Contacts of the helix formed by residues 261 - 266 (chain B) in PDB entry 3NJ4
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 THR 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A LYS* 3.8 19.0 - - + +
406A LEU 4.0 9.0 - - - +
407A THR* 3.6 23.1 - - + +
242B THR* 4.0 2.7 - - - -
260B THR* 1.3 83.9 - - - +
262B MET* 1.3 54.8 + - - +
263B ASP* 3.7 18.7 + - - +
264B GLU* 2.9 23.0 + - - +
265B ALA* 2.7 34.3 + - - +
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Residues in contact with MET 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A THR* 4.9 1.4 + - - -
217B VAL* 4.1 18.8 - - + +
219B ALA* 3.9 15.7 - - + +
242B THR* 3.9 13.5 - - + +
261B THR* 1.3 70.0 - - - +
263B ASP* 1.3 59.1 + - - +
264B GLU 2.9 5.2 - - - -
265B ALA* 4.2 2.9 - - - +
266B CYS* 2.8 38.9 + - - +
272B PHE* 3.9 28.7 - - + -
281B ILE* 3.5 43.5 - - + +
282B ILE* 4.1 15.0 - - + -
286B HIS* 3.5 23.3 - - + +
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Residues in contact with ASP 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B THR* 3.1 16.1 + - - +
262B MET* 1.3 78.3 - - - +
264B GLU* 1.3 59.9 + - + +
266B CYS* 3.4 9.5 - - - -
267B GLN* 3.3 16.3 - - - +
285B ARG* 2.6 37.9 + - - -
286B HIS* 3.2 13.4 + - - -
289B GLN* 4.3 2.4 - - - +
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Residues in contact with GLU 264 (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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405A LYS* 3.7 17.9 - - + -
258B GLU* 5.4 0.9 - - - +
260B THR* 3.6 29.7 - - + +
261B THR* 2.9 20.0 + - - +
263B ASP* 1.3 81.4 - - + +
265B ALA* 1.3 64.4 + - - +
266B CYS 3.3 1.1 - - - -
267B GLN* 3.1 29.6 + - - +
268B GLU* 4.1 11.0 - - - +
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Residues in contact with ALA 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B VAL* 3.6 33.7 - - + +
240B ILE* 4.4 14.8 - - + -
242B THR* 4.5 2.2 - - + -
260B THR* 4.6 1.7 + - - +
261B THR 2.7 20.0 + - - +
262B MET* 4.2 5.8 - - - -
264B GLU* 1.3 69.1 - - - +
266B CYS* 1.3 56.1 + - - +
267B GLN 2.8 11.4 + - - -
268B GLU* 2.9 24.0 + - - -
269B GLY 2.9 13.2 + - - -
272B PHE* 3.8 3.4 - - - -
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Residues in contact with CYS 266 (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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262B MET* 2.8 30.9 + - + +
263B ASP* 3.4 18.2 - - - -
264B GLU 3.3 0.2 - - - -
265B ALA* 1.3 71.6 - - - +
267B GLN* 1.3 58.0 + - - +
268B GLU 3.5 0.4 - - - -
269B GLY 4.8 0.2 + - - -
272B PHE* 3.7 18.6 - - + -
285B ARG 4.8 0.2 - - - -
286B HIS* 3.7 42.8 - - + +
289B GLN* 3.1 41.8 - - - +
290B MET* 3.3 11.0 - - + +
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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
------------------------------------------------------------
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