Contacts of the helix formed by residues 179 - 193 (chain E) in PDB entry 1N86
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 ILE 179 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147D MET* 3.2 42.4 - - + -
175E LEU* 2.8 18.1 + - - +
176E ARG 4.2 5.8 - - - +
178E LYS* 1.3 77.3 - - - +
180E GLN* 1.3 68.1 + - - +
181E LYS 3.1 1.8 - - - -
182E LEU* 2.9 16.4 + - - +
183E GLU* 2.9 31.9 + - + +
117F ASN* 4.6 19.7 - - + +
120F LYS* 4.5 14.6 - - + -
121F ILE* 3.4 22.9 - - + +
124F LEU* 4.4 11.2 - - + -
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Residues in contact with GLN 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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176E ARG 4.2 6.5 + - - +
177E SER* 3.1 14.4 + - - +
179E ILE* 1.3 75.8 - - - +
181E LYS* 1.3 56.1 - - - +
183E GLU* 3.1 26.4 + - - +
184E SER* 2.7 47.3 + - - +
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Residues in contact with LYS 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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151D GLU* 5.3 3.1 - - - +
169D LEU* 6.0 0.2 - - - +
171D ARG* 5.3 8.7 - - - +
177E SER 3.7 4.8 + - - +
178E LYS* 4.1 18.4 - - + +
180E GLN* 1.3 80.7 - - - +
182E LEU* 1.3 58.2 + - + +
184E SER* 2.9 9.4 - - - -
185E ASP* 2.7 64.2 + - - +
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Residues in contact with LEU 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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147D MET* 4.1 9.6 - - + -
150D LEU* 4.0 26.0 - - + -
151D GLU* 3.4 50.3 - - + +
154D ILE* 4.1 17.5 - - + -
171D ARG* 4.8 3.6 - - - +
178E LYS 3.6 14.8 - - - +
179E ILE 2.9 7.3 + - - +
181E LYS* 1.3 80.8 - - + +
183E GLU* 1.3 56.9 + - - +
184E SER 2.5 15.9 + - - -
185E ASP* 2.7 25.6 + - - +
186E VAL* 3.0 15.3 + - - +
124F LEU* 3.9 10.8 - - + -
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Residues in contact with GLU 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E ILE* 2.9 25.8 + - + +
180E GLN* 3.1 36.8 + - - +
182E LEU* 1.3 72.0 - - - +
184E SER* 1.3 56.6 + - - +
186E VAL* 4.0 4.1 - - - +
187E SER* 3.1 32.0 + - - -
120F LYS* 3.6 38.5 + - - +
123F ASN* 6.1 0.2 - - - +
124F LEU* 4.1 27.2 - - + +
127F LYS* 4.4 10.4 + - + +
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Residues in contact with SER 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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180E GLN* 2.7 25.5 + - - +
181E LYS* 2.9 18.8 - - - -
182E LEU 2.5 4.2 + - - -
183E GLU* 1.3 71.0 - - - +
185E ASP* 1.3 67.3 + - - +
186E VAL 3.2 1.1 - - - -
187E SER* 3.2 18.8 + - - -
188E ALA* 3.3 10.2 + - - +
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Residues in contact with ASP 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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154D ILE* 5.7 0.9 - - + -
158D ILE* 3.7 20.2 - - + -
169D LEU* 3.7 17.7 - - + +
171D ARG* 2.6 35.8 + - - +
181E LYS* 2.7 52.2 + - - +
182E LEU* 2.7 13.9 + - + +
184E SER* 1.3 70.1 - - - +
186E VAL* 1.3 57.2 + - + +
188E ALA* 2.7 27.7 - - - +
189E GLN* 2.9 9.0 + - - +
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Residues in contact with VAL 186 (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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154D ILE* 3.7 30.3 - - + -
158D ILE* 4.3 2.0 - - + -
182E LEU 3.0 16.4 + - - +
183E GLU* 4.0 4.5 - - - +
185E ASP* 1.3 72.3 - - - +
187E SER* 1.3 56.7 + - - +
188E ALA 2.4 17.6 + - - -
189E GLN* 2.8 17.2 + - - +
190E MET* 2.8 36.8 + - + +
124F LEU* 4.8 3.4 - - + -
127F LYS* 4.6 16.6 - - + -
128F VAL* 4.3 12.8 - - + +
131F LEU* 4.2 19.5 - - + -
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Residues in contact with SER 187 (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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183E GLU 3.1 15.0 + - - -
184E SER* 3.2 15.9 + - - -
186E VAL* 1.3 79.4 - - - +
188E ALA* 1.3 56.9 + - - +
190E MET* 4.2 8.8 - - - +
191E GLU* 3.6 15.6 + - - +
127F LYS* 3.7 21.8 - - - +
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Residues in contact with ALA 188 (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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169D LEU* 5.1 7.4 - - + -
184E SER 3.3 10.6 + - - +
185E ASP* 2.7 17.7 - - - +
186E VAL 2.4 8.1 + - - -
187E SER* 1.3 73.5 - - - +
189E GLN* 1.3 50.7 + - - +
190E MET 3.0 1.8 - - - -
191E GLU* 2.5 36.0 + - - +
192E TYR* 2.8 20.7 + - + -
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Residues in contact with GLN 189 (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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158D ILE* 4.1 22.0 - - + -
161D CYS* 3.4 29.6 - - + +
165D CYS* 4.2 0.2 - - - -
167D ARG 3.5 13.9 + - - +
168D ALA* 3.7 17.5 - - - -
169D LEU* 4.0 6.5 - - + +
185E ASP 2.9 10.5 + - - +
186E VAL* 2.8 10.2 + - - +
188E ALA* 1.3 72.3 - - - +
190E MET* 1.3 61.3 + - - +
192E TYR* 3.1 23.9 + - - -
193E CYS* 2.9 45.7 + - - -
131F LEU* 4.3 19.3 - - + -
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Residues in contact with MET 190 (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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186E VAL* 2.8 25.1 + - + +
187E SER* 4.2 7.6 - - - +
189E GLN* 1.3 78.3 - - - +
191E GLU* 1.3 63.8 + - - +
193E CYS* 3.5 12.2 + - - +
194E ARG* 3.8 8.1 + - - +
127F LYS* 3.8 28.9 - - + +
130F GLN* 4.4 8.5 - - + +
131F LEU* 3.5 45.6 - - + +
134F GLN* 3.6 29.8 + - - +
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Residues in contact with GLU 191 (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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187E SER 3.6 11.7 + - - +
188E ALA* 2.5 24.9 + - - +
190E MET* 1.3 71.8 - - - +
192E TYR* 1.3 70.9 + - + +
194E ARG* 3.4 30.6 + - - +
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Residues in contact with TYR 192 (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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165D CYS* 4.8 0.2 - - - -
166D SER* 3.4 9.4 + - - +
167D ARG* 3.0 57.6 + - + +
168D ALA 3.5 13.5 - - - -
169D LEU* 4.4 16.9 - - + +
188E ALA* 2.8 25.9 + - + -
189E GLN* 3.1 27.3 + - - +
191E GLU* 1.3 79.7 - - + +
193E CYS* 1.3 57.3 + - - +
194E ARG* 2.8 7.8 + - - +
195E THR* 3.1 20.4 + - - -
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Residues in contact with CYS 193 (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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161D CYS* 3.3 16.6 - - - -
165D CYS* 2.0 51.6 - - - -
189E GLN* 2.9 26.1 + - - +
190E MET* 3.6 8.5 - - - +
191E GLU 3.3 0.4 - - - -
192E TYR* 1.3 71.9 - - - +
194E ARG* 1.3 52.3 + - - +
195E THR 2.7 21.6 + - - -
196E PRO* 4.3 1.6 - - - +
131F LEU* 5.1 1.1 - - - -
134F GLN* 3.9 20.7 + - + +
135F CYS* 4.2 2.9 - - - -
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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