Contacts of the strand formed by residues 160 - 167 (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 GLY 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ASP* 3.6 1.0 - - - -
157A THR 2.9 31.4 + - - +
158A PRO 3.5 0.6 - - - -
159A LEU* 1.3 81.1 - - - +
161A LYS* 1.3 62.6 + - - -
163A LEU* 3.4 18.6 - - - +
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Residues in contact with LYS 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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81A GLU* 4.2 23.5 + - - +
84A LYS* 3.2 26.9 - - - +
116A VAL* 5.8 2.0 - - - +
156A ASP* 3.1 32.3 + - + +
160A GLY* 1.3 73.2 - - - -
162A ASN* 1.3 81.4 + - - +
163A LEU* 3.2 11.0 + - - +
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Residues in contact with ASN 162 (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* 2.9 33.7 + - - +
119A ASP* 4.3 6.2 + - - +
154A ALA* 3.5 15.4 - - + +
155A ILE 3.2 9.5 + - - -
156A ASP* 2.9 13.1 + - - -
161A LYS* 1.3 86.1 - - - +
163A LEU* 1.3 63.1 + - - +
164A ILE 3.6 1.1 - - - -
129B MET* 5.1 4.9 - - - +
130B ARG* 3.6 33.3 + - - +
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Residues in contact with LEU 163 (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 ILE 3.3 3.8 + - - -
157A THR* 3.1 28.5 - - + +
159A LEU* 3.7 8.1 - - + +
160A GLY* 3.4 26.4 + - - +
161A LYS 3.5 15.3 - - - +
162A ASN* 1.3 78.0 - - - +
164A ILE* 1.3 63.8 + - + +
97B LEU* 4.1 26.9 - - + +
128B TYR* 5.1 0.5 - - - -
129B MET* 2.7 63.6 + - + +
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Residues in contact with ILE 164 (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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86A ARG* 4.2 11.4 - - + +
123A PHE* 3.5 14.1 - - + -
154A ALA* 3.2 3.5 - - - +
155A ILE* 3.0 42.0 + - + +
157A THR* 4.2 20.4 - - + -
163A LEU* 1.3 90.7 - - - +
165A GLY* 1.3 59.5 + - - +
89B LYS* 4.1 4.3 - - - +
93B GLU* 3.5 33.9 - - + +
97B LEU* 4.3 10.1 - - + -
127B THR* 3.3 27.8 - - - +
128B TYR* 4.3 15.3 - - + -
130B ARG* 5.3 0.2 - - - -
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Residues in contact with GLY 165 (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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123A PHE* 3.5 17.2 - - - -
153A THR 3.4 13.0 - - - -
154A ALA* 3.7 2.9 - - - -
164A ILE* 1.3 76.8 - - - +
166A ALA* 1.3 61.6 + - - -
127B THR* 3.0 21.4 + - - +
130B ARG* 2.8 26.3 - - - +
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Residues in contact with ALA 166 (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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123A PHE* 3.9 4.4 - - + -
126A SER* 4.0 24.9 - - - +
127A THR* 5.7 1.6 - - + -
153A THR* 2.6 41.0 + - - +
165A GLY* 1.3 76.0 - - - +
167A ILE* 1.3 66.5 + - - +
168A TRP* 3.7 1.1 - - + -
126B SER 4.8 7.6 - - - +
127B THR* 5.0 3.8 - - + -
130B ARG* 3.7 12.2 - - - +
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Residues in contact with ILE 167 (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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150A GLY 4.5 2.2 - - - +
151A GLY 3.2 4.0 - - - +
152A LYS* 3.7 25.4 - - + -
166A ALA* 1.3 72.3 - - - +
168A TRP* 1.3 68.2 + - - +
169A GLN* 3.6 25.4 - - + +
130B ARG* 3.7 37.9 + - + +
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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