Contacts of the helix formed by residues 165 - 179 (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 LEU 165 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133D ILE* 3.1 32.5 - - + -
136D LEU* 5.7 0.2 - - + -
161E ILE* 3.0 21.3 - - + +
162E PRO* 4.5 0.7 - - + -
163E THR 2.7 2.2 - - - -
164E ASN* 1.3 78.1 - - - +
166E ARG* 1.3 63.5 + - - +
167E VAL 3.0 3.6 + - - -
168E LEU* 3.3 14.9 + - + +
169E ARG* 3.1 45.4 + - - +
103F HIS* 4.6 9.6 - - + +
106F SER* 4.6 7.2 - - - -
107F ILE* 4.6 17.5 - - + +
110F LEU* 3.2 30.7 - - + -
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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
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162E PRO 3.0 27.4 - - - +
163E THR* 3.1 16.8 + - - +
165E LEU* 1.3 76.9 - - - +
167E VAL* 1.3 66.8 + - - +
169E ARG* 3.2 27.2 - - - +
170E SER* 3.0 24.7 + - - -
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Residues in contact with VAL 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D GLN* 4.1 24.7 - - + +
185D LEU* 5.4 1.8 - - - -
188D VAL* 3.3 32.8 - - + -
163E THR 3.7 14.1 - - - +
164E ASN 4.9 0.2 - - - -
165E LEU 3.0 0.6 - - - -
166E ARG* 1.3 75.2 - - + +
168E LEU* 1.3 67.6 + - + +
169E ARG 2.5 15.5 + - - -
170E SER* 2.5 30.2 + - - +
171E ILE* 3.0 27.9 + - + -
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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
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133D ILE* 5.6 3.4 - - + +
136D LEU* 3.5 31.6 - - + -
137D GLN* 3.8 16.2 - - + +
140D VAL* 3.5 28.9 - - + -
188D VAL* 5.7 1.3 - - + -
164E ASN 3.7 23.3 - - - +
165E LEU* 3.6 4.9 - - + +
167E VAL* 1.3 92.9 - - + +
169E ARG* 1.3 54.1 + - - +
171E ILE* 3.7 6.3 - - - -
172E LEU* 2.6 41.8 + - + +
110F LEU* 3.3 34.1 - - + -
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Residues in contact with ARG 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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162E PRO* 3.9 7.3 + - - +
165E LEU* 3.1 36.9 - - - +
166E ARG* 3.2 46.7 - - - +
167E VAL 2.5 4.9 + - - -
168E LEU* 1.3 69.5 - - - +
170E SER* 1.3 50.9 + - - +
171E ILE 2.6 16.4 + - - -
173E GLU* 2.8 41.9 + - - +
103F HIS* 4.5 8.9 + - - -
106F SER* 3.4 27.9 + - - -
109F TYR* 5.8 5.8 - - + -
110F LEU* 3.8 18.1 - - + +
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Residues in contact with SER 170 (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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181D GLN* 3.6 14.2 - - - +
184D GLN* 3.9 16.8 + - - -
166E ARG* 3.0 12.7 + - - -
167E VAL* 2.5 29.7 + - - -
169E ARG* 1.3 72.8 - - - +
171E ILE* 1.3 58.9 + - - +
173E GLU* 3.1 24.0 + - - +
174E ASN* 3.6 6.9 - - - +
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Residues in contact with ILE 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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140D VAL* 3.8 27.8 - - + -
144D LEU* 4.3 12.6 - - + -
181D GLN* 3.8 46.4 - - + +
184D GLN* 5.0 4.3 - - + +
185D LEU* 5.4 2.9 - - + +
167E VAL* 3.0 27.4 + - + +
168E LEU* 3.8 6.3 - - - +
169E ARG 2.6 6.7 + - - -
170E SER* 1.3 80.2 - - - +
172E LEU* 1.3 57.4 + - - +
173E GLU 2.5 5.1 + - - -
174E ASN* 2.4 31.2 + - - -
175E LEU* 2.9 26.0 + - + -
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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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136D LEU* 4.9 3.8 - - + -
140D VAL* 3.4 31.6 - - + -
143D GLN* 4.3 11.9 - - - +
168E LEU* 2.6 28.7 + - + +
169E ARG* 5.2 0.4 - - - -
171E ILE* 1.3 75.2 - - - +
173E GLU* 1.3 55.2 + - - -
175E LEU* 4.6 4.7 - - + -
176E ARG* 3.1 26.3 + - - +
110F LEU* 3.1 44.6 - - + +
113F ILE* 3.3 22.2 - - + +
114F TYR* 3.7 29.8 - - + -
117F ASN* 4.0 3.6 + - - +
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Residues in contact with GLU 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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169E ARG* 2.8 36.7 + - - +
170E SER* 3.1 25.1 + - - +
171E ILE 2.5 5.1 + - - -
172E LEU* 1.3 76.7 - - - +
174E ASN* 1.3 66.9 + - + +
176E ARG* 3.6 9.1 - - - +
177E SER* 3.3 22.5 + - - -
113F ILE* 5.4 0.9 - - - -
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Residues in contact with ASN 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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177D ASP* 4.3 4.4 + - - -
181D GLN* 3.1 39.5 + - - +
170E SER 3.6 9.2 - - - +
171E ILE 2.4 22.6 + - - +
173E GLU* 1.3 71.2 - - + +
175E LEU* 1.3 63.7 + - - +
177E SER* 2.8 7.7 + - - -
178E LYS* 2.4 67.3 + - - +
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Residues in contact with LEU 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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140D VAL* 4.7 3.6 - - + -
143D GLN* 3.1 29.2 - - - +
144D LEU* 3.1 41.1 - - + -
147D MET* 4.4 16.6 - - + -
178D TYR* 5.0 11.4 - - + +
181D GLN* 3.9 7.0 - - - +
171E ILE* 2.9 19.2 + - + +
172E LEU* 4.7 3.6 - - + -
174E ASN* 1.3 83.9 + - - +
176E ARG* 1.3 56.9 + - - +
177E SER 2.6 15.8 + - - -
178E LYS* 2.7 15.6 + - - +
179E ILE* 2.8 20.4 + - + +
117F ASN* 3.7 10.1 - - - +
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Residues in contact with ARG 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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172E LEU 3.1 20.5 + - - +
173E GLU* 3.6 11.9 - - - +
175E LEU* 1.3 78.8 - - - +
177E SER* 1.3 62.2 + - - +
179E ILE* 4.2 7.7 + - - +
180E GLN* 4.2 9.2 + - - +
109F TYR* 4.3 10.7 + - - -
113F ILE* 3.2 36.1 - - + +
116F SER* 5.3 5.5 + - - -
117F ASN* 3.1 29.5 - - - +
120F LYS* 6.1 2.9 - - - +
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Residues in contact with SER 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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173E GLU 3.3 13.2 + - - -
174E ASN* 2.8 12.7 + - - -
175E LEU 2.6 4.4 + - - -
176E ARG* 1.3 76.9 - - - +
178E LYS* 1.3 53.8 + - - -
179E ILE 2.9 10.1 + - - -
180E GLN* 3.1 21.9 + - - +
181E LYS* 3.7 4.2 + - - +
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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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147D MET* 4.8 0.6 - - - +
151D GLU* 3.9 10.8 - - - +
174D ASP* 4.7 7.0 + - + -
177D ASP* 2.9 41.9 + - - +
178D TYR* 3.3 42.9 + - + +
181D GLN* 4.6 1.0 - - - +
174E ASN* 2.4 55.3 + - - +
175E LEU* 2.7 8.5 + - + +
177E SER* 1.3 64.4 - - - +
179E ILE* 1.3 59.4 + - - +
181E LYS* 4.1 14.1 - - + +
182E LEU* 3.6 17.5 - - - +
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Residues in contact with ILE 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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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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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