Contacts of the helix formed by residues 317 - 323 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79T VAL* 5.8 0.5 - - - +
80T HIS* 3.3 40.3 + + - -
107T GLU* 4.8 1.6 - - - -
257T GLY* 5.0 13.6 + - - -
259T ILE* 3.0 28.5 - - + -
280T PRO* 3.9 17.5 - - + -
281T VAL* 4.8 10.1 - - + -
313T GLY* 3.1 17.4 + - - +
314T THR 3.7 2.5 - - - -
315T PHE 3.0 0.4 - - - -
316T HIS* 1.3 114.0 - + + +
318T GLY* 1.3 68.2 + - - +
319T ASP* 3.4 2.7 - - - -
320T LYS* 3.5 12.1 + - + +
321T LEU* 3.3 20.1 + - - +
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Residues in contact with GLY 318 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113S LEU* 3.6 17.3 - - - -
117S ILE* 3.1 21.2 - - - +
314T THR 2.9 20.9 + - - -
315T PHE 3.0 6.1 + - - -
316T HIS 3.7 0.2 - - - -
317T TYR* 1.3 75.6 - - - +
319T ASP* 1.3 66.7 + - - +
321T LEU* 2.8 21.3 - - - +
322T LEU* 3.5 1.9 + - - +
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Residues in contact with ASP 319 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229Q ASN* 2.9 30.6 + - - +
232Q LYS* 2.4 34.2 + - - +
108S LEU* 3.4 41.7 - - - +
113S LEU* 4.1 3.6 - - - +
109T LYS* 5.0 7.4 + - - -
317T TYR 3.4 0.6 - - - -
318T GLY* 1.3 67.1 + - - +
320T LYS* 1.3 54.6 + - - +
321T LEU 2.5 4.1 + - - -
322T LEU* 2.3 38.1 + - - +
323T SER 3.4 1.0 + - - -
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Residues in contact with LYS 320 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161Q PRO* 6.1 2.6 - - - +
229Q ASN* 4.4 0.8 - - - +
233Q GLU* 4.4 14.9 + - + +
237Q LEU* 5.9 4.8 - - - +
259T ILE* 3.7 47.1 + - + +
317T TYR* 3.5 16.8 + - + +
318T GLY 3.5 0.2 - - - -
319T ASP* 1.3 77.1 - - + +
321T LEU* 1.3 55.4 + - - +
322T LEU 3.4 0.4 - - - -
323T SER* 3.9 11.0 + - - +
324T LEU* 2.9 43.5 - - + +
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Residues in contact with LEU 321 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117S ILE* 3.3 30.5 - - + -
259T ILE* 4.5 13.7 - - + -
264T ALA* 3.4 37.7 - - + +
267T ILE* 4.1 16.4 - - + -
280T PRO* 4.5 11.0 - - + -
314T THR* 3.9 24.2 - - + +
317T TYR 3.3 14.2 + - - +
318T GLY 2.8 11.1 + - - +
319T ASP 2.5 5.9 + - - -
320T LYS* 1.3 75.1 - - - +
322T LEU* 1.3 53.3 + - - -
324T LEU* 3.5 6.9 + - - +
325T LEU* 2.6 44.0 + - + +
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Residues in contact with LEU 322 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226Q LYS* 6.0 1.6 - - - -
229Q ASN* 3.7 8.5 - - + +
108S LEU* 3.7 41.7 - - + -
113S LEU* 4.5 2.7 - - + -
116S LYS* 4.2 12.6 - - + -
117S ILE* 3.0 49.4 - - + +
268T ARG* 5.4 0.9 - - - +
318T GLY 3.7 4.9 - - - +
319T ASP* 2.3 30.8 + - - +
321T LEU* 1.3 65.1 - - - +
323T SER* 1.3 57.4 + - - +
324T LEU 2.7 10.6 + - - -
325T LEU* 3.1 23.1 + - + +
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Residues in contact with SER 323 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155Q PRO* 5.1 10.7 - - - +
160Q SER* 5.9 0.2 - - - -
161Q PRO* 4.4 15.5 - - - +
226Q LYS* 6.5 0.4 - - - +
229Q ASN* 4.1 6.1 + - - +
230Q LEU* 5.5 1.3 - - - -
233Q GLU* 2.3 43.9 + - - -
319T ASP 3.4 1.8 + - - -
320T LYS* 3.5 7.1 + - - +
322T LEU* 1.3 77.2 - - - +
324T LEU* 1.3 74.9 - - - +
325T LEU 4.8 1.1 - - - +
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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