Contacts of the helix formed by residues 160 - 175 (chain E) in PDB entry 3P05
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 160 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E LYS 3.5 7.5 - - - +
159E GLU* 1.3 92.7 - - + +
161E PHE* 1.3 65.7 + - - +
162E ARG* 4.4 5.6 - - + +
163E ASP* 3.2 39.2 + - - +
164E TYR* 3.3 8.8 + - - +
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Residues in contact with PHE 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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155E GLN* 3.7 27.0 - - - +
159E GLU 3.5 2.0 + - - -
160E PRO* 1.3 71.4 - - - +
162E ARG* 1.3 58.0 + - - +
164E TYR* 3.3 25.9 + + - +
165E VAL* 2.9 52.1 + - + +
190E LEU* 4.9 5.6 - - + -
194E ALA* 4.4 2.0 - - + -
198E CYS* 4.2 7.8 - - - -
202E LEU* 3.8 28.5 - - + -
211E LEU* 5.2 0.9 - - + -
214E MET* 3.9 30.7 - - + -
215E MET* 4.0 23.8 - - + +
218E CYS* 3.6 35.7 + - + +
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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
----------------------------------------------------------
64A ALA* 4.5 5.4 - - + -
144A MET* 3.9 9.9 + - - +
145A TYR* 3.4 78.3 + - + +
147A PRO* 5.8 1.8 - - - +
160E PRO* 3.2 4.4 - - + +
161E PHE* 1.3 77.3 - - - +
163E ASP* 1.3 74.0 + - - +
165E VAL* 3.3 3.1 + - - +
166E ASP* 2.9 31.7 + - - +
215E MET* 3.5 33.3 - - + +
219E GLN* 5.6 1.6 + - - -
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Residues in contact with ASP 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E GLU* 3.7 15.2 - - + +
160E PRO* 3.2 36.1 + - - +
162E ARG* 1.3 86.5 + - - +
164E TYR* 1.3 62.4 + - - +
166E ASP* 3.2 12.8 + - - +
167E ARG* 3.1 26.4 + - + +
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Residues in contact with TYR 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E ILE* 3.8 19.7 - - + -
154E ARG 3.7 6.7 - - - -
155E GLN* 3.4 44.2 - - + -
159E GLU* 3.5 21.7 + - - +
160E PRO 3.3 3.6 + - - +
161E PHE* 3.3 29.8 + + - +
162E ARG 3.2 0.4 - - - -
163E ASP* 1.3 77.9 - - - +
165E VAL* 1.3 59.2 + - + +
167E ARG* 3.1 11.6 + - - +
168E PHE* 2.8 32.1 + + - +
189E LEU 3.5 3.3 + - - -
190E LEU* 2.8 46.7 + - + +
193E ASN* 3.4 22.3 - - - +
194E ALA* 4.2 3.6 - - - -
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Residues in contact with VAL 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA* 3.4 24.9 + - + -
161E PHE* 2.9 57.3 + - + +
162E ARG* 3.8 6.1 - - - +
163E ASP 3.3 0.2 - - - -
164E TYR* 1.3 80.8 - - + +
166E ASP* 1.3 60.8 + - - +
168E PHE* 3.4 5.3 + - - +
169E TYR* 3.0 47.1 + - + +
190E LEU* 4.4 9.2 - - + -
211E LEU* 4.3 13.0 - - + -
215E MET* 4.7 2.9 - - + -
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Residues in contact with ASP 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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61A GLY* 6.2 0.2 - - - -
62A HIS* 3.6 18.4 + - - +
63A GLN* 3.3 10.2 + - - +
64A ALA* 2.9 32.6 + - - +
145A TYR* 4.3 8.5 + - - -
162E ARG* 2.9 28.1 + - - +
163E ASP* 3.2 15.1 + - - +
165E VAL* 1.3 76.8 - - - +
167E ARG* 1.3 62.2 + - + +
169E TYR* 4.2 0.2 - - - -
170E LYS* 3.0 27.2 + - - +
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Residues in contact with ARG 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E ASP 5.3 0.2 + - - -
153E ILE* 3.4 43.7 - - + +
154E ARG 3.0 24.0 + - - +
156E GLY* 4.1 1.0 - - - +
159E GLU* 2.6 42.3 + - - +
163E ASP* 3.1 12.0 + - + +
164E TYR* 3.1 9.0 + - - +
166E ASP* 1.3 72.9 - - + +
168E PHE* 1.3 60.9 + - - +
170E LYS* 3.7 6.1 - - - +
171E THR* 2.8 37.4 + - - +
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Residues in contact with PHE 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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150E ILE* 3.4 29.1 - - + +
153E ILE* 3.9 16.9 - - + +
164E TYR* 2.8 28.7 + + + +
165E VAL 3.6 6.1 - - - +
167E ARG* 1.3 78.1 - - - +
169E TYR* 1.3 78.6 + + - +
172E LEU* 3.1 42.1 + - + +
185E ALA* 3.2 36.6 - - + -
186E THR* 4.6 1.3 - - - -
189E LEU* 3.6 22.7 - - + -
190E LEU* 3.7 36.1 - - + -
193E ASN* 5.2 1.6 - - - -
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Residues in contact with TYR 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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63A GLN* 3.3 30.6 - - + +
67A GLN* 3.8 43.8 + - + +
165E VAL* 3.0 43.7 + - + +
168E PHE* 1.3 89.2 - + - +
170E LYS* 1.3 62.4 + - - +
172E LEU* 3.7 26.8 - - + +
173E ARG* 2.9 29.5 + - - +
182E LYS* 6.2 0.9 - - + -
186E THR* 3.3 33.5 + - - +
190E LEU* 4.2 10.5 - - + +
211E LEU* 4.5 6.6 - - + +
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Residues in contact with LYS 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY* 5.2 6.7 - - - +
63A GLN* 4.0 12.4 - - + +
33E SER* 3.7 22.2 - - - +
34E PRO* 4.1 9.3 - - + +
146E SER* 6.0 4.9 - - - +
166E ASP 3.0 20.2 + - - +
167E ARG* 3.7 5.4 - - - +
169E TYR* 1.3 77.1 - - - +
171E THR* 1.3 65.6 + - - +
173E ARG* 3.2 5.9 + - - +
174E ALA* 3.0 25.5 + - + +
232E IOD 3.5 22.4 - - + -
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Residues in contact with THR 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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146E SER* 4.7 6.5 + - - +
148E THR* 3.4 27.7 - - - +
150E ILE* 3.9 17.7 - - - +
153E ILE* 3.5 23.4 - - + +
167E ARG* 2.8 23.7 + - - +
168E PHE 3.7 4.0 - - - -
170E LYS* 1.3 79.1 - - - +
172E LEU* 1.3 64.1 + - - +
174E ALA* 3.1 16.3 + - - +
175E GLU* 3.1 24.9 + - + +
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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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150E ILE* 3.6 35.2 - - + -
168E PHE* 3.1 30.7 + - + +
169E TYR* 3.7 26.9 - - + +
171E THR* 1.3 77.0 - - - +
173E ARG* 1.3 62.9 + - - +
175E GLU* 3.3 14.6 + - - +
176E GLN 3.6 6.4 + - - -
177E ALA* 3.6 33.4 + - + +
181E VAL* 5.2 3.1 - - + +
182E LYS* 4.2 25.8 - - + +
185E ALA* 4.3 11.0 - - + -
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Residues in contact with ARG 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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57A ASN* 2.6 35.5 + - - +
59A VAL 3.4 22.4 + - - -
63A GLN* 3.9 21.9 + - - +
34E PRO* 3.9 21.7 + - + +
35E GLU* 3.9 11.2 - - - +
38E PRO* 3.9 15.2 - - - +
169E TYR 2.9 17.8 + - - +
170E LYS* 3.2 6.3 + - - +
172E LEU* 1.3 76.9 - - - +
174E ALA* 1.3 63.6 + - - +
176E GLN* 3.2 20.5 + - - +
232E IOD 3.6 19.6 - - - +
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Residues in contact with ALA 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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34E PRO* 3.6 19.0 - - + +
142E VAL* 3.7 6.8 - - + +
143E ARG* 3.7 17.7 - - - +
146E SER* 3.0 40.8 - - - +
170E LYS* 3.0 18.1 + - + +
171E THR 3.1 4.2 + - - +
173E ARG* 1.3 78.4 - - - +
175E GLU* 1.3 55.7 + - - +
176E GLN* 3.2 17.0 + - - -
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Residues in contact with GLU 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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143E ARG* 3.2 27.5 + - + -
146E SER 4.8 8.1 - - - +
147E PRO 4.7 1.5 - - - +
148E THR 2.7 27.2 - - - +
149E SER* 3.2 6.1 + - - -
150E ILE* 3.1 34.5 + - - +
171E THR* 3.1 20.3 + - + +
172E LEU* 3.3 10.2 + - - +
173E ARG 3.2 1.0 - - - -
174E ALA* 1.3 76.7 - - - +
176E GLN* 1.3 69.9 + - - +
177E ALA* 3.2 7.5 + - + +
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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