Contacts of the helix formed by residues 295 - 302 (chain B) in PDB entry 2NUD
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 VAL 295 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B ALA* 4.4 5.2 - - + +
49B ARG 4.2 8.3 - - - +
50B TRP* 3.4 64.8 - - + +
51B PRO* 5.0 1.8 - - + -
293B GLY 3.9 1.6 + - - -
294B ASN* 1.3 70.5 - - - +
296B SER* 1.3 60.3 + - - +
297B ASP* 2.9 28.3 - - - +
298B ILE* 3.0 8.3 + - + +
299B GLU* 2.9 30.4 + - - +
1502B TRS 3.3 22.9 - - - +
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Residues in contact with SER 296 (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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255B HIS* 3.7 20.3 + - - -
269B ALA* 5.3 2.8 + - - +
273B GLU* 3.9 15.8 + - - +
290B PHE* 3.5 42.8 - - - +
294B ASN 3.3 5.5 + - - -
295B VAL* 1.3 72.1 - - - +
297B ASP* 1.3 64.7 + - - +
299B GLU* 3.3 7.5 + - - +
300B ALA* 3.0 23.4 + - - +
308B PHE* 4.1 5.7 - - - -
315B LEU* 5.8 0.2 - - - -
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Residues in contact with ASP 297 (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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255B HIS* 5.4 1.3 - - + -
259B ALA* 4.2 21.9 - - + +
269B ALA* 3.3 27.7 - - + +
295B VAL* 2.9 15.1 - - - +
296B SER* 1.3 79.6 + - - +
298B ILE* 1.3 64.2 + - - +
300B ALA* 3.2 2.9 + - - +
301B MET* 3.0 40.4 + - + +
1502B TRS 2.7 46.6 + - - -
2002B ETF 4.4 1.6 + - - -
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Residues in contact with ILE 298 (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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50B TRP* 4.0 25.4 - - + -
131B TYR* 4.3 17.0 - - + -
134B VAL* 4.0 23.6 - - + -
137B ARG* 5.0 3.4 - - + +
178B PHE* 5.3 4.5 - - + -
215B ILE* 5.0 9.4 - - + -
295B VAL* 3.0 18.3 + - + +
297B ASP* 1.3 96.4 + - - +
299B GLU* 1.3 78.5 + - - +
301B MET* 3.3 12.6 + - - +
302B LEU* 3.1 42.3 + - + +
1502B TRS 4.4 0.2 - - - -
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Residues in contact with GLU 299 (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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137B ARG* 3.0 41.4 + - - -
293B GLY 4.3 5.5 - - - +
294B ASN* 3.5 30.3 + - + +
295B VAL 2.9 22.2 + - - +
296B SER* 3.7 8.1 - - - +
298B ILE* 1.3 82.5 - - - +
300B ALA* 1.3 62.5 + - - +
302B LEU* 3.4 9.7 + - - +
303B SER* 3.3 17.0 + - - -
308B PHE* 3.9 13.3 - - + -
311B LYS* 4.4 13.6 + - + -
315B LEU* 4.2 20.4 - - + +
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Residues in contact with ALA 300 (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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164B GLN* 3.0 15.1 - - - +
255B HIS* 5.5 0.7 - - - +
256B TRP* 3.1 23.5 + - + -
259B ALA* 4.3 15.7 - - + -
260B SER* 4.0 6.7 - - - +
296B SER 3.0 13.9 + - - +
297B ASP 3.5 9.2 - - - +
298B ILE 3.1 0.2 - - - -
299B GLU* 1.3 78.4 - - - +
301B MET* 1.3 61.4 + - - +
303B SER* 3.1 8.5 + - - -
308B PHE* 3.4 25.5 - - + -
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Residues in contact with MET 301 (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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162B TYR* 3.3 11.3 - - - -
164B GLN* 3.4 19.2 - - - +
176B ASN* 3.6 28.7 - - - +
178B PHE* 3.3 36.0 - - + -
215B ILE* 4.7 4.0 - - - -
217B HIS* 3.6 34.1 - - + +
259B ALA 3.5 21.1 - - - +
260B SER* 4.3 7.6 - - - +
262B MET* 4.3 14.4 - - + -
297B ASP* 3.0 27.1 + - + +
298B ILE* 3.9 11.0 - - - +
300B ALA* 1.3 74.6 - - - +
302B LEU* 1.3 56.0 + - - +
303B SER 3.3 1.1 - - - -
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Residues in contact with LEU 302 (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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134B VAL* 4.9 4.5 - - + -
137B ARG* 3.8 48.7 - - + +
138B VAL* 4.3 11.0 - - + -
141B HIS* 2.9 36.3 + - + -
162B TYR* 3.4 14.5 + - + -
178B PHE* 3.6 38.6 - - + -
298B ILE* 3.1 34.3 + - + +
299B GLU* 3.9 5.4 - - - +
300B ALA 3.1 0.8 - - - -
301B MET* 1.3 77.6 - - - +
303B SER* 1.3 59.8 + - - +
307B GLU* 4.4 1.4 - - - +
311B LYS* 5.5 1.0 + - - +
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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