Contacts of the helix formed by residues 198 - 212 (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 PRO 198 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E PHE* 4.4 4.7 - - + -
39E THR* 3.6 7.2 - - - +
51E VAL* 4.0 27.1 - - + -
109E ASP* 3.4 7.0 - - - +
193E VAL* 3.7 20.8 - - + +
194E ALA 3.4 12.6 - - - +
195E GLU 3.5 13.2 - - - +
196E GLN 3.6 1.3 - - - -
197E THR* 1.3 90.7 - - - +
199E LEU* 1.3 68.5 + - + +
200E THR 3.6 0.2 - - - -
201E ALA* 3.5 6.5 + - - +
202E LEU* 3.2 26.8 + - + +
222E PRO* 4.2 13.9 - - + -
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Residues in contact with LEU 199 (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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17E VAL* 3.9 33.2 - - + -
19E CYS 4.0 11.3 - - - +
20E ASN* 4.8 0.2 - - + -
39E THR* 3.9 7.6 - - + -
48E ILE* 3.9 18.4 - - + -
49E CYS* 3.6 21.5 - - - -
51E VAL* 3.9 18.4 - - + -
105E LEU* 4.0 23.9 - - + +
109E ASP* 3.2 28.9 + - + +
197E THR 3.5 0.4 - - - -
198E PRO* 1.3 77.6 - - + +
200E THR* 1.3 64.7 + - - +
202E LEU* 3.2 7.5 + - + +
203E TYR* 3.1 20.6 + - - +
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Residues in contact with THR 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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102E LEU* 3.7 15.5 - - + +
105E LEU* 3.8 18.4 - - + +
106E GLU* 2.7 55.3 + - + +
109E ASP* 4.8 2.5 + - + +
171E PRO* 3.8 10.6 - - - +
172E LEU* 3.5 22.3 - - + +
197E THR* 4.8 2.3 + - - -
198E PRO 3.6 0.8 - - - -
199E LEU* 1.3 75.0 - - - +
201E ALA* 1.3 64.2 + - - +
203E TYR* 3.2 4.0 + - - +
204E VAL* 3.0 25.8 + - - +
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Residues in contact with ALA 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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166E ILE* 5.0 2.5 - - + -
171E PRO* 5.3 4.3 - - + +
172E LEU* 4.4 0.4 - - - +
175E GLN* 3.2 39.2 - - + +
193E VAL* 3.5 33.2 - - + -
197E THR 5.1 3.1 + - - +
198E PRO 3.5 7.0 + - - +
199E LEU 3.3 0.4 - - - -
200E THR* 1.3 81.7 + - - +
202E LEU* 1.3 60.9 + - - +
204E VAL 3.3 0.5 + - - -
205E ALA 3.2 16.5 + - - -
220E ILE* 3.5 8.2 - - + +
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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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19E CYS* 3.8 27.6 - - + +
20E ASN* 3.8 13.2 - - - -
21E GLN 3.6 26.5 - - - +
28E TRP* 3.2 30.6 - - + -
51E VAL* 4.1 15.7 - - + -
193E VAL* 5.0 0.2 - - + -
198E PRO* 3.2 20.0 - - + +
199E LEU* 3.2 10.2 + - + +
201E ALA* 1.3 74.4 - - - +
203E TYR* 1.3 65.5 + - - +
205E ALA* 3.2 11.0 + - - +
206E ASN 3.5 0.2 + - - -
220E ILE* 3.8 30.3 - - + +
222E PRO* 4.2 10.5 - - + -
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Residues in contact with TYR 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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18E PHE* 4.2 14.6 - + + -
19E CYS* 4.0 21.9 - - + +
97E ARG* 4.5 1.9 + - - -
98E ASP* 2.9 32.4 + - + -
101E TYR* 3.8 31.9 - + - -
102E LEU* 3.8 21.5 - - + -
105E LEU* 4.5 7.4 - - + -
199E LEU 3.1 11.6 + - - +
200E THR 3.2 7.8 + - - +
202E LEU* 1.3 77.4 - - - +
204E VAL* 1.3 62.7 + - - +
206E ASN* 3.0 26.7 + - + +
207E LEU* 3.2 27.8 + - + +
3119I EDO 3.0 26.5 + - - -
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Residues in contact with VAL 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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91E LEU* 4.3 7.6 - - + -
95E ILE* 4.3 23.8 - - + -
102E LEU* 4.3 16.6 - - + -
172E LEU* 3.5 24.0 - - + -
175E GLN* 3.4 24.9 - - - +
179E LEU* 5.1 2.2 - - + -
200E THR 3.0 14.6 + - - +
201E ALA 3.6 2.5 - - - +
202E LEU 3.2 0.4 - - - -
203E TYR* 1.3 73.6 - - - +
205E ALA* 1.3 58.5 + - - +
207E LEU* 2.8 10.0 + - - +
208E ILE* 2.8 39.7 + - + +
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Residues in contact with ALA 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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23E PHE* 3.3 48.1 - - + -
28E TRP* 3.9 3.8 - - + -
201E ALA 3.2 4.8 + - - -
202E LEU* 3.2 12.5 + - - +
203E TYR 3.1 0.4 - - - -
204E VAL* 1.3 75.7 - - - +
206E ASN* 1.3 62.8 + - - +
208E ILE* 3.1 14.1 + - + +
209E LYS 3.1 17.8 + - - -
220E ILE* 3.8 19.3 - - + +
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Residues in contact with ASN 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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18E PHE* 5.8 2.0 - - - +
19E CYS* 3.9 24.4 - - - -
23E PHE* 4.7 0.8 - - - -
28E TRP* 3.0 25.6 + - - -
202E LEU 3.5 1.8 + - - -
203E TYR* 3.0 23.1 + - + +
205E ALA* 1.3 79.1 - - - +
207E LEU* 1.3 60.6 + - + +
209E LYS* 3.4 14.8 + - - +
210E GLU* 3.0 27.0 + - - +
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Residues in contact with LEU 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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91E LEU* 3.7 12.8 - - + -
94E LEU* 3.5 14.3 - - + +
95E ILE* 3.7 41.5 - - + +
97E ARG* 3.6 15.5 - - - +
98E ASP* 3.6 6.5 - - - +
102E LEU* 4.3 4.5 - - + -
203E TYR* 3.2 35.6 + - + +
204E VAL* 2.8 10.8 + - - +
206E ASN* 1.3 78.8 - - + +
208E ILE* 1.3 55.2 + - - +
210E GLU* 3.6 22.7 - - - +
211E ALA* 2.7 36.0 + - - +
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Residues in contact with ILE 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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23E PHE* 4.9 2.7 - - + -
26E ASN* 4.8 7.4 - - - +
91E LEU* 3.9 22.9 - - + -
175E GLN* 5.1 2.2 - - - +
179E LEU* 3.8 27.6 - - + -
183E LEU* 5.6 1.1 - - + -
204E VAL* 2.8 23.1 + - + +
205E ALA* 3.4 16.6 - - + +
207E LEU* 1.3 76.7 - - - +
209E LYS* 1.3 63.2 + - - +
211E ALA 3.2 7.8 + - - -
212E GLY 3.3 8.5 + - - -
213E PHE* 3.4 39.8 + - + -
218E VAL* 3.8 35.2 - - + +
220E ILE* 5.3 0.4 - - + -
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Residues in contact with LYS 209 (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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23E PHE* 4.1 6.7 - - + -
26E ASN* 3.3 57.4 + - + +
27E GLU* 5.5 2.2 - - - +
28E TRP* 5.9 4.1 - - - +
205E ALA 3.1 11.8 + - - +
206E ASN* 3.7 16.8 - - - +
208E ILE* 1.3 77.0 - - - +
210E GLU* 1.3 63.7 + - - +
212E GLY* 3.1 14.9 + - - -
213E PHE 4.5 0.9 + - - +
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Residues in contact with GLU 210 (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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90E ARG* 4.6 11.1 + - - +
94E LEU* 3.9 13.9 - - + +
97E ARG* 2.8 43.2 + - - -
206E ASN 3.0 16.6 + - - +
207E LEU* 3.6 14.3 - - - +
209E LYS* 1.3 78.3 - - - +
211E ALA* 1.3 62.2 + - - +
212E GLY* 3.2 1.6 + - - -
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Residues in contact with ALA 211 (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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87E LEU* 3.4 17.5 - - - +
90E ARG* 3.8 27.5 - - + +
91E LEU* 3.9 16.4 - - + +
94E LEU* 3.6 8.9 - - + +
207E LEU 2.7 21.4 + - - +
208E ILE 3.6 6.3 - - - +
209E LYS 3.2 0.6 - - - -
210E GLU* 1.3 74.0 - - - +
212E GLY* 1.3 57.4 + - - +
213E PHE* 4.0 15.9 - - + -
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Residues in contact with GLY 212 (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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79E MET* 5.5 0.5 - - - +
87E LEU* 4.0 13.9 - - - +
208E ILE 3.3 0.4 + - - -
209E LYS 3.1 13.1 + - - -
210E GLU 3.1 1.5 - - - -
211E ALA* 1.3 80.4 - - - +
213E PHE* 1.3 67.4 + - - +
214E PRO* 3.5 6.4 - - - +
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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