Contacts of the helix formed by residues 198 - 208 (chain E) in PDB entry 1U1C
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 198 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26E GLY* 4.0 1.9 - - - -
67E THR* 4.1 2.2 - - - +
68E GLY 3.5 12.1 - - - +
69E ILE* 3.4 5.9 - - - +
70E GLY 2.8 29.2 + - - +
71E GLY* 4.8 1.3 - - - +
74E THR* 3.2 27.9 - - + +
91E ARG* 2.9 39.2 + - - +
158E SER* 3.5 1.0 + - - -
196E GLU* 3.0 1.6 + - - -
197E MET* 1.3 96.2 - - - +
199E SER* 1.3 68.0 + - - +
200E ALA 3.4 3.0 + - - -
201E THR* 3.4 7.4 + - - -
202E LEU* 3.2 20.8 + - - +
3042E PO4 2.9 24.9 + - - -
5041E BAU 5.1 0.3 - - - +
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Residues in contact with SER 199 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91E ARG* 4.0 4.0 - - - +
113E SER* 2.6 27.1 + - - -
156E THR* 4.2 3.7 - - - +
158E SER* 3.3 2.8 + - - -
196E GLU* 2.6 33.1 + - - -
198E GLU* 1.3 77.4 - - - +
200E ALA* 1.3 55.1 + - - +
202E LEU* 3.3 5.6 + - - -
203E LEU* 2.8 42.9 + - - +
215E MET* 3.8 25.4 - - - -
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Residues in contact with ALA 200 (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 SER* 4.0 9.6 - - - -
114E VAL 4.2 0.9 - - - +
115E ARG* 4.0 19.5 - - + -
117E ASP* 3.5 25.4 - - + +
120E SER* 3.7 0.6 - - - -
130E ALA* 4.0 3.8 - - - +
158E SER* 3.0 27.8 + - - +
199E SER* 1.3 76.9 + - - +
201E THR* 1.3 61.3 + - - +
204E THR* 2.7 32.6 + - - -
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Residues in contact with THR 201 (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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71E GLY* 3.2 43.1 - - - +
74E THR* 4.6 2.7 - - - -
75E SER* 4.0 14.8 - - - +
117E ASP* 2.6 24.8 + - - +
119E ALA* 3.3 18.3 - - + +
120E SER* 4.2 7.0 - - - +
123E PHE* 4.9 1.3 - - + -
198E GLU 3.4 6.4 + - - -
199E SER 3.3 0.6 - - - -
200E ALA* 1.3 75.9 - - - +
202E LEU* 1.3 66.6 + - - +
204E THR* 4.0 0.7 - - - -
205E MET* 3.0 35.1 + - - +
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Residues in contact with LEU 202 (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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24E VAL* 4.8 6.3 - - + -
74E THR* 4.2 12.3 - - + +
78E VAL* 3.8 24.5 - - + -
89E PHE* 3.9 16.4 - - + +
91E ARG* 3.5 40.8 - - + +
198E GLU 3.2 13.9 + - - +
199E SER* 3.8 4.3 - - - +
201E THR* 1.3 80.2 - - - +
203E LEU* 1.3 71.8 + - + +
205E MET* 3.5 7.9 - - - +
206E CYS* 3.1 44.4 + - - +
213E ALA* 4.3 6.3 - - + -
214E GLY 4.1 10.5 - - - +
215E MET* 5.3 1.1 - - + -
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Residues in contact with LEU 203 (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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110E THR* 4.2 14.4 - - + -
112E ALA* 4.4 0.7 - - - -
113E SER* 3.9 17.5 - - - +
130E ALA* 3.4 31.2 - - + +
131E VAL 3.7 5.1 - - - +
132E ALA* 3.9 31.6 - - + +
199E SER* 2.8 27.5 + - - +
202E LEU* 1.3 81.7 - - + +
204E THR* 1.3 56.9 + - - +
206E CYS* 4.1 0.3 - - - +
207E ALA* 3.0 33.1 + - - +
213E ALA* 3.8 28.7 - - + +
215E MET* 4.5 10.5 - - + -
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Residues in contact with THR 204 (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 ARG* 3.7 15.5 - - - +
120E SER* 3.6 35.1 - - - +
123E PHE* 4.9 0.4 - - + -
124E ALA* 3.9 20.6 - - + +
128E PHE* 4.3 6.5 - - + -
129E PRO 4.9 2.5 - - - -
130E ALA* 3.3 21.9 - - - +
200E ALA 2.7 24.6 + - - -
201E THR 4.0 0.2 - - - -
203E LEU* 1.3 77.8 - - - +
205E MET* 1.3 54.8 + - - +
207E ALA* 4.0 1.4 - - - +
208E SER* 2.8 35.5 + - - -
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Residues in contact with MET 205 (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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75E SER* 3.4 43.7 - - - +
78E VAL* 3.7 34.8 - - + -
79E GLU* 4.0 9.9 - - + +
123E PHE* 3.6 43.3 - - + -
201E THR* 3.0 26.2 + - - +
202E LEU* 3.5 7.6 - - - +
204E THR* 1.3 76.4 - - - +
206E CYS* 1.3 59.7 + - - +
208E SER* 3.6 5.8 + - - -
209E GLN* 2.7 43.6 + - - +
211E LEU* 5.2 0.4 - - + -
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Residues in contact with CYS 206 (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 VAL* 4.1 12.6 - - - -
89E PHE* 3.8 26.2 - - - -
202E LEU* 3.1 32.6 + - - +
203E LEU 4.1 1.1 - - - +
205E MET* 1.3 75.3 - - - +
207E ALA* 1.3 63.8 + - - +
208E SER 3.2 2.0 - - - -
209E GLN 3.1 6.4 + - - -
210E GLY 3.2 0.5 + - - -
211E LEU* 2.9 50.6 + - - +
213E ALA* 3.6 25.4 - - + -
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Residues in contact with ALA 207 (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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155D VAL* 5.1 5.7 - - + +
190D MET 3.1 13.0 - - - +
191D GLY* 5.1 1.4 - - - -
128E PHE* 3.9 22.0 - - + -
129E PRO 4.8 1.1 - - - +
131E VAL* 3.7 25.4 - - + +
203E LEU 3.0 19.8 + - - +
206E CYS* 1.3 76.4 - - - +
208E SER* 1.3 57.1 + - - +
209E GLN 3.4 1.0 + - - -
210E GLY* 4.4 3.4 + - - -
211E LEU 4.4 3.6 - - - -
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Residues in contact with SER 208 (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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189D ALA 3.8 1.2 - - - +
190D MET* 3.4 35.2 - - - -
123E PHE* 3.9 14.9 + - - +
124E ALA* 4.3 7.9 - - - -
128E PHE* 4.0 11.7 - - - -
204E THR 2.8 22.3 + - - -
205E MET* 3.6 9.7 + - - -
207E ALA* 1.3 76.9 - - - +
209E GLN* 1.3 59.7 + - - +
210E GLY 3.8 0.4 - - - -
175F ARG* 2.6 31.5 + - - -
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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