Contacts of the helix formed by residues 317 - 323 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80U HIS* 2.7 52.6 + + + +
107U GLU* 4.7 3.1 - - - -
257U GLY 5.5 6.5 - - - -
259U ILE* 3.2 30.3 - - + -
280U PRO* 4.0 15.5 - - + -
281U VAL* 4.1 13.7 - - + -
313U GLY* 2.9 19.1 + - - +
314U THR 3.7 1.8 - - - -
316U HIS* 1.3 102.7 + + + +
318U GLY* 1.3 68.2 + - - +
319U ASP* 3.7 0.9 - - - -
320U LYS* 3.3 11.0 + - + +
321U LEU* 2.9 18.0 + - - +
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Residues in contact with GLY 318 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314U THR 3.0 17.2 + - - -
315U PHE 4.0 1.6 - - - -
316U HIS 2.5 15.2 + - - -
317U TYR* 1.3 67.2 - - - +
319U ASP* 1.3 54.5 + - - +
321U LEU* 2.3 34.3 + - - -
322U LEU* 3.0 7.9 + - - -
113V LEU* 3.8 22.4 - - - -
117V ILE* 4.0 7.4 - - - -
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Residues in contact with ASP 319 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229K ASN* 2.6 35.7 + - - +
232K LYS* 2.4 46.1 + - - +
315U PHE 5.2 0.2 + - - -
316U HIS 4.3 3.5 + - - +
317U TYR 3.7 0.4 - - - -
318U GLY* 1.3 71.9 - - - +
320U LYS* 1.3 63.5 + - - +
322U LEU* 3.1 13.4 + - - -
323U SER* 3.4 1.6 + - - -
108V LEU* 3.7 34.9 - - - +
113V LEU* 4.4 4.5 - - - +
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Residues in contact with LYS 320 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161K PRO* 6.1 1.0 - - - +
233K GLU* 3.7 23.7 + - + +
259U ILE* 3.7 46.5 + - + +
317U TYR* 3.3 15.6 + - + +
318U GLY 2.6 4.0 + - - -
319U ASP* 1.3 77.6 - - - +
321U LEU* 1.3 55.0 + - - +
323U SER* 2.9 6.7 + - - -
324U LEU* 2.8 39.6 - - + +
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Residues in contact with LEU 321 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259U ILE* 3.3 29.4 - - + -
264U ALA* 4.2 16.8 - - + -
267U ILE* 4.4 7.0 - - + -
280U PRO* 3.5 28.7 - - + -
314U THR* 3.9 21.3 - - + +
317U TYR 2.9 21.7 + - - +
318U GLY* 2.3 23.4 + - - +
320U LYS* 1.3 66.7 - - - +
322U LEU* 1.3 53.0 + - - +
324U LEU* 2.5 36.9 + - - +
325U LEU* 3.2 18.8 + - + +
117V ILE* 3.7 27.6 - - + -
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Residues in contact with LEU 322 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225K SER 5.6 1.3 - - - +
226K LYS* 6.1 1.0 - - - -
229K ASN* 3.3 15.9 - - + +
268U ARG* 4.8 2.2 - - - +
318U GLY 3.0 6.2 + - - +
319U ASP* 3.1 7.4 + - - +
321U LEU* 1.3 77.0 - - - +
323U SER* 1.3 59.8 + - - +
324U LEU 3.1 1.1 + - - -
325U LEU* 3.5 26.9 + - + +
108V LEU* 3.4 47.3 - - + -
113V LEU* 5.0 4.9 - - + -
116V LYS* 3.8 37.0 - - + +
117V ILE* 4.4 8.5 - - + +
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Residues in contact with SER 323 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155K PRO* 5.4 8.1 - - - +
161K PRO* 5.1 12.6 - - - +
229K ASN* 3.5 5.8 + - - -
230K LEU* 6.1 1.1 - - - -
233K GLU* 2.6 44.7 + - - -
319U ASP 3.4 1.4 + - - -
320U LYS 2.9 13.2 + - - -
321U LEU 2.9 0.2 + - - -
322U LEU* 1.3 78.6 - - - +
324U LEU* 1.3 66.0 + - - +
325U LEU 4.1 3.7 - - - +
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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