Contacts of the helix formed by residues 270 - 282 (chain T) in PDB entry 5JPQ
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 GLY 270 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266T THR* 3.0 25.5 + - - -
267T ALA 4.9 0.2 + - - -
268T LEU 3.7 0.6 - - - -
269T VAL* 1.3 79.6 - - - +
271T PRO* 1.3 67.5 - - - +
272T ALA 3.5 2.0 - - - -
273T LEU 4.6 0.2 - - - -
274T GLY* 3.2 18.0 + - - -
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Residues in contact with PRO 271 (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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251T ASN 5.1 1.1 - - - +
254T LEU* 4.3 5.6 - - + -
255T GLU* 3.7 38.1 - - + +
258T MET* 4.1 19.7 - - + +
266T THR* 4.5 5.8 - - - -
270T GLY* 1.3 69.3 - - - +
272T ALA* 1.3 55.2 + - - +
274T GLY* 3.1 2.9 + - - -
275T ALA* 2.8 36.6 + - - +
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Residues in contact with ALA 272 (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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144T VAL* 4.5 7.0 - - + +
254T LEU* 5.6 4.5 - - - +
270T GLY 3.5 0.4 - - - -
271T PRO* 1.3 76.8 - - - +
273T LEU* 1.3 59.1 + - - +
275T ALA* 3.2 9.0 + - - +
276T ARG* 2.8 29.6 + - - +
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Residues in contact with LEU 273 (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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269T VAL* 3.7 29.5 + - + +
270T GLY 4.1 1.0 + - - -
272T ALA* 1.3 79.2 - - - +
274T GLY* 1.3 62.1 + - - +
276T ARG* 3.2 10.1 + - - +
277T LEU* 3.0 22.7 + - - +
319T ILE 5.6 3.6 - - - +
322T GLN* 5.2 15.0 - - + -
323T TYR* 5.9 2.9 - - - +
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Residues in contact with GLY 274 (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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265T VAL* 5.2 16.7 - - - +
266T THR* 5.7 0.7 - - - -
269T VAL* 4.5 6.5 - - - +
270T GLY 3.2 13.4 + - - -
271T PRO 3.1 7.6 + - - -
273T LEU* 1.3 76.9 - - - +
275T ALA* 1.3 62.2 + - - +
277T LEU* 3.2 9.3 + - - +
278T LEU* 3.1 19.1 + - - +
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Residues in contact with ALA 275 (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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140T ALA* 3.9 21.5 - - + +
141T ILE* 4.9 2.6 - - - -
144T VAL* 3.6 23.1 - - + -
254T LEU* 5.9 5.4 - - + -
258T MET* 5.7 6.5 - - + +
271T PRO 2.8 16.4 + - - +
272T ALA* 3.4 9.0 - - - +
274T GLY* 1.3 71.4 - - - -
276T ARG* 1.3 51.8 + - - +
278T LEU* 2.9 12.4 + - - +
279T SER* 2.8 34.0 + - - -
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Residues in contact with ARG 276 (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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144T VAL* 4.5 6.7 - - + +
272T ALA 2.8 14.6 + - - +
273T LEU* 3.3 15.3 - - - +
274T GLY 3.1 0.2 - - - -
275T ALA* 1.3 75.9 - - - +
277T LEU* 1.3 61.4 + - - +
279T SER* 3.4 10.0 + - - -
280T ILE* 3.2 22.3 + - - +
319T ILE* 5.4 13.5 - - + +
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Residues in contact with LEU 277 (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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273T LEU 3.0 10.8 + - - +
274T GLY* 3.2 10.1 + - - +
276T ARG* 1.3 75.2 - - - +
278T LEU* 1.3 59.1 + - - +
280T ILE* 3.3 5.6 + - - +
281T ALA* 2.9 31.7 + - - +
287T LEU* 5.5 4.9 - - + -
319T ILE* 5.9 3.8 - - + +
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Residues in contact with LEU 278 (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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137T ASP* 5.6 8.3 - - + +
140T ALA* 6.0 2.7 - - + -
141T ILE* 5.1 9.4 - - + +
274T GLY 3.1 11.0 + - - +
275T ALA* 2.9 14.2 + - - +
277T LEU* 1.3 76.3 - - - +
279T SER* 1.3 51.8 + - - +
281T ALA* 3.2 4.4 + - - -
282T GLY* 2.6 40.6 + - - -
283T SER* 3.4 15.3 + - - +
284T LEU* 5.1 4.0 - - + +
287T LEU* 5.2 4.2 - - - +
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Residues in contact with SER 279 (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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141T ILE* 4.4 27.1 - - - +
144T VAL* 5.8 2.0 - - - -
145T ARG* 5.8 5.2 - - - -
275T ALA 2.8 11.5 + - - -
276T ARG* 3.4 14.4 - - - -
277T LEU 3.2 0.2 - - - -
278T LEU* 1.3 77.1 - - - +
280T ILE* 1.3 61.7 + - - +
282T GLY* 3.5 9.2 + - - -
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Residues in contact with ILE 280 (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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276T ARG 3.2 12.4 + - - +
277T LEU* 3.8 4.5 - - - +
279T SER* 1.3 78.1 - - - +
281T ALA* 1.3 64.4 + - - +
282T GLY* 3.4 0.7 + - - -
298T LEU* 4.5 20.9 - - + -
299T GLY* 4.9 7.4 - - - +
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Residues in contact with ALA 281 (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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277T LEU 2.9 16.9 + - - +
278T LEU 3.7 2.5 - - - +
280T ILE* 1.3 76.8 - - - +
282T GLY* 1.3 56.9 + - - +
283T SER 3.5 5.2 - - - +
286T GLU* 3.5 16.8 - - + +
287T LEU* 3.8 35.2 - - + +
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Residues in contact with GLY 282 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141T ILE* 5.5 5.9 - - - +
278T LEU 2.6 17.2 + - - -
279T SER* 3.5 8.9 + - - -
280T ILE 3.2 2.8 - - - -
281T ALA* 1.3 73.2 - - - +
283T SER* 1.3 60.4 + - - -
286T GLU* 5.0 0.4 - - - -
119X LEU* 5.8 1.9 - - - +
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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