Contacts of the strand formed by residues 152 - 157 (chain A) in PDB entry 1NUA
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 LYS 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A GLY 5.7 0.3 - - - -
119A ASP* 3.6 15.6 - - - +
136A GLN* 5.7 2.3 + - - -
147A SER 4.8 9.9 + - - +
150A GLY* 3.3 9.1 - - - +
151A GLY* 1.3 76.1 - - - +
153A THR* 1.3 63.1 + - - +
167A ILE* 3.7 22.9 - - + -
130B ARG* 3.8 32.3 - - - +
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Residues in contact with THR 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLY 4.7 2.7 - - - +
119A ASP* 3.5 8.5 - - - +
122A GLY* 3.4 23.6 + - - +
123A PHE* 3.3 26.1 - - - +
126A SER* 4.3 2.8 + - - -
134A TYR* 3.5 20.2 - - - +
136A GLN* 5.8 1.6 - - - +
151A GLY 4.0 7.6 - - - +
152A LYS* 1.3 79.2 - - - +
154A ALA* 1.3 67.6 + - - +
166A ALA* 2.6 36.2 + - - +
168A TRP* 4.2 3.6 - - + +
130B ARG* 2.9 12.6 + - - +
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS* 3.4 16.8 - - - -
119A ASP* 3.2 21.9 + - - +
120A LEU 3.7 0.5 + - - -
123A PHE* 3.8 5.1 - - - +
153A THR* 1.3 79.5 - - - +
155A ILE* 1.3 67.7 + - - +
162A ASN* 3.5 26.9 - - - +
164A ILE 3.2 17.7 - - - +
165A GLY* 3.7 6.7 - - - -
130B ARG* 3.7 12.6 - - + +
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Residues in contact with ILE 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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84A LYS* 3.7 14.8 - - + +
85A SER* 3.8 16.2 - - - +
86A ARG* 3.3 44.0 - - + +
89A LYS* 4.7 4.9 - - + -
120A LEU* 4.0 20.0 - - + -
123A PHE* 3.9 24.0 - - + -
154A ALA* 1.3 79.2 - - - +
156A ASP* 1.3 70.3 + - - +
157A THR* 4.9 0.8 - - + +
162A ASN* 3.2 18.9 + - - -
163A LEU 3.3 7.4 + - - -
164A ILE* 3.0 26.8 + - + +
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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
----------------------------------------------------------
81A GLU* 4.4 10.7 - - - +
84A LYS* 3.0 37.2 + - - +
85A SER* 4.1 13.2 - - - -
86A ARG* 4.6 2.4 + - - +
155A ILE* 1.3 80.5 - - - +
157A THR* 1.3 68.8 + - - +
160A GLY 3.6 8.1 - - - +
161A LYS* 3.1 36.6 + - + +
162A ASN 2.9 21.7 + - - -
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Residues in contact with THR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 4.1 35.7 - - + +
155A ILE* 4.9 2.5 - - + +
156A ASP* 1.3 81.1 - - - +
158A PRO* 1.3 70.8 - - - +
159A LEU* 2.9 10.4 + - - +
160A GLY* 2.9 25.5 + - - +
163A LEU* 3.1 31.2 - - + +
164A ILE* 4.2 17.3 - - + -
94B ASP* 4.8 2.9 - - - -
97B LEU* 4.2 3.5 - - + +
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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