Contacts of the helix formed by residues 317 - 324 (chain B) in PDB entry 1J0B
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 TYR 317 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B VAL* 5.3 1.9 - - - +
80B HIS* 3.0 41.4 + + + -
107B GLU* 3.9 7.2 - - - -
257B GLY* 5.6 5.8 - - - -
259B ILE* 3.3 33.7 - - + -
280B PRO* 4.4 8.5 - - + -
281B VAL* 5.3 10.3 - - + -
313B GLY* 2.8 23.3 + - - +
316B HIS* 1.3 108.9 + + + +
318B GLY* 1.3 59.7 + - - +
319B ASP* 3.3 3.4 - - - +
320B LYS* 3.9 6.1 + - + +
321B LEU* 3.1 29.1 + - - +
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Residues in contact with GLY 318 (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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113A LEU* 3.4 22.1 - - - +
117A ILE* 3.8 7.0 - - - +
314B THR 3.4 19.2 + - - -
315B PHE 3.4 3.8 + - - -
316B HIS 3.4 4.9 + - - -
317B TYR* 1.3 77.0 - - - +
319B ASP* 1.3 60.3 + - - +
320B LYS 3.5 0.2 - - - -
321B LEU* 3.7 4.0 - - - +
322B LEU* 3.1 30.1 + - - +
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Residues in contact with ASP 319 (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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108A LEU* 3.5 33.7 - - - +
113A LEU* 4.8 2.1 - - - +
109B LYS* 3.9 19.6 + - - +
316B HIS 5.0 0.4 + - - +
317B TYR* 3.3 1.7 - - - +
318B GLY* 1.3 75.6 - - - +
320B LYS* 1.3 68.7 + - - +
322B LEU* 3.3 7.8 + - - +
323B SER* 3.2 18.2 + - - -
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Residues in contact with LYS 320 (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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259B ILE* 3.6 42.2 - - + -
317B TYR* 3.9 10.2 + - + +
318B GLY 3.5 0.2 - - - -
319B ASP* 1.3 74.4 - - - +
321B LEU* 1.3 68.9 + - - +
322B LEU 2.7 1.9 + - - -
323B SER* 2.6 28.3 + - - +
324B LEU* 3.0 35.3 - - + +
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Residues in contact with LEU 321 (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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117A ILE* 4.5 19.1 - - + -
259B ILE* 3.4 24.9 - - + -
264B ALA* 3.8 21.8 - - + +
267B ILE* 3.9 16.4 - - + -
280B PRO* 3.6 31.6 - - + -
314B THR* 4.3 11.7 - - + +
317B TYR 3.1 23.8 + - - +
318B GLY* 3.7 10.8 - - - +
320B LYS* 1.3 78.7 - - - +
322B LEU* 1.3 60.3 + - - +
324B LEU* 3.4 6.5 + - - +
325B LEU* 2.8 32.2 - - + +
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Residues in contact with LEU 322 (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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108A LEU* 3.3 37.7 - - + -
113A LEU* 3.6 15.5 - - + -
116A LYS* 3.7 17.3 - - + +
117A ILE* 3.4 41.7 - - + +
268B ARG* 5.4 0.9 - - - +
318B GLY 3.1 16.1 + - - +
319B ASP* 3.5 8.7 - - - +
320B LYS 2.7 4.6 + - - -
321B LEU* 1.3 70.3 - - - +
323B SER* 1.3 53.4 + - - +
324B LEU 2.6 16.7 + - - -
325B LEU* 2.7 23.8 + - + +
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Residues in contact with SER 323 (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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319B ASP 3.2 6.0 + - - -
320B LYS* 2.6 41.2 + - - +
322B LEU* 1.3 73.1 - - - +
324B LEU* 1.3 63.6 + - - +
325B LEU 4.8 1.9 - - - +
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Residues in contact with LEU 324 (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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259B ILE* 3.3 21.1 - - + +
260B THR* 3.2 37.0 - - - +
261B GLY* 3.2 12.5 - - - +
264B ALA* 3.9 7.9 - - + -
265B GLN* 4.7 5.4 - - - +
320B LYS* 3.0 53.6 - - + +
321B LEU* 3.6 8.5 - - - +
322B LEU 2.6 6.5 + - - -
323B SER* 1.3 81.7 - - - +
325B LEU* 1.3 66.1 + - + +
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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