Contacts of the strand formed by residues 284 - 290 (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 ALA 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ILE* 3.2 21.8 - - + -
275A LEU* 3.6 20.6 - - + -
282A THR 3.1 2.9 + - - +
283A GLY* 1.3 75.4 - - - +
285A ARG* 1.3 62.7 + - - +
286A ILE 4.1 0.9 - - - -
342A GLY 4.9 1.4 + - - -
343A HIS* 3.5 28.3 - - + +
344A VAL* 3.2 29.8 + - - +
402A PHE* 3.9 6.7 - - - -
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Residues in contact with ARG 285 (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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130A ILE 2.6 14.9 + - - +
131A PHE* 3.5 29.7 - - + -
132A LEU* 2.8 29.2 + - - -
275A LEU* 5.0 0.2 - - - +
284A ALA* 1.3 75.8 - - - +
286A ILE* 1.3 57.4 + - - +
287A MET* 3.3 23.5 + - + +
344A VAL* 3.9 21.4 - - + +
346A ASP* 2.8 32.6 + - - +
368A GLY 4.5 3.2 + - - -
370A TYR* 3.1 41.3 + - - -
389A VAL* 4.7 2.9 - - - +
400A MET* 4.0 20.4 - - - +
401A GLY 5.6 0.2 + - - -
402A PHE* 3.5 28.4 - - + -
450A GLY* 5.3 4.6 - - - -
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Residues in contact with ILE 286 (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 10.3 - - + -
134A VAL* 3.7 25.1 - - + -
268A LEU* 4.0 19.5 - - + -
271A ALA* 4.1 4.0 - - + -
272A VAL* 3.9 39.7 - - + +
275A LEU* 3.8 26.5 - - + -
285A ARG* 1.3 68.9 - - - +
287A MET* 1.3 54.3 + - - +
288A MET* 4.9 1.1 - - + +
338A ALA* 5.2 0.7 - - + -
343A HIS* 4.8 10.8 - - + +
344A VAL 2.9 16.4 + - - +
345A ILE* 4.3 13.7 - - + -
346A ASP* 2.7 33.9 + - - +
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Residues in contact with MET 287 (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* 3.6 32.8 - - + -
132A LEU 3.0 9.0 + - - +
133A TYR* 3.6 43.0 - - + +
134A VAL* 2.9 25.0 + - - -
285A ARG* 3.6 19.1 - - + +
286A ILE* 1.3 70.3 - - - +
288A MET* 1.3 60.8 + - - +
289A PHE* 3.2 18.8 - - + -
346A ASP* 3.5 23.3 - - - +
348A TYR* 3.9 12.6 - - + -
386A PHE* 5.0 4.3 - - - -
390A PHE* 3.9 25.1 - - + -
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Residues in contact with MET 288 (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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134A VAL* 3.4 19.7 - - + +
169A PHE* 3.6 30.1 - - + -
264A SER* 3.2 31.4 - - - +
267A ALA* 4.1 7.2 - - + -
268A LEU* 3.4 34.3 - - + +
286A ILE 3.6 1.5 + - - +
287A MET* 1.3 71.2 - - - +
289A PHE* 1.3 59.9 + - - +
290A ILE* 3.2 23.6 - - + -
331A PHE* 5.9 0.2 - - + -
346A ASP 2.9 18.7 + - - +
347A ILE* 3.5 6.2 - - + -
348A TYR* 2.7 37.8 + - - -
360A MET* 5.5 6.3 - - - +
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Residues in contact with PHE 289 (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 16.8 - + + -
134A VAL 3.0 14.3 + - - +
135A VAL* 4.7 3.1 - - - -
136A ASP* 3.1 26.5 + - - +
147A LEU* 3.3 44.6 - - + -
151A MET* 4.3 15.5 - - + -
169A PHE* 4.4 1.2 - - - -
287A MET* 3.2 32.5 - - + -
288A MET* 1.3 73.7 - - - +
290A ILE* 1.3 65.2 + - - +
348A TYR* 3.3 33.9 - + + +
377A PHE* 4.2 5.6 - + + -
382A PHE* 4.2 5.4 - + - -
386A PHE* 3.9 35.4 - + - -
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Residues in contact with ILE 290 (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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136A ASP* 4.2 2.2 - - - +
169A PHE* 5.0 2.5 - - + -
262A ARG* 5.3 0.4 - - - -
264A SER* 5.0 8.3 - - - +
288A MET* 3.2 45.5 - - + +
289A PHE* 1.3 84.3 - - - +
291A GLY* 1.3 58.4 + - - +
292A GLY 2.9 32.1 - - - +
347A ILE* 4.6 9.6 - - + -
348A TYR 2.7 13.0 + - - +
349A ALA* 4.0 3.8 - - + -
350A CYS 3.0 27.2 + - - -
355A THR* 3.1 32.3 - - + +
360A MET* 4.7 11.0 - - + -
377A PHE* 3.2 9.2 - - - -
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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