Contacts of the helix formed by residues 154 - 166 (chain A) in PDB entry 2NO5
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A THR* 5.4 0.6 + - - +
150A ILE* 3.6 18.2 - - + +
151A TYR 3.3 16.4 + - - +
153A PRO* 1.3 79.8 - - - +
155A PRO* 1.3 77.5 - - - +
156A ARG* 2.9 63.6 + - - +
157A ILE* 3.2 18.2 + - - +
158A TYR* 3.8 0.7 - - - -
54B LEU* 3.5 26.7 - - + +
56B HIS* 5.1 4.6 + - - -
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Residues in contact with PRO 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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153A PRO 3.3 3.8 - - - +
154A ASP* 1.3 89.6 - - - +
156A ARG* 1.3 66.1 + - + +
158A TYR* 2.9 26.6 + - + +
159A GLN* 2.9 13.0 + - - +
184A GLY 5.8 0.2 - - - +
188A PHE* 4.0 21.2 - - + -
54B LEU 3.3 15.3 - - - +
55B MET* 4.5 3.4 - - + +
56B HIS* 3.4 28.7 - - + +
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Residues in contact with ARG 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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56A HIS* 6.2 1.4 - - - -
148A LEU* 3.7 10.1 - - + +
150A ILE* 3.2 39.1 - - + +
154A ASP* 2.9 37.8 + - - +
155A PRO* 1.3 79.7 - - + +
157A ILE* 1.3 56.1 + - - +
159A GLN* 3.4 11.8 - - + +
160A PHE* 2.9 27.4 + - - +
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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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118A LEU* 3.9 21.6 - - + +
119A SER 5.4 0.4 - - - +
145A ALA* 3.5 25.6 - - + +
148A LEU* 3.0 32.5 - - + +
150A ILE* 3.4 25.9 - - + +
151A TYR 4.7 1.3 - - - +
152A LYS* 3.8 33.7 - - + +
154A ASP* 3.2 17.4 + - - +
155A PRO 3.1 1.0 - - - -
156A ARG* 1.3 78.2 - - - +
158A TYR* 1.3 77.0 + - + +
160A PHE* 3.1 23.1 - - + +
161A ALA 3.3 4.5 + - - -
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Residues in contact with TYR 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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118A LEU* 3.8 19.7 - - + -
152A LYS* 4.0 1.5 - - + +
153A PRO* 3.1 47.8 - - + +
154A ASP 3.8 8.3 - - - -
155A PRO* 2.9 11.0 + - + +
157A ILE* 1.3 77.1 - - + +
159A GLN* 1.3 67.2 + - - +
161A ALA* 3.0 14.9 + - - +
162A CYS 3.2 9.7 + - - -
174A PHE* 4.1 7.2 - + - -
181A ASP* 2.7 35.6 + - - -
184A GLY 3.5 16.8 - - - -
185A ALA* 3.4 22.0 - - + -
188A PHE* 3.5 24.7 - - + -
190A PHE* 3.4 23.7 - + + -
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Residues in contact with GLN 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 PRO 2.9 12.0 + - - +
156A ARG* 3.4 16.8 - - + +
158A TYR* 1.3 76.0 - - - +
160A PHE* 1.3 56.5 + - - +
162A CYS* 3.2 14.2 + - - +
163A ASP* 2.8 58.2 + - - +
169A PRO* 5.8 0.9 - - - +
188A PHE* 3.1 30.9 - - + -
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Residues in contact with PHE 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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118A LEU* 4.5 6.5 - - + -
143A LEU* 4.0 24.5 - - + -
144A SER 3.9 13.5 - - - -
147A ASP* 3.5 33.7 - - + -
148A LEU* 3.9 33.0 - - + -
156A ARG 2.9 14.7 + - - +
157A ILE* 3.1 14.5 + - + +
159A GLN* 1.3 73.4 - - - +
161A ALA* 1.3 62.8 + - - +
163A ASP* 3.3 8.6 + - + -
164A ARG* 2.9 67.7 + - + +
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Residues in contact with ALA 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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9A VAL* 4.9 5.6 - - + -
118A LEU* 4.3 19.7 - - + -
143A LEU* 3.7 20.4 - - + -
157A ILE 3.3 1.8 + - - -
158A TYR 3.0 12.7 + - - +
160A PHE* 1.3 80.4 - - - +
162A CYS* 1.4 65.2 + - - +
164A ARG 3.2 0.5 + - - -
165A LEU* 2.9 38.3 + - + +
190A PHE* 4.0 14.1 - - + -
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Residues in contact with CYS 162 (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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158A TYR 3.2 2.8 + - - -
159A GLN* 3.2 19.0 + - - +
161A ALA* 1.4 74.9 - - - +
163A ASP* 1.3 68.2 + - - +
166A GLY* 2.8 22.2 + - - -
167A VAL* 3.4 26.4 + - - +
168A ASN 4.0 1.3 - - - -
169A PRO* 3.7 39.7 - - + -
172A VAL* 5.0 1.1 - - - -
188A PHE* 3.9 10.5 - - - -
190A PHE* 3.7 21.7 - - - -
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Residues in contact with ASP 163 (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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159A GLN* 2.8 45.0 + - - +
160A PHE* 3.3 9.4 + - + +
162A CYS* 1.3 76.3 - - - +
164A ARG* 1.3 64.1 - - + +
166A GLY* 3.2 9.8 + - - -
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Residues in contact with ARG 164 (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 LEU* 3.8 35.0 - - + +
147A ASP* 4.4 11.5 + - - +
160A PHE* 2.9 57.2 + - + +
161A ALA 4.0 1.8 - - - +
163A ASP* 1.3 75.6 - - + +
165A LEU* 1.3 63.7 + - + +
166A GLY 3.3 0.2 - - - -
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Residues in contact with LEU 165 (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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6A ARG* 5.0 0.3 + - - -
7A ALA* 4.6 11.9 - - + -
9A VAL* 3.8 29.2 - - + -
114A ILE* 4.1 31.3 - - + +
116A ALA* 4.2 11.2 - - + -
141A SER* 4.2 24.7 - - - +
143A LEU* 4.3 9.2 - - + -
161A ALA* 2.9 27.6 + - + +
162A CYS 4.0 1.1 - - - +
164A ARG* 1.3 83.0 - - + +
166A GLY* 1.3 64.3 + - - +
167A VAL* 3.3 23.5 + - + +
172A VAL* 5.4 0.7 - - + -
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Residues in contact with GLY 166 (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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6A ARG* 3.6 11.6 + - - -
162A CYS 2.8 9.7 + - - -
163A ASP 3.2 9.7 + - - -
164A ARG 3.3 0.6 - - - -
165A LEU* 1.3 79.8 - - - +
167A VAL* 1.3 62.0 + - - +
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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