Contacts of the helix formed by residues 154 - 161 (chain A) in PDB entry 3NUI
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 THR 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER* 4.0 13.4 + - - -
119A GLU* 5.2 2.2 - - + +
122A ASP* 2.5 30.9 + - - +
153A VAL* 1.3 83.3 - - + +
155A ALA* 1.3 68.9 + - - +
157A SER* 2.7 19.3 + - - -
158A ALA* 2.7 22.9 + - - +
119B GLU* 4.0 29.6 - - + +
122B ASP* 3.3 24.7 - - + +
123B THR* 6.1 0.2 - - - +
126B LYS* 4.5 0.7 - - - -
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Residues in contact with ALA 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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154A THR* 1.3 73.0 - - - +
156A VAL* 1.3 57.2 + - - +
158A ALA* 3.8 1.6 - - - +
159A SER* 2.8 32.9 + - - -
171A LEU* 4.1 11.9 - - + +
173A LEU* 4.2 9.0 - - + -
122B ASP* 2.9 13.1 + - - +
126B LYS* 4.5 3.1 - - + +
129B TRP* 4.4 16.2 - - + -
173B LEU* 3.6 40.4 - - + -
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASP* 3.4 22.2 + - - +
125A VAL* 4.1 28.3 - - + -
126A LYS* 5.0 13.0 - - - +
129A TRP* 4.5 13.7 - - + -
154A THR* 3.3 0.6 + - - -
155A ALA* 1.3 72.7 - - - +
157A SER* 1.3 61.3 + - - +
159A SER* 2.9 9.4 + - - -
160A MET* 2.8 29.1 + - - +
173A LEU* 4.2 16.2 - - + -
176A PHE* 3.8 24.4 - - + -
122B ASP* 4.9 0.6 + - - -
173B LEU* 4.8 10.5 - - + +
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Residues in contact with SER 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 SER* 3.6 10.1 - - - -
121A ASN* 4.2 7.2 - - - -
122A ASP* 2.9 18.4 + - - -
151A HIS* 3.5 23.1 - - - +
152A GLY* 3.4 5.4 + - - -
153A VAL 3.3 6.8 + - - -
154A THR* 2.7 31.4 + - - -
156A VAL* 1.3 72.3 - - - +
158A ALA* 1.3 50.1 + - - +
160A MET* 3.4 12.7 + - - +
161A THR* 2.8 34.5 + - - -
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Residues in contact with ALA 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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152A GLY 3.5 15.0 + - - +
153A VAL* 4.1 8.7 - - - +
154A THR 2.7 25.9 + - - +
157A SER* 1.3 71.1 + - - +
159A SER* 1.3 61.9 + - - +
161A THR* 3.2 12.8 - - - +
166A ASN* 3.0 35.5 + - - +
171A LEU* 3.9 21.3 - - + +
172A PRO* 5.3 0.5 - - - +
126B LYS* 4.3 2.9 - - - +
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Residues in contact with SER 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 ALA 2.8 19.5 + - - -
156A VAL 2.9 9.7 + - - -
158A ALA* 1.3 73.5 - - - +
160A MET* 1.3 62.7 + - - +
161A THR 3.4 0.7 - - - +
171A LEU* 3.7 3.2 - - - +
172A PRO* 3.6 12.4 - - - +
173A LEU* 2.9 33.0 + - - +
176A PHE* 3.5 31.7 - - - +
178A HIS* 3.0 28.6 + - - -
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Residues in contact with MET 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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121A ASN* 4.0 11.0 - - - +
125A VAL* 3.6 21.1 - - - -
143A ILE* 4.1 7.6 - - + -
145A THR* 2.7 32.6 + - + -
149A ALA* 4.3 1.4 - - - +
151A HIS* 3.6 26.8 - - + -
156A VAL* 2.8 14.3 + - - +
157A SER* 3.4 23.3 - - - +
159A SER* 1.3 74.3 - - - +
161A THR* 1.3 63.3 + - - +
162A GLY 3.6 0.7 + - - -
176A PHE* 3.7 19.3 - - + -
178A HIS* 3.2 2.3 + - - -
221A PHE* 3.4 50.3 - - + -
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Residues in contact with THR 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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149A ALA 3.4 16.2 - - - +
150A TYR* 3.6 18.6 - - + -
151A HIS* 2.8 18.4 + - - +
152A GLY 3.3 9.7 + - - +
157A SER 2.8 18.3 + - - -
158A ALA* 3.2 23.7 - - - +
159A SER 3.3 0.9 - - - +
160A MET* 1.3 73.8 - - - +
162A GLY* 1.3 61.7 + - - +
163A LYS* 3.7 17.4 + - + -
165A TYR* 4.0 3.4 - - - +
166A ASN* 3.8 15.8 + - - +
172A PRO* 5.5 2.3 - - - +
178A HIS* 3.1 14.0 + - - -
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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