Contacts of the helix formed by residues 145 - 161 (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 ASP 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A VAL 3.6 3.2 + - - +
144A LEU* 1.3 74.7 - - - +
146A PHE* 1.3 58.0 + - - +
147A ARG* 3.0 28.1 + - - +
148A GLU* 2.8 58.5 + - - +
149A LYS* 3.1 6.6 + - - +
187A PHE* 5.5 0.5 - - - -
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Residues in contact with PHE 146 (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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144A LEU* 3.9 4.4 + - - +
145A ASP* 1.3 73.6 + - - +
147A ARG* 1.3 56.3 + - - +
149A LYS* 4.0 15.5 - - + -
150A ILE* 2.8 54.7 + - + +
180A ILE* 4.3 6.5 - - + -
186A TYR* 4.3 15.7 - - + +
187A PHE* 3.6 27.3 - + + -
189A TYR* 5.0 10.8 + - + +
266A MET* 3.8 30.7 - - + -
267A LYS* 4.3 16.4 - - - -
270A TYR* 3.8 31.4 - + - -
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Residues in contact with ARG 147 (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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145A ASP* 3.0 16.3 + - - +
146A PHE* 1.3 78.6 - - - +
148A GLU* 1.3 56.4 + - - +
150A ILE* 3.5 1.4 + - - +
151A ASN* 2.9 42.7 + - - +
181A LEU* 3.2 47.1 + - + +
184A GLU* 4.3 14.1 + - - +
187A PHE* 3.5 44.8 - - + +
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Residues in contact with GLU 148 (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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143A VAL 5.5 1.0 - - - +
145A ASP* 2.8 39.3 + - + +
147A ARG* 1.3 76.7 - - - +
149A LYS* 1.3 61.2 + - - +
151A ASN* 3.3 6.6 + - - +
152A GLU* 2.8 49.6 + - + +
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Residues in contact with LYS 149 (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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145A ASP 3.1 9.6 + - - +
146A PHE* 3.5 22.4 - - + +
148A GLU* 1.3 74.9 - - - +
150A ILE* 1.3 64.1 + - - +
152A GLU* 3.2 16.7 + - - +
153A ASP* 2.9 39.6 + - - +
156A LYS* 5.8 4.0 - - - +
270A TYR* 3.9 12.3 - - + +
274A GLU* 4.0 20.8 + - - -
278A TYR* 5.1 6.1 + - - -
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Residues in contact with ILE 150 (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* 2.8 41.7 + - + +
147A ARG 3.6 4.0 - - - +
149A LYS* 1.3 73.9 - - - +
151A ASN* 1.3 58.7 + - - +
153A ASP* 3.9 1.6 - - - +
154A ASN* 3.0 28.5 + - + +
177A TYR* 3.6 27.5 - - + +
180A ILE* 3.6 19.7 - - + -
181A LEU* 3.5 42.0 - - + -
187A PHE* 3.6 22.4 - - + -
270A TYR* 3.7 14.6 - - + +
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Residues in contact with ASN 151 (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* 2.9 30.3 + - - +
148A GLU* 3.9 6.1 - - - +
149A LYS 3.3 0.2 - - - -
150A ILE* 1.3 76.3 - - - +
152A GLU* 1.3 62.9 + - + +
154A ASN* 3.7 8.7 - - - +
155A LYS* 3.2 23.7 + - - +
181A LEU* 3.7 25.2 - - - +
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Residues in contact with GLU 152 (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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148A GLU* 2.8 43.9 + - + +
149A LYS* 3.6 15.1 + - - +
151A ASN* 1.3 76.7 - - + +
153A ASP* 1.3 62.7 + - - +
155A LYS* 3.2 7.2 + - - +
156A LYS* 2.9 46.8 + - - +
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Residues in contact with ASP 153 (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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149A LYS* 2.9 39.1 + - - +
150A ILE 3.9 3.1 - - - +
152A GLU* 1.3 75.4 - - - +
154A ASN* 1.3 63.8 + - - +
156A LYS* 3.3 16.8 + - - +
157A ILE* 2.9 32.9 + - + +
177A TYR* 3.7 18.3 + - - +
270A TYR* 2.7 31.7 + - - +
274A GLU* 4.1 14.6 - - - +
277A ILE* 5.2 7.4 - - + +
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Residues in contact with ASN 154 (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* 3.0 19.2 + - + +
151A ASN* 3.7 11.2 - - - +
153A ASP* 1.3 76.7 - - - +
155A LYS* 1.3 60.5 + - - +
157A ILE* 3.9 1.7 - - - +
158A LYS* 3.1 31.3 + - - +
173A VAL* 3.9 7.5 - - - +
174A ASP* 3.0 32.7 + - - +
177A TYR* 3.4 37.3 - - + +
181A LEU* 6.0 0.3 - - - +
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Residues in contact with LYS 155 (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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151A ASN 3.2 14.2 + - - +
152A GLU* 3.2 7.7 + - - +
154A ASN* 1.3 76.6 - - - +
156A LYS* 1.3 66.3 + - + +
158A LYS* 3.4 7.4 + - - +
159A LYS* 3.1 60.2 + - - +
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Residues in contact with LYS 156 (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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149A LYS* 5.8 3.8 - - - +
152A GLU* 2.9 32.9 + - - +
153A ASP* 3.7 15.2 + - - +
155A LYS* 1.3 77.4 - - + +
157A ILE* 1.3 52.3 + - - +
159A LYS* 3.2 7.4 + - - +
160A LEU* 2.7 42.5 + - + +
277A ILE* 3.9 29.8 - - + +
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Residues in contact with ILE 157 (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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153A ASP* 2.9 16.4 + - + +
154A ASN 3.9 2.5 - - - +
156A LYS* 1.3 77.0 - - - +
158A LYS* 1.3 59.1 + - - +
160A LEU* 3.4 6.4 - - - +
161A LEU* 2.8 52.1 + - + +
170A MET* 5.5 0.2 - - - -
173A VAL* 3.8 24.7 - - + -
177A TYR* 3.3 28.0 - - + +
273A PHE* 3.5 34.1 - - + +
276A ILE* 4.6 8.5 - - + -
277A ILE* 3.1 22.9 - - + -
295A ILE* 4.9 2.7 - - + -
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Residues in contact with LYS 158 (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* 3.1 26.5 + - - +
155A LYS* 3.8 6.7 - - - +
157A ILE* 1.3 77.0 - - - +
159A LYS* 1.3 64.7 + - + +
162A SER* 3.0 23.2 + - - -
170A MET* 3.5 44.0 - - + +
173A VAL* 4.5 4.9 - - + -
174A ASP* 3.1 35.9 + - - +
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Residues in contact with LYS 159 (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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155A LYS* 3.1 51.2 + - + +
156A LYS* 3.8 5.2 - - - +
158A LYS* 1.3 75.4 - - + +
160A LEU* 1.3 65.3 + - + +
161A LEU 3.1 0.9 + - - -
162A SER* 3.2 21.8 + - - -
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Residues in contact with LEU 160 (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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156A LYS* 2.7 20.7 + - + +
157A ILE* 3.4 5.4 - - + +
159A LYS* 1.3 75.2 - - + +
161A LEU* 1.3 69.0 + - + +
162A SER 3.7 0.7 + - - -
163A ARG 5.0 0.9 + - - -
164A GLU* 5.6 0.7 - - - +
276A ILE* 4.6 3.8 - - + +
277A ILE* 3.3 54.7 - - + +
280A LYS* 3.4 49.0 + - + +
288A TYR* 5.4 0.2 + - - -
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Residues in contact with LEU 161 (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* 2.8 35.5 + - + +
158A LYS 3.6 2.5 - - - +
159A LYS 3.2 0.2 - - - -
160A LEU* 1.3 91.2 - - + +
162A SER* 1.3 63.4 + - - +
163A ARG 3.2 2.7 - - - -
164A GLU* 3.1 10.7 + - + -
165A LEU* 3.0 52.1 + - + -
170A MET* 3.6 7.1 - - + +
276A ILE* 3.7 23.8 - - + -
280A LYS* 5.2 0.7 - - + -
288A TYR* 4.2 17.0 - - + +
292A LEU* 4.2 16.6 - - + -
295A ILE* 3.8 15.5 - - + -
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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