Contacts of the helix formed by residues 170 - 185 (chain E) in PDB entry 1ZUM
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 PHE 170 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106E GLU* 4.3 0.7 - - - -
112E LYS* 3.2 25.4 - - - +
121E ASP* 3.4 14.1 - - - +
124E MET* 5.5 3.6 - - + -
167E PRO 4.7 0.2 - - - -
168E TRP 4.7 0.2 - - - -
169E ASN* 1.3 95.8 + - - +
171E PRO* 1.3 68.2 - - - +
172E LEU 3.5 2.2 - - - -
173E LEU* 3.4 27.5 + - + -
174E MET* 2.9 38.5 + - + +
296E PHE* 3.9 34.1 - + - -
297E ASN* 3.5 24.5 - - + -
300E GLN 3.7 10.1 - - - -
301E CYS* 4.4 16.2 - - + -
302E CYS* 5.5 0.4 - - - -
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Residues in contact with PRO 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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106E GLU* 3.4 28.7 - - - +
110E ASN* 3.8 7.9 - - + +
112E LYS* 4.6 1.8 - - - +
166E ILE* 3.7 10.3 - - + +
167E PRO 4.2 10.3 - - - +
168E TRP 3.3 13.0 - - - +
169E ASN 3.5 3.1 - - - +
170E PHE* 1.3 87.5 - - - +
172E LEU* 1.3 61.8 + - - +
175E GLN* 3.3 20.7 + - - +
197E THR* 3.3 43.7 - - + +
200E THR* 3.8 8.5 - - - +
201E ALA* 5.3 3.9 - - + +
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Residues in contact with LEU 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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95E ILE* 6.1 0.7 - - + -
102E LEU* 4.3 13.2 - - + +
106E GLU* 3.0 24.5 + - - +
121E ASP* 5.6 1.8 - - + -
122E LEU* 3.9 30.5 - - + -
125E VAL* 3.7 19.3 - - + +
171E PRO* 1.3 72.7 - - - +
173E LEU* 1.3 62.5 + - - +
175E GLN* 3.2 15.1 + - - +
176E ALA* 3.0 28.1 + - - +
200E THR* 3.5 35.7 - - + +
201E ALA 4.4 0.2 - - - +
204E VAL* 3.5 32.1 - - + -
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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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106E GLU* 4.7 0.4 + - - -
121E ASP* 4.8 8.8 + - - +
124E MET* 3.3 66.2 - - + +
125E VAL* 3.7 12.2 - - + +
128E CYS* 4.8 1.8 - - + -
170E PHE* 3.4 27.1 + - + -
172E LEU* 1.3 79.0 - - - +
174E MET* 1.3 61.5 + - + +
176E ALA* 3.2 1.7 + - - +
177E TRP* 2.8 69.2 + - + +
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Residues in contact with MET 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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166E ILE* 4.1 20.2 - - + -
167E PRO* 4.0 28.0 - - + +
169E ASN* 4.2 5.2 - - - +
170E PHE* 2.9 41.0 + - + +
171E PRO 4.2 1.6 - - - +
173E LEU* 1.3 74.8 - - + +
175E GLN* 1.3 65.7 + - - +
177E TRP* 3.3 53.8 + - + +
178E LYS* 3.2 33.8 + - - +
244E THR* 4.3 15.9 - - - -
476E GLU* 5.5 0.2 - - - +
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Residues in contact with GLN 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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166E ILE* 3.8 12.8 - - + +
171E PRO 3.3 12.3 + - - +
172E LEU* 3.2 16.8 + - - +
173E LEU 3.2 0.4 - - - -
174E MET* 1.3 78.0 - - - +
176E ALA* 1.3 57.7 + - - +
178E LYS* 3.1 4.2 + - - +
179E LEU* 2.9 41.7 + - + +
191E MET* 3.9 17.8 - - - +
201E ALA* 3.2 36.4 - - + +
204E VAL* 3.4 40.4 - - - +
208E ILE* 5.1 0.2 - - - +
220E ILE* 3.6 14.6 - - - +
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Residues in contact with ALA 176 (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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125E VAL* 4.0 28.5 - - + +
128E CYS* 3.4 20.1 - - + -
129E LEU* 4.1 21.6 - - + +
172E LEU 3.0 13.4 + - - +
173E LEU* 3.2 7.6 + - + +
175E GLN* 1.3 78.9 - - - +
177E TRP* 1.3 57.0 + - - +
179E LEU* 4.5 2.7 - - - +
180E GLY* 2.9 25.3 + - - -
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Residues in contact with TRP 177 (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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124E MET* 6.3 0.2 - - - -
128E CYS* 3.8 14.6 - - - +
132E TYR* 5.2 0.5 - - - -
173E LEU* 2.8 55.9 + - + +
174E MET* 3.3 36.1 - - + +
175E GLN 3.3 0.4 - - - -
176E ALA* 1.3 71.6 - - - +
178E LYS* 1.3 58.9 + - + +
181E PRO* 3.2 23.2 - - - +
302E CYS* 6.2 0.7 - - - -
459E PHE* 4.4 22.0 - + + -
461E ALA* 6.1 0.2 - - - +
465E PHE* 4.0 30.5 - + - -
476E GLU* 3.4 40.7 - - + +
477E LEU* 3.6 43.7 + - + +
485E TYR* 5.6 0.2 - - - -
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Residues in contact with LYS 178 (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 GLN* 3.0 40.1 + - + +
165E ILE 4.6 0.9 - - - -
166E ILE* 3.7 19.3 - - + +
174E MET* 3.2 19.6 + - - +
175E GLN 3.1 6.9 + - - +
176E ALA 3.1 0.4 - - - -
177E TRP* 1.3 78.6 - - - +
179E LEU* 1.3 65.3 + - - +
180E GLY 3.4 0.4 + - - -
181E PRO* 3.6 4.3 - - - +
182E ALA* 3.3 13.7 + - - +
191E MET* 3.9 5.6 - - + -
242E ALA* 4.0 20.4 - - - -
244E THR* 2.8 29.5 + - - +
268E GLU* 3.6 5.8 + - - -
476E GLU* 2.7 32.2 + - - +
485E TYR* 4.0 16.8 - - - +
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Residues in contact with LEU 179 (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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88E LEU* 5.1 0.4 - - + -
91E LEU* 5.0 8.3 - - + -
129E LEU* 4.9 6.5 - - + -
164E GLN* 3.8 8.5 - - - +
175E GLN* 2.9 36.6 + - + +
176E ALA* 4.4 3.6 - - - +
178E LYS* 1.3 72.8 - - - +
180E GLY* 1.3 68.3 + - - +
182E ALA* 4.5 1.3 - - - -
183E LEU* 2.9 46.5 + - + +
189E VAL* 4.0 19.3 - - + -
191E MET* 3.7 20.9 - - + -
204E VAL* 5.1 1.8 - - + -
208E ILE* 3.8 28.7 - - + -
218E VAL* 4.3 11.0 - - + -
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Residues in contact with GLY 180 (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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88E LEU* 4.1 6.4 - - - +
129E LEU* 4.4 13.1 - - - +
132E TYR* 3.6 23.2 - - - +
176E ALA 2.9 15.9 + - - -
179E LEU* 1.3 79.7 - - - +
181E PRO* 1.3 62.6 - - - +
184E ALA* 3.0 26.5 + - - +
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Residues in contact with PRO 181 (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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132E TYR* 3.7 42.0 - - + +
177E TRP 3.2 29.2 - - - +
178E LYS 3.6 4.9 - - - +
180E GLY* 1.3 87.5 - - - +
182E ALA* 1.3 60.9 + - - +
184E ALA* 4.0 0.6 - - + +
185E THR* 2.8 33.0 + - - +
476E GLU* 6.5 0.4 - - + -
477E LEU 5.8 1.8 - - - +
481E GLY* 4.0 16.2 - - - +
482E LEU* 3.9 10.5 - - + -
485E TYR* 4.0 15.4 - - + +
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Residues in contact with ALA 182 (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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162E CYS* 5.2 0.2 - - - -
164E GLN* 3.6 16.2 - - - +
178E LYS 3.3 17.0 + - - +
179E LEU 3.4 1.5 + - - +
180E GLY 3.4 0.8 - - - -
181E PRO* 1.3 80.8 - - - +
183E LEU* 1.3 60.2 + - - +
185E THR* 3.1 10.3 + - - -
187E ASN* 3.0 31.7 + - + +
189E VAL* 4.0 18.2 - - + -
485E TYR* 3.6 23.0 - - + -
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Residues in contact with LEU 183 (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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76E TRP* 3.6 14.3 - - + -
84E ARG* 3.5 15.2 - - - +
88E LEU* 4.1 21.3 - - + -
91E LEU* 5.5 2.7 - - + -
179E LEU* 2.9 44.5 + - + +
182E ALA* 1.3 69.2 - - + +
184E ALA* 1.3 65.6 + - - +
185E THR 3.1 2.0 - - - -
186E GLY 3.1 10.0 + - - -
187E ASN 3.8 11.2 - - - +
189E VAL* 4.8 6.3 - - + -
208E ILE* 5.6 0.4 - - + -
213E PHE* 4.0 18.8 - - + -
217E VAL* 3.6 32.8 - - + +
218E VAL* 3.9 23.8 - - + -
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Residues in contact with ALA 184 (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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84E ARG* 2.9 24.1 + - - -
88E LEU* 3.8 11.3 - - + +
132E TYR* 3.4 30.3 - - + +
135E TRP* 4.7 1.6 - - + -
136E ALA* 3.5 22.5 - - - +
180E GLY 3.0 20.5 + - - +
181E PRO* 4.0 5.8 - - + +
182E ALA 3.4 0.2 - - - -
183E LEU* 1.3 76.6 - - - +
185E THR* 1.3 59.1 + - + +
482E LEU* 4.7 6.1 - - + -
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Residues in contact with THR 185 (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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84E ARG* 4.0 10.6 + - - +
139E TYR* 4.7 8.5 - - + -
156E HIS 5.7 0.3 - - - +
157E GLU 5.0 0.3 - - - -
158E PRO* 3.2 24.3 - - - +
181E PRO 2.8 23.1 + - - +
182E ALA 3.1 0.2 + - - -
183E LEU 3.1 0.2 - - - -
184E ALA* 1.3 79.4 - - + +
186E GLY* 1.3 56.1 + - - +
187E ASN* 2.9 23.5 + - - -
482E LEU* 3.7 28.5 - - + +
485E TYR* 3.4 4.8 - - + +
486E THR* 3.8 28.7 - - + +
500H SER* 5.2 0.2 - - - -
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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