Contacts of the helix formed by residues 165 - 184 (chain E) in PDB entry 4WYV
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 SER 165 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E ASP* 2.8 12.7 + - - -
164E TYR* 1.3 80.7 - - - +
166E ARG* 1.3 65.3 + - - -
167E PRO 3.5 0.7 - - - -
168E LEU* 3.1 21.6 + - - +
169E HIS* 3.2 26.5 + - - -
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Residues in contact with ARG 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E VAL* 6.0 3.0 - - - +
54E ILE* 5.1 15.2 - - - +
107E TYR* 4.3 18.2 + - - -
108E LEU* 4.9 20.3 + - - +
111E GLU* 3.8 24.9 + - - +
154E LEU* 4.2 27.3 - - - +
158E SER* 3.4 16.2 - - - +
163E ASP* 2.7 25.9 + - - +
165E SER* 1.3 72.4 + - - +
167E PRO* 1.3 71.9 - - + +
169E HIS* 3.1 11.5 + - + +
170E ILE* 2.9 31.7 + - + +
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Residues in contact with PRO 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E SER* 3.7 39.1 + - - +
158E SER* 3.3 11.9 - - - +
159E VAL* 3.9 13.2 - - + -
163E ASP 3.4 14.8 - - - +
164E TYR 4.1 0.9 - - - -
165E SER 3.6 2.2 - - - -
166E ARG* 1.3 94.3 - - + +
168E LEU* 1.3 57.0 + - + +
170E ILE* 3.7 6.1 - - + +
171E SER* 2.9 27.9 + - - -
205E VAL* 5.0 1.4 - - - +
208E VAL* 3.9 12.3 - - + -
209E VAL* 3.8 7.0 - - + +
212E LEU* 3.9 14.1 - - + -
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Residues in contact with LEU 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E TYR 3.3 24.9 - - - +
165E SER* 3.1 11.4 + - - +
166E ARG 3.1 1.2 - - - -
167E PRO* 1.3 77.4 - - + +
169E HIS* 1.3 67.7 + - + +
171E SER* 3.3 10.4 + - - -
172E THR* 3.3 18.4 + - - +
209E VAL* 4.2 24.0 - - + -
212E LEU* 4.0 17.5 - - + -
217E PHE 4.7 17.0 - - - +
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Residues in contact with HIS 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E TYR* 3.8 11.2 + - - +
111E GLU* 3.1 35.1 + - - +
165E SER* 3.2 35.9 + - - -
166E ARG* 3.1 9.5 + - + +
168E LEU* 1.3 76.0 - - + +
170E ILE* 1.3 65.8 + - - +
172E THR* 3.1 9.8 + - - -
173E PHE* 3.0 23.7 + - - +
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Residues in contact with ILE 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E TYR* 3.6 22.9 - - + +
151E LEU* 3.5 45.1 - - + +
154E LEU* 4.1 15.9 - - + -
155E SER* 3.9 24.2 - - - +
166E ARG* 2.9 36.3 + - + +
167E PRO* 3.7 5.4 - - + +
169E HIS* 1.3 75.6 - - - +
171E SER* 1.3 57.2 + - - +
173E PHE* 3.3 2.9 + - - +
174E ILE* 2.8 39.0 + - + +
205E VAL* 4.3 7.6 - - + -
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Residues in contact with SER 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E PRO 2.9 14.3 + - - -
168E LEU 3.4 10.8 - - - -
169E HIS 3.1 0.4 - - - -
170E ILE* 1.3 77.1 - - - +
172E THR* 1.3 58.6 - - - +
174E ILE* 3.9 0.9 - - - +
175E ASN* 2.8 45.4 + - - -
205E VAL* 3.8 18.9 - - - +
206E GLU* 4.1 9.2 - - - +
209E VAL* 3.6 22.2 - - - +
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Residues in contact with THR 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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168E LEU 3.3 10.6 + - - +
169E HIS* 3.1 17.2 + - - -
171E SER* 1.3 80.0 - - - +
173E PHE* 1.3 51.6 + - - +
175E ASN* 3.2 7.6 + - - +
176E GLU* 2.8 46.2 + - - +
47F GLN* 5.4 12.6 - - + -
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Residues in contact with PHE 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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3A VAL* 4.6 6.5 - - + -
107E TYR* 3.6 33.4 - + + +
111E GLU 4.2 6.5 - - - -
112E THR* 3.7 5.8 - - - -
113E LEU* 3.5 46.4 - - + -
147E LEU* 4.1 13.0 - - + -
151E LEU* 3.7 27.8 - - + -
169E HIS 3.0 17.8 + - - +
170E ILE 3.6 2.7 - - - +
172E THR* 1.3 77.0 + - - +
174E ILE* 1.3 63.9 + - + +
176E GLU* 3.2 20.2 + - - +
177E LEU* 3.0 44.6 + - + +
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Residues in contact with ILE 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E ALA* 3.5 35.7 - - + +
151E LEU* 4.5 4.5 - - + -
152E SER 4.4 3.6 - - - +
170E ILE* 2.8 31.5 + - + +
171E SER 4.0 2.9 - - - +
173E PHE* 1.3 74.6 - - + +
175E ASN* 1.3 57.8 + - - +
177E LEU* 3.1 16.2 + - + +
178E ASP* 2.9 26.2 + - - +
198E LEU* 4.4 8.5 - - + +
201E ASP* 4.4 6.1 - - + -
202E VAL* 3.4 35.9 - - + +
205E VAL* 4.1 24.7 - - + -
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Residues in contact with ASN 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E SER* 2.8 40.6 + - - +
172E THR* 3.6 7.6 - - - +
174E ILE* 1.3 77.0 - - - +
176E GLU* 1.3 55.8 + - - +
178E ASP* 3.3 8.9 + - - +
179E SER* 2.9 30.9 + - - -
202E VAL* 3.9 10.7 - - - +
205E VAL* 5.1 2.4 - - - +
206E GLU* 3.3 29.9 + - - +
47F GLN* 4.0 23.0 + - - +
153F ARG* 3.6 12.3 + - - -
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Residues in contact with GLU 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 3.3 43.4 - - + +
172E THR* 2.8 29.4 + - - +
173E PHE* 3.2 16.9 + - - +
175E ASN* 1.3 72.7 - - - +
177E LEU* 1.3 52.9 + - - +
179E SER* 3.3 8.1 + - - -
180E GLY 2.8 28.8 + - - -
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Residues in contact with LEU 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 4.9 5.2 - - + -
7A PHE* 4.3 8.6 - - + -
113E LEU* 4.0 20.6 - - + -
144E VAL* 3.8 31.0 - - + +
147E LEU* 5.4 0.9 - - + -
148E ALA* 4.1 30.1 - - + +
173E PHE* 3.0 45.0 + - + +
174E ILE* 3.1 14.6 + - + +
176E GLU* 1.3 77.2 - - - +
178E ASP* 1.3 56.4 + - - +
180E GLY* 3.3 2.4 + - - -
181E PHE* 3.0 43.3 + - + -
198E LEU* 4.4 5.4 - - + -
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Residues in contact with ASP 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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174E ILE 2.9 12.1 + - - +
175E ASN* 3.6 12.4 - - - +
177E LEU* 1.3 73.5 - - - +
179E SER* 1.3 66.1 + - - +
181E PHE* 3.5 1.9 + - - +
182E ARG* 3.2 46.0 + - - +
195E TYR* 3.4 21.8 + - - -
198E LEU* 3.9 12.6 - - + +
199E LYS* 5.5 5.4 + - - +
202E VAL* 4.0 27.3 - - + +
43F GLN* 4.8 0.9 - - - +
153F ARG* 4.8 8.3 + - - -
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Residues in contact with SER 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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175E ASN 2.9 15.7 + - - -
176E GLU* 3.4 12.1 - - - -
178E ASP* 1.3 75.6 - - - +
180E GLY* 1.3 64.1 + - - +
182E ARG* 3.2 18.9 + - - +
183E LEU* 3.4 18.4 + - - +
40F THR* 4.2 20.7 - - - +
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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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3A VAL* 5.2 2.0 - - - -
4A SER* 5.7 2.2 - - - -
7A PHE* 3.3 37.9 - - - +
176E GLU 2.8 17.6 + - - -
177E LEU 3.3 4.0 + - - -
179E SER* 1.3 72.2 - - - +
181E PHE* 1.3 56.3 + - - +
183E LEU* 3.0 32.5 + - - +
184E LEU* 3.7 1.6 + - - +
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Residues in contact with PHE 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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7A PHE* 3.7 16.6 - + - -
141E LEU* 3.8 36.8 - - + -
144E VAL* 4.5 12.6 - - + -
145E LEU* 3.6 41.5 - - + -
177E LEU* 3.0 33.5 + - + +
178E ASP 4.1 1.1 - - - +
179E SER 3.4 0.2 - - - -
180E GLY* 1.3 69.9 - - - +
182E ARG* 1.3 66.8 + - - +
183E LEU 3.1 2.0 - - - -
184E LEU* 3.0 39.1 + - + +
186E LEU* 4.3 14.3 - - + +
191E LEU* 5.7 0.4 - - + -
195E TYR* 3.3 36.3 - + + -
198E LEU* 3.8 13.0 - - + -
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Residues in contact with ARG 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E ASP* 3.2 44.3 + - - +
179E SER* 3.2 16.7 + - - +
181E PHE* 1.3 77.2 - - - +
183E LEU* 1.3 62.8 + - - +
184E LEU 3.4 1.3 - - - +
195E TYR* 4.0 13.4 + - - +
36F ARG* 3.3 61.5 + - + +
39F LEU* 3.8 17.4 - - - +
40F THR* 3.9 38.1 - - + +
43F GLN* 2.9 35.4 + - - +
97F ARG* 5.9 0.2 - - - +
153F ARG* 5.5 1.0 - - - +
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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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4A SER* 4.3 7.0 - - - +
7A PHE* 4.0 9.4 - - + +
8A VAL* 3.7 41.7 - - + +
11A GLN* 3.3 31.4 + - + +
179E SER* 3.4 15.5 - - - +
180E GLY* 3.0 18.9 + - - +
182E ARG* 1.3 78.9 - - - +
184E LEU* 1.3 61.6 + - + +
185E ASN 3.7 0.9 + - - -
33F GLN* 4.3 9.2 + - - -
36F ARG* 4.8 0.7 + - - -
40F THR* 4.9 13.5 - - + +
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Residues in contact with LEU 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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7A PHE* 3.9 21.5 - - + +
10A LEU* 4.0 6.5 - - + -
11A GLN* 3.6 37.9 - - + +
14A LEU* 3.7 15.0 - - + -
141E LEU* 3.6 29.2 - - + -
180E GLY 4.1 6.5 - - - +
181E PHE* 3.0 40.3 + - + +
182E ARG 3.4 5.9 - - - +
183E LEU* 1.3 79.6 - - + +
185E ASN* 1.3 60.9 + - - +
186E LEU* 3.5 18.4 + - + +
36F ARG* 4.0 8.3 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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