Contacts of the helix formed by residues 150 - 160 (chain B) in PDB entry 2NTZ
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 SER 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B ILE* 1.3 70.1 + - - +
152B ARG* 3.0 12.2 + - - +
153B GLU* 3.4 23.3 + - - +
154B ILE* 2.9 33.4 + - - +
202B GLN* 4.2 17.8 + - - +
203B SER* 4.0 25.4 + - - +
205B LEU 5.8 2.5 + - - -
210B TYR* 4.5 2.8 + - - -
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B SER* 1.3 79.0 - - - +
152B ARG* 1.3 60.0 + - - +
154B ILE* 3.5 14.0 - - + +
155B GLY* 2.9 23.9 + - - -
181B LYS* 3.8 31.0 - - + -
184B ARG* 4.4 2.5 - - + -
185B ALA* 3.3 44.8 - - + +
188B ALA* 4.2 9.6 - - + -
205B LEU 5.3 4.3 - - - +
207B PHE* 4.2 22.2 - - + +
210B TYR* 4.0 24.2 - - + -
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Residues in contact with ARG 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B SER 3.0 5.7 - - - +
151B ILE* 1.3 79.6 - - - +
153B GLU* 1.3 59.2 + - + +
155B GLY* 2.5 23.8 + - - -
156B LEU* 2.7 46.1 + - + +
188B ALA* 3.4 23.1 + - - +
189B ALA* 3.4 21.1 + - - +
191B ALA 3.1 26.3 + - - -
193B GLU* 3.6 30.1 + - - +
196B VAL* 3.6 23.1 - - - +
202B GLN* 4.9 7.1 - - - +
210B TYR* 3.3 41.7 - - + +
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B SER* 3.7 23.4 - - - +
152B ARG* 1.3 74.6 - - + +
154B ILE* 1.3 59.3 + - + +
155B GLY 2.7 10.7 + - - -
156B LEU* 2.9 11.6 + - - +
157B ARG* 2.8 25.3 + - - +
202B GLN* 5.4 8.0 + - - +
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Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B SER* 2.9 24.9 - - - +
151B ILE* 3.5 21.8 - - + +
153B GLU* 1.3 75.2 - - + +
155B GLY* 1.3 55.2 + - - +
157B ARG* 3.7 8.4 - - + +
158B LEU* 2.9 50.4 + - + +
175B GLU* 6.3 0.7 - - + -
177B LEU* 4.6 15.5 - - + -
181B LYS* 5.7 8.3 - - + +
185B ALA* 4.7 4.0 - - + -
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Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ILE 2.9 10.7 + - - -
152B ARG 2.5 17.7 + - - -
154B ILE* 1.3 68.0 - - - +
156B LEU* 1.3 50.4 + - - -
157B ARG 3.0 4.0 - - - -
158B LEU* 2.9 5.8 + - - +
159B MSE 2.7 35.0 + - - +
185B ALA* 3.9 16.4 - - - -
186B LEU* 4.7 1.8 - - - +
189B ALA* 3.7 17.4 - - - +
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ARG* 2.7 76.7 + - + +
153B GLU* 2.9 7.8 + - - +
155B GLY* 1.3 71.7 - - - -
157B ARG* 1.3 59.7 + - - +
159B MSE 3.4 23.7 - - + +
160B ARG* 3.5 15.6 + - - +
189B ALA* 3.5 31.4 - - + +
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B GLU 2.8 16.7 + - - +
154B ILE* 3.7 11.9 - - - +
156B LEU* 1.3 79.8 - - - +
158B LEU* 1.3 58.6 + - - +
159B MSE 3.5 0.2 + - - -
160B ARG* 3.6 39.8 + - - +
161B MSE 2.6 43.9 - - - +
175B GLU* 2.8 35.5 + - - +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ILE* 2.9 35.1 + - + +
155B GLY* 2.9 4.6 + - - +
157B ARG* 1.3 75.0 - - + +
159B MSE 1.3 65.6 + - - +
161B MSE 3.1 23.3 + - + +
162B LYS* 3.3 11.8 + - - +
171B ILE* 3.3 34.8 - - + +
175B GLU* 4.1 21.5 - - + +
177B LEU* 4.4 13.9 - - + -
181B LYS* 5.1 0.9 - - + +
182B VAL* 4.8 17.0 - - + +
185B ALA* 3.7 25.8 - - + -
186B LEU* 4.5 10.9 - - + +
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Residues in contact with MSE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B GLY 2.7 12.8 + - - +
156B LEU* 3.4 20.6 - - + +
158B LEU* 1.3 72.2 - - - +
160B ARG* 1.3 51.4 + - - +
161B MSE 3.0 4.3 - - - -
162B LYS* 2.6 34.8 + - - +
163B ASN* 2.7 32.2 - - - +
186B LEU* 4.4 12.1 - - + +
189B ALA* 4.2 28.7 - - + +
190B SER* 5.6 4.5 - - - -
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Residues in contact with ARG 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B LEU 3.5 12.2 + - - +
157B ARG* 3.8 42.9 + - - +
158B LEU 3.4 0.6 - - - -
159B MSE 1.3 78.9 - - + +
161B MSE 1.3 62.8 + - + +
162B LYS 3.2 0.4 - - - -
163B ASN* 3.4 9.4 + - - +
164B ASP* 3.0 26.3 + - - +
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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