Contacts of the strand formed by residues 126 - 133 (chain B) in PDB entry 2NS2
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 TRP 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B VAL 3.9 0.5 - - - +
113B GLU* 3.3 5.0 - - - -
114B HIS* 2.8 45.8 + + + +
115B MET* 6.3 1.1 - - - -
125B GLU* 1.3 82.6 - - - +
127B ARG* 1.3 63.8 + - - +
128B GLY 4.1 0.3 + - - -
145B TYR* 3.8 32.5 - + + -
147B LYS* 3.2 42.0 - - + -
148B ASP* 6.1 1.6 - - + -
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ALA* 4.5 19.4 - - - +
112B VAL 3.2 12.3 - - - +
113B GLU* 3.4 26.2 + - + +
125B GLU 4.2 0.6 + - - -
126B TRP* 1.3 77.4 - - - +
128B GLY* 1.3 61.6 + - - +
145B TYR* 3.6 8.6 - - - +
146B GLU* 2.6 59.9 + - + +
147B LYS 4.8 0.7 + - - -
168B MET* 6.2 2.2 - - - -
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ALA* 3.4 3.3 - - - +
112B VAL* 2.6 43.4 + - - -
126B TRP 4.1 0.4 + - - -
127B ARG* 1.3 77.6 - - - +
129B MET* 1.3 56.8 + - - -
143B ILE* 5.1 1.8 - - - -
144B THR 3.2 14.4 - - - -
145B TYR* 3.8 10.3 - - - -
146B GLU* 3.7 14.5 - - - +
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Residues in contact with MET 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLY* 4.3 7.6 - - - +
110B LYS 3.5 17.7 - - - +
111B ALA* 4.6 4.3 - - - +
112B VAL* 4.5 0.4 - - - +
128B GLY* 1.3 75.0 - - - +
130B VAL* 1.3 77.1 + - - +
131B LEU* 3.5 22.3 + - + +
143B ILE* 3.3 19.0 - - - +
144B THR* 3.0 25.1 + - + +
146B GLU* 5.0 10.5 - - - +
211B VAL* 5.9 0.7 - - - -
214B LYS* 3.1 49.8 - - - +
217B VAL* 4.8 6.7 - - + -
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B MET* 3.9 23.3 - - + +
108B ILE* 3.8 20.2 - - + +
109B GLY* 3.1 20.7 + - - -
110B LYS 3.3 4.6 + - - +
112B VAL* 3.9 22.0 - - + -
129B MET* 1.3 84.0 - - - +
131B LEU* 1.3 61.9 + - - +
132B ALA 4.4 0.9 - - - +
141B PHE* 3.6 31.0 - - + -
142B TYR 3.9 7.0 - - - +
143B ILE* 4.3 5.6 - - + -
156B LEU* 3.8 23.6 - - + -
165B LEU* 6.5 1.1 - - + -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ILE* 3.6 17.0 - - - +
129B MET* 3.7 31.0 - - + +
130B VAL* 1.3 75.2 - - - +
132B ALA* 1.3 66.9 + - + +
142B TYR* 2.9 12.1 + - + +
143B ILE* 3.9 19.5 - - - +
144B THR* 3.9 13.0 - - + +
151B LEU* 3.8 28.5 - - + -
211B VAL* 3.7 43.7 - - + +
213B ALA* 3.9 4.2 + - - +
217B VAL* 4.5 2.5 - - + -
219B PHE* 3.9 13.0 - - + -
230B VAL* 4.1 13.2 - - + -
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ILE* 4.3 12.3 - - + -
130B VAL* 4.0 0.8 - - - +
131B LEU* 1.3 83.8 - - + +
133B ARG* 1.3 65.8 + - - +
134B ALA 3.7 0.4 - - - -
141B PHE* 3.4 16.3 - - - -
142B TYR* 3.0 37.8 + - + +
211B VAL* 5.7 1.1 - - + -
219B PHE* 6.2 0.7 - - + -
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA* 3.0 33.6 - - - +
105B ASP* 3.8 16.7 + - - -
108B ILE* 4.1 13.8 - - + +
132B ALA* 1.3 78.4 - - - +
134B ALA* 1.3 70.6 + - - +
135B PRO* 3.4 4.9 - - - +
138B ASN* 3.1 37.0 + - - +
139B THR* 5.5 2.4 - - - +
140B TRP 3.7 6.5 - - - +
141B PHE* 3.9 15.8 - - + -
142B TYR* 5.5 0.2 - - - -
157B LEU* 3.9 17.0 - - - +
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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