Contacts of the helix formed by residues 249 - 260 (chain A) in PDB entry 5JNO
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A GLN* 5.9 0.4 - - + +
248A LEU* 1.3 75.7 - - - +
250A ALA* 1.3 59.8 + - - +
251A ALA* 3.4 10.6 + - - +
252A GLU* 2.8 47.3 + - - +
253A LEU* 2.8 28.2 + - - +
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Residues in contact with ALA 250 (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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248A LEU 4.0 0.4 + - - -
249A THR* 1.3 72.9 - - - +
251A ALA* 1.3 57.6 + - - +
253A LEU* 3.4 8.8 + - - +
254A LYS* 2.9 31.2 + - - +
314A TYR* 4.5 4.1 + - - +
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Residues in contact with ALA 251 (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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249A THR* 3.2 9.0 + - - +
250A ALA* 1.3 78.3 - - - +
252A GLU* 1.3 62.8 + - + +
254A LYS* 3.4 6.3 + - - +
255A GLN* 3.1 24.3 + - - +
54B GLU* 6.3 0.4 - - + -
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Residues in contact with GLU 252 (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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247A GLN 4.3 3.1 - - - +
248A LEU* 3.5 23.3 - - + +
249A THR* 2.8 54.0 + - - +
251A ALA* 1.3 72.3 - - + +
253A LEU* 1.3 66.4 + - - +
255A GLN* 3.5 9.1 + - - +
256A ILE* 3.3 27.0 + - + +
53B ASN* 6.5 0.2 - - + -
54B GLU* 4.0 27.6 - - + +
55B LYS* 3.4 40.3 - - - +
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Residues in contact with LEU 253 (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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248A LEU* 4.1 10.0 - - + +
249A THR 2.8 17.1 + - - +
250A ALA* 3.7 7.9 - - - +
252A GLU* 1.3 76.2 - - - +
254A LYS* 1.3 62.8 + - - +
256A ILE* 3.1 7.1 + - + +
257A VAL* 3.0 31.2 + - + +
266A LEU* 5.1 1.6 - - + -
270A LEU* 4.0 28.0 - - + -
310A TYR* 4.0 34.5 - - + +
313A VAL* 4.0 22.9 - - + -
314A TYR* 3.7 25.6 - - + -
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Residues in contact with LYS 254 (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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250A ALA 2.9 20.7 + - - +
251A ALA* 3.4 7.6 + - - +
253A LEU* 1.3 71.5 - - - +
255A GLN* 1.3 58.2 + - - +
257A VAL* 3.2 6.0 + - - +
258A ASP* 2.7 67.2 + - - +
314A TYR* 3.2 39.9 + - + +
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Residues in contact with GLN 255 (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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251A ALA 3.1 11.2 + - - +
252A GLU* 3.6 11.0 - - - +
254A LYS* 1.3 79.1 - - - +
256A ILE* 1.3 58.4 + - + +
258A ASP* 3.3 17.6 + - - +
259A GLN* 2.6 36.4 + - + +
52B PRO* 3.7 21.3 + - - +
53B ASN* 3.5 16.5 - - + +
54B GLU* 3.1 27.8 + - - +
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Residues in contact with ILE 256 (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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248A LEU* 4.1 16.6 - - + -
252A GLU* 3.3 16.1 + - + +
253A LEU* 3.1 6.8 + - - +
255A GLN* 1.3 77.4 - - + +
257A VAL* 1.3 61.8 + - - +
259A GLN* 3.1 20.7 + - - +
260A SER* 2.8 17.7 + - - -
266A LEU* 3.5 21.1 - - + -
269A ARG* 3.7 27.4 - - + -
270A LEU* 4.0 23.3 - - + -
273A GLN* 4.0 22.2 - - + +
51B PHE* 4.4 14.8 - - + -
53B ASN* 5.7 4.3 - - + -
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Residues in contact with VAL 257 (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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253A LEU* 3.0 17.7 + - + +
254A LYS* 3.5 11.2 - - - +
256A ILE* 1.3 73.6 - - - +
258A ASP* 1.3 71.6 + - - +
260A SER* 2.9 27.6 + - - +
266A LEU* 3.8 24.9 - - + -
314A TYR* 3.6 50.7 - - + -
315A TYR* 5.2 7.1 + - + +
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Residues in contact with ASP 258 (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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254A LYS* 2.7 57.6 + - - +
255A GLN* 3.6 10.0 - - - +
256A ILE 3.3 0.4 - - - -
257A VAL* 1.3 77.8 - - - +
259A GLN* 1.3 62.1 + - + +
260A SER 3.7 2.1 + - - +
10B ALA* 5.7 3.1 + - - +
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Residues in contact with GLN 259 (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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255A GLN* 2.6 43.1 + - - +
256A ILE* 3.1 12.3 + - - +
257A VAL 3.1 1.0 - - - -
258A ASP* 1.3 78.8 - - + +
260A SER* 1.3 61.2 + - - +
269A ARG* 3.4 29.4 + - - +
10B ALA* 3.5 16.1 - - - +
11B GLU 3.5 7.6 - - - +
51B PHE* 3.5 16.0 - - - -
52B PRO* 3.1 45.4 + - + +
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Residues in contact with SER 260 (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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256A ILE 2.8 16.5 + - - -
257A VAL* 2.9 19.2 + - - +
258A ASP 4.7 1.9 - - - +
259A GLN* 1.3 78.9 - - - +
261A LEU* 1.3 62.4 + - - +
262A SER 3.6 3.3 + - - -
265A ASP* 3.4 5.4 - - - -
266A LEU* 3.2 43.3 - - - +
269A ARG* 3.2 8.2 - - - +
315A TYR* 4.6 7.0 + - - -
10B ALA 6.1 0.9 - - - -
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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