Contacts of the helix formed by residues 267 - 281 (chain B) in PDB entry 5JMO
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 ALA 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ASP* 3.5 28.5 + - + +
236B GLU* 5.1 0.6 + - - -
265B GLY 3.5 3.5 + - - +
266B PRO* 1.3 75.2 - - - +
268B ARG* 1.3 68.3 + - - +
269B LEU 3.4 1.3 - - - -
270B ALA* 3.3 2.6 + - - +
271B GLU* 2.9 21.4 + - - +
308B TYR* 4.7 1.0 + - - -
3H ARG* 5.6 0.4 - - - +
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Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 6.0 3.4 - - - +
233B ASP* 3.4 2.6 + - - +
267B ALA* 1.3 78.0 - - - +
269B LEU* 1.3 88.4 + - + +
271B GLU* 3.4 6.6 + - - +
272B GLU* 3.0 43.4 + - + +
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 6.2 3.1 - - + +
234A ALA* 4.7 14.8 - - + -
269A LEU* 5.8 2.5 - - + -
233B ASP* 2.7 27.8 + - + +
234B ALA* 3.8 30.5 - - + +
237B ALA* 3.4 21.1 - - + +
268B ARG* 1.3 106.8 - - + +
270B ALA* 1.3 56.1 + - - +
272B GLU* 3.3 22.6 + - - +
273B ALA* 2.9 22.5 + - - +
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ASP* 2.9 18.2 + - - +
236B GLU* 3.7 30.3 - - + +
237B ALA* 3.8 10.7 - - - +
240B LEU* 4.1 10.0 - - + +
266B PRO* 3.8 17.0 - - + -
267B ALA 3.3 0.6 + - - +
269B LEU* 1.3 73.2 - - - +
271B GLU* 1.3 60.6 + - - +
273B ALA* 3.1 2.9 + - - +
274B PHE* 2.9 33.3 + - - -
308B TYR* 5.0 0.2 - - + -
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Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PRO* 3.7 24.3 - - + +
267B ALA 2.9 18.8 + - - +
268B ARG* 3.7 7.0 - - - +
270B ALA* 1.3 76.4 - - - +
272B GLU* 1.3 63.6 + - - +
274B PHE* 3.3 10.6 + - - +
275B PHE* 3.1 24.1 + - + +
311B SER* 5.0 3.7 + - - -
313B TYR* 3.4 31.0 - - - -
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLU* 4.9 8.1 - - - +
268B ARG* 3.0 31.8 + - + +
269B LEU* 3.4 25.3 - - - +
271B GLU* 1.3 77.6 - - - +
273B ALA* 1.3 57.4 + - - +
275B PHE* 3.3 6.1 + - - +
276B ARG* 2.9 34.2 + - + +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLN* 5.6 3.8 - - - +
237B ALA* 3.6 31.6 - - + +
240B LEU* 4.0 15.1 - - + +
241B GLY* 4.3 8.3 - - - +
269B LEU 2.9 14.2 + - - +
270B ALA 3.1 8.0 + - - +
272B GLU* 1.3 74.6 - - - +
274B PHE* 1.3 65.7 + - - +
276B ARG* 3.8 8.2 - - - +
277B GLY* 2.9 21.3 + - - -
289B PHE* 4.4 3.1 - - - -
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Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 3.7 27.3 - - + +
266B PRO* 4.3 15.3 - - + -
270B ALA 2.9 21.4 + - - -
271B GLU* 3.5 14.6 - - - +
273B ALA* 1.3 76.8 - - - +
275B PHE* 1.3 61.2 + - - +
277B GLY* 3.1 3.1 + - - -
278B VAL* 3.1 23.6 + - - +
289B PHE* 3.6 38.1 - + - -
291B TRP* 3.6 23.8 - + - -
308B TYR* 4.1 19.1 - + - -
311B SER* 4.8 7.9 - - - -
313B TYR* 3.7 24.5 - + + -
314B THR* 3.6 24.7 - - + -
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Residues in contact with PHE 275 (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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271B GLU* 3.1 17.0 + - + +
272B GLU* 3.8 6.3 - - - +
273B ALA 3.3 0.2 - - - -
274B PHE* 1.3 73.4 - - - +
276B ARG* 1.3 60.9 + - - +
278B VAL* 3.4 9.6 + - + +
279B SER* 2.8 55.6 + - - -
313B TYR* 3.4 31.9 - + + +
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Residues in contact with ARG 276 (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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176A ASN 3.3 25.4 + - - -
177A ASP* 3.5 24.2 + - - +
178A GLN* 3.2 30.5 - - - +
241B GLY* 6.1 3.6 - - - -
244B PRO* 5.8 9.0 - - + +
272B GLU* 2.9 23.0 + - + +
273B ALA* 3.8 7.2 - - - +
275B PHE* 1.3 78.1 - - - +
277B GLY* 1.3 56.8 + - - +
279B SER* 3.4 7.2 - - - -
280B GLN* 2.7 70.4 + - + +
281B GLY 3.6 0.2 + - - -
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Residues in contact with GLY 277 (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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240B LEU 5.7 0.9 - - - -
241B GLY* 6.4 1.3 - - - -
244B PRO* 5.4 4.3 - - - -
273B ALA 2.9 15.8 + - - -
274B PHE 3.1 4.2 + - - -
276B ARG* 1.3 76.3 - - - +
278B VAL* 1.3 57.1 + - - +
281B GLY* 2.8 25.5 + - - -
287B SER* 2.9 35.1 + - - -
289B PHE* 4.2 4.7 - - - -
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B PHE 3.1 13.0 + - - +
275B PHE* 3.6 15.9 - - + +
277B GLY* 1.3 75.8 - - - +
279B SER* 1.3 62.4 + - - +
284B GLY 4.4 2.3 - - - +
285B LEU 4.3 1.2 - - - -
286B GLY* 3.3 21.5 + - - -
287B SER 4.0 12.1 - - - +
289B PHE* 4.3 4.9 - - + -
313B TYR* 3.7 44.0 - - + +
390B TRP* 3.5 51.8 + - + +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B PHE* 2.8 45.8 + - - -
276B ARG* 3.3 9.4 + - - -
278B VAL* 1.3 82.2 - - - +
280B GLN* 1.3 68.4 + - - +
284B GLY* 3.8 16.4 - - - +
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Residues in contact with GLN 280 (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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244B PRO* 5.4 4.4 - - + +
245B ASN* 3.7 7.6 + - - +
276B ARG* 2.7 59.5 + - + +
279B SER* 1.3 81.6 + - - +
281B GLY* 1.3 68.3 + - - +
283B GLY* 3.6 4.5 + - - -
284B GLY* 3.2 13.4 + - - -
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Residues in contact with GLY 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B PRO* 3.7 19.7 - - - +
276B ARG 3.6 1.6 + - - -
277B GLY* 2.8 24.2 + - - -
280B GLN* 1.3 73.7 - - - +
282B ARG* 1.3 64.4 + - - -
284B GLY 2.9 6.8 + - - -
286B GLY* 2.8 25.0 + - - -
287B SER* 3.7 10.1 - - - -
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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