Contacts of the strand formed by residues 130 - 136 (chain A) in PDB entry 2NUP
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 ILE 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A MET* 6.4 0.4 - - - -
128A PRO 3.6 10.5 - - - +
129A LEU* 1.3 79.7 - - - +
131A PHE* 1.3 64.5 + - - +
163A LEU* 3.5 15.7 - - + +
230A LEU* 4.1 18.6 - - + -
275A LEU* 3.8 27.4 - - + -
279A PHE* 3.4 48.0 - - + +
282A THR* 5.1 6.5 - - + +
283A GLY 3.5 13.4 + - - +
284A ALA* 3.2 16.2 - - + +
285A ARG* 2.6 33.0 + - - +
402A PHE* 5.7 0.7 - - - -
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Residues in contact with PHE 131 (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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129A LEU* 4.0 23.1 - - + -
130A ILE* 1.3 79.2 - - - +
132A LEU* 1.3 60.8 + - - +
133A TYR* 4.1 3.9 + - + -
158A LEU* 3.5 33.0 - - + -
159A PRO* 4.6 0.9 - - + -
162A ALA* 4.2 17.0 - - + -
163A LEU 2.9 10.4 + - - +
164A VAL* 3.2 16.2 - - + +
165A GLY 3.0 22.5 + - - +
230A LEU* 4.6 1.2 - - - +
285A ARG* 3.5 27.6 - - + -
287A MET* 3.6 28.7 - - + -
390A PHE* 3.9 12.1 - + - -
398A PHE* 4.0 19.7 - + - -
400A MET* 4.6 9.0 - - - -
402A PHE* 5.0 5.6 - + - -
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Residues in contact with LEU 132 (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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131A PHE* 1.3 72.7 - - - +
133A TYR* 1.3 65.5 + - - +
134A VAL* 3.6 11.6 + - + +
165A GLY* 3.4 29.8 - - - +
166A LEU 4.0 2.2 - - - +
167A ILE* 4.2 12.3 - - + -
230A LEU* 4.5 2.9 - - + -
271A ALA* 3.5 35.2 - - + +
274A LEU* 3.9 23.8 - - + -
275A LEU* 3.6 31.0 - - + -
285A ARG 2.8 12.9 + - - +
286A ILE* 3.6 8.2 - - + -
287A MET* 3.0 27.6 + - - +
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Residues in contact with TYR 133 (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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131A PHE* 4.3 4.3 - - + -
132A LEU* 1.3 72.7 - - - +
134A VAL* 1.3 56.8 + - - +
135A VAL* 3.9 7.0 - - + -
151A MET* 3.8 34.0 + - + -
154A SER* 2.9 30.9 + - - -
155A LEU* 3.6 8.3 + - + -
158A LEU* 3.5 21.0 - - + +
164A VAL* 4.1 22.7 - - + -
165A GLY 3.0 18.7 + - - +
166A LEU* 3.5 15.6 - - + +
167A ILE* 2.7 32.7 + - - +
240A LEU* 4.9 11.2 - - + -
244A LEU* 5.2 6.3 - - + -
287A MET* 3.6 30.8 - - + +
289A PHE* 4.3 7.0 - + + -
386A PHE* 5.0 4.0 - + - -
390A PHE* 5.4 0.3 - - - -
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Residues in contact with VAL 134 (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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132A LEU* 3.6 16.4 - - + +
133A TYR* 1.3 76.9 - - - +
135A VAL* 1.3 60.4 + - - +
167A ILE* 3.1 19.3 - - + +
169A PHE* 4.5 2.5 - - + -
267A ALA* 4.1 30.7 - - + +
268A LEU* 4.7 0.4 - - - +
271A ALA* 3.8 12.1 - - + -
286A ILE* 3.7 24.9 - - + -
287A MET 2.9 10.1 + - - +
288A MET* 3.4 23.2 - - + +
289A PHE* 3.0 27.4 + - - +
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Residues in contact with VAL 135 (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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133A TYR* 4.3 2.0 - - + -
134A VAL* 1.3 79.9 - - - +
136A ASP* 1.3 72.7 + - - +
137A THR* 3.7 1.3 + - + -
144A LEU* 4.8 4.3 - - + -
147A LEU* 4.1 12.8 - - + -
151A MET* 3.4 43.1 - - + -
166A LEU* 4.0 21.3 - - + -
167A ILE 2.6 13.9 + - - +
168A THR* 3.1 11.7 - - + -
169A PHE* 2.8 36.9 + - - -
247A LEU* 4.4 9.6 - - + -
289A PHE* 4.3 4.0 - - + -
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Residues in contact with ASP 136 (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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135A VAL* 1.3 88.2 - - - +
137A THR* 1.3 72.6 + - - +
138A CYS* 2.8 24.8 + - - +
139A MET* 3.2 18.4 - - + +
144A LEU* 3.9 2.8 - - - +
169A PHE* 3.2 21.5 - - + +
262A ARG* 3.2 31.8 + - - +
289A PHE 3.1 23.6 + - - +
290A ILE* 4.2 0.9 - - - -
291A GLY* 2.8 27.4 + - - +
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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