Contacts of the helix formed by residues 143 - 157 (chain A) in PDB entry 3NTY
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 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A VAL* 1.3 70.6 - - - +
144A LEU* 1.3 66.3 + - - +
145A CYS* 3.3 29.0 + - - +
146A ALA* 3.1 20.8 + - + +
147A THR* 3.1 20.1 + - - -
175A MET* 5.3 3.6 - - - +
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Residues in contact with LEU 144 (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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90A HIS* 3.7 34.1 - - + +
116A ILE* 4.5 12.3 - - + +
119A PRO* 3.6 35.9 - - + +
121A SER* 5.8 0.2 - - - +
142A VAL 3.4 5.3 + - - +
143A ASP* 1.3 74.7 + - - +
145A CYS* 1.3 51.8 + - - +
147A THR* 3.2 14.2 + - - +
148A TRP* 2.7 34.7 + - - +
168A PHE* 4.2 13.7 - - + -
172A GLN* 5.1 7.0 - - + +
175A MET* 4.4 21.2 - - + -
176A ILE* 3.9 10.0 - - + +
316A ASN* 3.8 17.9 + - - +
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Residues in contact with CYS 145 (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 ASP* 3.2 18.4 + - - +
144A LEU* 1.3 76.4 - - - +
146A ALA* 1.3 51.7 + - - +
148A TRP* 3.5 4.1 + - - +
149A GLU* 2.8 40.9 + - - +
175A MET* 3.6 37.0 - - - -
176A ILE* 4.5 3.6 - - - -
179A LYS* 3.4 37.4 - - + +
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Residues in contact with ALA 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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92A PRO* 4.1 28.5 - - + +
142A VAL* 5.3 0.2 - - + -
143A ASP* 3.1 25.6 + - + +
145A CYS* 1.3 73.9 - - - +
147A THR* 1.3 67.9 + - - +
149A GLU* 3.2 12.5 + - - +
150A ALA* 3.2 21.1 + - - +
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Residues in contact with THR 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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85A LEU* 3.7 24.9 - - + -
90A HIS* 2.8 40.2 + - + +
92A PRO* 5.0 0.2 - - - -
95A VAL* 4.3 5.1 - - + +
116A ILE* 3.7 20.2 - - + -
142A VAL* 3.5 7.8 - - - +
143A ASP 3.1 13.5 + - - -
144A LEU* 3.2 16.5 + - + +
146A ALA* 1.3 75.3 - - - +
148A TRP* 1.3 63.7 + - - +
150A ALA* 3.1 6.5 + - - +
151A VAL* 2.9 25.1 + - + +
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Residues in contact with TRP 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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116A ILE* 3.8 18.8 - - + +
144A LEU 2.7 19.5 + - - +
145A CYS* 3.6 5.4 - - - +
147A THR* 1.3 74.6 - - - +
149A GLU* 1.3 58.7 + - - +
151A VAL* 3.1 19.5 + - + +
152A GLU* 2.8 47.7 + - + +
163A ILE* 3.5 29.2 - - + -
164A GLY 3.6 24.7 - - - -
165A VAL* 4.1 9.0 - - + -
176A ILE* 3.5 32.1 - - + +
179A LYS* 4.4 7.2 - - - -
182A LEU* 3.3 9.6 - - + +
184A TYR 3.1 28.4 + - - -
186A PRO* 3.6 28.7 - - + -
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Residues in contact with GLU 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 CYS* 2.8 27.3 + - - +
146A ALA* 3.2 8.7 + - - +
148A TRP* 1.3 75.7 - - - +
150A ALA* 1.3 61.5 + - - +
152A GLU* 3.4 16.0 - - - +
153A LYS* 3.2 39.7 + - - +
179A LYS* 2.8 40.3 + - - +
180A PRO 4.6 1.4 - - - +
183A LYS* 5.1 1.2 - - - -
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Residues in contact with ALA 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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92A PRO* 3.3 36.6 - - + +
95A VAL* 3.7 16.6 - - + +
96A ARG* 5.5 0.8 + - - +
146A ALA 3.2 5.9 + - - +
147A THR 3.1 8.9 + - - +
149A GLU* 1.3 75.0 - - - +
151A VAL* 1.3 64.5 + - - +
153A LYS* 3.3 19.8 + - - +
154A CYS* 3.3 16.1 + - - -
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Residues in contact with VAL 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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85A LEU* 4.3 7.6 - - + -
95A VAL* 3.7 19.5 - - + -
114A TYR* 4.4 19.1 - - + +
116A ILE* 4.2 21.1 - - + +
147A THR 2.9 18.6 + - - +
148A TRP* 3.4 22.0 - - + +
150A ALA* 1.3 77.7 - - - +
152A GLU* 1.3 61.0 + - - +
154A CYS* 3.1 19.6 + - - +
155A LYS 3.4 3.8 + - - -
163A ILE* 3.5 33.2 - - + +
164A GLY 5.4 0.2 - - - +
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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 TRP* 2.8 39.2 + - - +
149A GLU* 3.4 26.2 - - - +
150A ALA 3.2 0.2 - - - -
151A VAL* 1.3 75.9 - - - +
153A LYS* 1.3 56.4 - - - +
155A LYS* 2.9 19.8 + - - +
156A ASP* 3.0 16.8 + - - -
163A ILE* 3.7 11.4 - - + -
179A LYS* 4.5 4.0 + - - -
181A GLY 5.0 0.2 - - - +
182A LEU* 3.6 2.5 - - - +
183A LYS* 2.8 51.6 + - - +
184A TYR* 2.8 27.4 + - + +
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Residues in contact with LYS 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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96A ARG* 5.0 5.9 + - - +
149A GLU* 3.2 30.3 + - - +
150A ALA* 3.3 11.1 + - - +
152A GLU* 1.3 75.9 - - - +
154A CYS* 1.3 57.3 + - - +
156A ASP* 3.7 10.5 - - + +
157A ALA* 2.9 29.6 + - - +
183A LYS* 4.2 20.3 - - - +
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Residues in contact with CYS 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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95A VAL* 4.1 19.3 - - - -
96A ARG* 4.1 24.5 - - - +
99A LEU* 3.6 33.0 - - + -
114A TYR* 5.1 4.0 - - + -
150A ALA 3.3 13.9 + - - -
151A VAL* 3.1 11.9 + - + +
153A LYS* 1.3 74.8 - - - +
155A LYS* 1.3 62.7 + - - +
157A ALA* 3.6 4.8 + - - -
158A GLY 3.2 2.6 + - - -
159A LEU* 3.0 30.8 + - - +
160A ALA* 3.3 8.3 + - + -
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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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12A ASP* 4.0 27.1 + - - +
14A HIS* 4.1 7.5 + - - -
151A VAL 3.4 2.0 + - - -
152A GLU 2.9 9.7 + - - +
154A CYS* 1.3 77.6 - - - +
156A ASP* 1.3 61.4 + - - +
158A GLY* 2.9 19.8 + - - -
160A ALA* 3.4 13.1 - - - +
161A LYS 2.8 31.0 + - - +
162A SER* 4.7 2.5 - - - -
163A ILE* 4.2 26.9 - - + -
184A TYR* 3.6 47.6 - - + +
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Residues in contact with ASP 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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152A GLU 3.0 12.2 + - - +
153A LYS* 3.7 12.5 - - - +
155A LYS* 1.3 77.3 - - - +
157A ALA* 1.3 58.3 - - - +
158A GLY* 3.4 1.0 + - - -
183A LYS* 2.7 35.0 + - - +
184A TYR* 2.3 33.6 + - - -
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Residues in contact with ALA 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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96A ARG* 3.5 28.9 - - - +
153A LYS 2.9 21.1 + - - +
154A CYS* 3.9 5.8 - - - +
155A LYS 3.2 0.2 - - - -
156A ASP* 1.3 71.7 - - - +
158A GLY* 1.3 59.1 + - - +
159A LEU* 3.3 17.1 + - + +
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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