
159E ARG* 4.0 3.1 - - - +
161E LYS* 1.3 75.6 - - - +
163E ASN* 1.3 71.5 + - - +
164E LYS* 3.6 30.9 - - + +
169E LEU* 4.2 11.7 - - + -
199E PHE* 3.6 37.0 - - + -
235E VAL* 3.7 41.9 - - + +
236E LYS 5.8 0.4 - - - +
263E PRO* 5.0 3.4 - - + -
290E PHE* 3.7 18.8 - - + -
13F GLU* 4.9 0.9 - - - +
66F LEU* 4.1 7.4 - - + -
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Residues in contact with ASN 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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183B LYS* 2.9 27.9 - - - +
159E ARG 2.8 12.0 + - - -
160E ASP 3.5 4.1 + - - +
161E LYS 3.3 2.6 - - - -
162E LEU* 1.3 80.7 - - - +
164E LYS* 1.3 57.2 + - - +
165E TYR* 3.6 17.1 - - - -
235E VAL* 5.4 1.3 - - + -
13F GLU* 4.0 15.6 - - - +
52F VAL* 5.9 1.0 - - + +
70F ASN 5.1 0.2 - - - +
71F ARG* 3.7 45.6 + - + +
106F ARG* 4.0 17.3 + - - +
117F GLN* 5.3 0.6 + - - -
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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