Contacts of the helix formed by residues 166 - 182 (chain A) in PDB entry 3N4U
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 LYS 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A GLU 3.9 6.8 + - - +
165A LEU* 1.3 74.3 - - - +
167A GLY* 1.3 68.1 + - - +
168A PRO* 3.3 11.9 - - + -
169A GLN* 3.0 23.5 + - + +
170A MET* 3.0 10.3 + - - +
296A ARG* 5.7 0.4 - - - +
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Residues in contact with GLY 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU 4.0 0.2 + - - -
166A LYS* 1.3 70.0 - - - +
168A PRO* 1.3 69.2 - - - +
170A MET* 3.0 17.9 + - - +
171A LYS* 3.0 23.9 + - - +
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Residues in contact with PRO 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LYS* 3.4 12.8 - - + -
167A GLY* 1.3 90.1 - - - +
169A GLN* 1.3 63.0 + - + +
171A LYS* 3.5 18.2 + - + +
172A LYS* 3.6 19.8 - - - +
300A ILE* 4.9 1.6 - - - +
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Residues in contact with GLN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.7 26.9 - - + -
166A LYS* 3.0 20.4 + - + +
168A PRO* 1.3 76.5 - - + +
170A MET* 1.3 66.8 + - - +
172A LYS* 2.9 53.1 + - - +
173A VAL 3.8 0.9 + - - -
295A ILE* 3.8 10.9 - - + +
296A ARG* 3.5 42.3 + - + +
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Residues in contact with MET 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ILE 4.9 0.2 - - - +
158A LYS* 3.5 62.1 - - + +
161A LEU* 3.6 23.1 - - - +
162A SER* 3.7 9.2 - - - -
165A LEU* 4.1 26.1 - - + +
166A LYS 3.0 11.9 + - - +
167A GLY* 3.0 11.9 + - - +
169A GLN* 1.3 78.3 - - - +
171A LYS* 1.3 62.0 + - + +
173A VAL* 3.0 26.3 + - - +
174A ASP* 3.4 9.4 + - - +
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLY* 3.0 23.9 + - - +
168A PRO* 3.6 12.8 - - + +
169A GLN 3.1 0.2 - - - -
170A MET* 1.3 76.7 - - + +
172A LYS* 1.3 58.6 + - - +
174A ASP* 3.4 16.8 + - + +
175A ASP* 2.9 29.6 + - - +
300A ILE* 3.8 14.5 - - + +
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Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A PRO* 3.6 15.7 - - - +
169A GLN* 2.9 41.1 + - - +
171A LYS* 1.3 75.6 - - - +
173A VAL* 1.3 59.9 + - - +
175A ASP* 3.8 1.7 - - - +
176A PHE* 2.9 29.6 + - - +
273A PHE* 5.3 0.2 - - - -
295A ILE* 3.3 19.5 - - + +
296A ARG 3.3 13.1 + - - -
298A ILE* 2.8 48.9 + - + +
299A LYS* 5.0 2.9 - - - +
300A ILE* 4.1 23.6 - - + +
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASN* 3.9 12.3 - - - +
157A ILE* 3.8 23.6 - - + -
158A LYS* 4.5 5.4 - - + -
165A LEU* 4.3 10.1 - - + -
169A GLN 4.1 8.5 - - - +
170A MET* 3.0 15.0 + - - +
172A LYS* 1.3 74.7 - - - +
174A ASP* 1.3 66.6 + - - +
176A PHE* 3.1 11.6 + - - +
177A TYR* 3.2 41.9 + - + -
273A PHE* 4.3 11.2 - - + -
295A ILE* 3.9 29.6 - - + -
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Residues in contact with ASP 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASN* 3.0 33.1 + - - +
158A LYS* 3.1 36.4 + - - +
170A MET* 3.4 9.6 + - - +
171A LYS* 3.4 19.9 + - + +
173A VAL* 1.3 74.6 - - - +
175A ASP* 1.3 57.3 + - - +
177A TYR* 3.6 1.6 + - - +
178A ARG* 2.9 29.9 + - - +
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Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LYS 2.9 17.9 + - - +
172A LYS 3.8 3.9 - - - +
174A ASP* 1.3 74.4 - - - +
176A PHE* 1.3 63.0 + - - +
178A ARG* 2.9 30.6 + - - +
179A ASP* 3.0 30.4 + - - +
298A ILE* 5.2 4.7 - - - +
300A ILE* 3.9 40.6 - - + +
301A LYS* 4.4 10.3 + - - -
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Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LYS 2.9 18.2 + - - +
173A VAL 3.5 3.4 - - - +
175A ASP* 1.3 81.1 - - - +
177A TYR* 1.3 83.6 + + - +
179A ASP* 3.6 7.1 + - - +
180A ILE* 3.1 43.7 + - + +
266A MET 5.1 0.2 - - - -
269A LYS* 4.0 28.7 - - + -
270A TYR* 4.0 30.5 - + - -
273A PHE* 3.6 54.7 - + + -
298A ILE* 4.8 9.2 - - + -
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ILE* 3.6 28.0 - - + -
153A ASP* 3.7 9.7 + - + +
154A ASN* 3.4 49.6 - - + +
157A ILE* 3.3 23.5 - - + +
173A VAL* 3.2 36.3 + - + +
174A ASP 4.1 0.4 - - - +
176A PHE* 1.3 92.6 - + - +
178A ARG* 1.3 67.7 + - - +
180A ILE* 3.2 5.3 + - + +
181A LEU* 2.9 33.0 + - + +
270A TYR* 3.6 31.7 - + - -
273A PHE* 3.5 14.1 - + - +
274A GLU 4.9 0.7 + - - -
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Residues in contact with ARG 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ASP 2.9 21.1 + - - +
175A ASP* 2.9 37.4 + - - +
176A PHE 3.4 0.2 - - - -
177A TYR* 1.3 75.6 - - - +
179A ASP* 1.3 84.9 + - - +
181A LEU* 3.1 13.5 + - + +
182A GLU* 3.1 50.5 + - - +
301A LYS* 5.0 11.1 - - - +
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Residues in contact with ASP 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ASP* 3.0 20.5 + - - +
176A PHE* 3.6 8.2 - - - +
178A ARG* 1.3 96.8 + - - +
180A ILE* 1.3 73.2 + - - +
182A GLU* 3.3 14.9 + - - +
183A ASN* 3.8 8.0 + - - +
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PHE* 4.3 9.9 - - + -
150A ILE* 3.6 25.1 - - + -
176A PHE* 3.1 41.3 + - + +
177A TYR* 3.2 12.0 + - + +
179A ASP* 1.3 85.6 - - - +
181A LEU* 1.3 63.4 + - - +
183A ASN* 3.1 17.7 + - - +
186A TYR* 3.5 21.8 - - + +
187A PHE* 3.4 9.1 - - + -
266A MET* 3.5 31.0 - - + -
269A LYS* 6.4 0.7 - - - -
270A TYR* 5.1 2.5 - - + -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ARG* 3.2 52.2 + - + +
150A ILE* 3.5 36.8 - - + -
151A ASN* 3.7 21.3 - - - +
154A ASN* 6.0 0.2 - - - +
177A TYR* 2.9 28.8 + - + +
178A ARG* 3.1 10.5 + - + +
180A ILE* 1.3 76.7 - - - +
182A GLU* 1.3 59.7 + - - +
183A ASN 3.2 2.2 + - - -
187A PHE* 3.7 10.6 - - + -
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ARG* 3.1 39.9 + - - +
179A ASP* 3.6 12.8 - - - +
180A ILE 3.1 0.8 - - - -
181A LEU* 1.3 77.8 - - - +
183A ASN* 1.3 59.0 + - - +
184A GLU* 3.8 4.1 + - - +
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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