Contacts of the strand formed by residues 145 - 151 (chain A) in PDB entry 2NUN
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 HIS 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 ASP 4.6 5.2 + - - +
144A ALA* 1.3 76.0 - - - +
146A ASP* 1.3 76.3 + - - +
147A GLU* 2.6 31.0 + - + -
160A LYS* 4.7 2.5 - - - -
161A VAL* 2.8 60.4 + - + +
162A TYR* 5.0 0.2 - - - -
163A ARG* 3.7 29.6 + - + -
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Residues in contact with ASP 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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145A HIS* 1.3 82.7 - - - +
147A GLU* 1.3 62.0 + - - +
148A ILE* 5.7 1.1 - - + -
159A VAL 3.7 6.4 - - - +
160A LYS* 3.0 40.3 + - - +
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Residues in contact with GLU 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 HIS* 2.6 35.3 + - + +
146A ASP* 1.3 77.5 - - - +
148A ILE* 1.3 81.7 - - - +
149A MET* 5.8 0.9 - - - -
158A ASN* 3.7 0.9 - - - -
159A VAL* 3.0 37.3 + - + +
161A VAL* 3.7 17.0 - - + +
163A ARG* 3.5 28.8 + - - -
179A ARG* 4.8 4.2 + - - -
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Residues in contact with ILE 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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146A ASP* 5.7 0.9 - - + -
147A GLU* 1.3 94.5 - - - +
149A MET* 1.3 70.6 + - - +
150A GLN* 4.0 12.9 + - + +
156A ASP* 4.4 20.4 - - + +
157A LEU 3.5 4.7 - - - +
158A ASN* 3.7 23.3 - - - +
159A VAL* 4.7 0.7 - - - -
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Residues in contact with MET 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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147A GLU* 4.0 1.9 + - - +
148A ILE* 1.3 74.6 - - - +
150A GLN* 1.3 73.8 + - - +
151A ASP* 4.9 10.3 - - + -
154A PHE* 6.5 0.2 - - + -
155A GLY 3.8 0.7 - - - +
156A ASP* 3.2 5.7 - - - +
157A LEU* 2.9 63.1 + - + +
159A VAL* 3.6 25.4 - - + -
179A ARG* 3.9 32.8 - - - +
210A TYR 5.3 2.5 - - - +
212A PRO* 4.1 21.8 - - + +
214A ARG* 3.9 26.7 - - - +
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Residues in contact with GLN 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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148A ILE* 4.0 9.9 + - + +
149A MET* 1.3 90.1 - - - +
151A ASP* 1.3 61.8 + - - +
156A ASP* 3.8 17.7 - - - +
179A ARG* 5.6 3.6 + - - -
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Residues in contact with ASP 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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149A MET* 4.9 15.0 - - + -
150A GLN* 1.3 74.7 - - - +
152A ASN* 1.3 66.7 + - - +
153A LEU* 3.0 11.7 + - - +
154A PHE* 2.8 43.5 + - + +
155A GLY* 2.7 43.4 + - - +
156A ASP* 5.1 0.5 - - - +
210A TYR* 3.7 35.0 - - - +
214A ARG* 5.4 1.8 + - - +
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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