Contacts of the helix formed by residues 278 - 293 (chain B) in PDB entry 5LQF
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 THR 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B ALA* 4.7 3.8 - - - -
277B TYR* 1.3 75.3 - - - +
279B LYS* 1.3 65.3 + - - +
280B HIS* 4.0 10.9 - - + +
281B GLN* 2.6 41.4 + - - +
282B ILE* 3.0 23.1 + - - +
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Residues in contact with LYS 279 (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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41A GLU* 3.1 34.0 + - - +
266B ILE* 3.6 19.9 - - + +
267B GLY* 4.0 19.3 - - - +
270B ALA* 4.1 19.1 - - + +
278B THR* 1.3 70.4 - - - +
280B HIS* 1.3 60.6 + - - +
282B ILE* 3.1 12.1 + - - +
283B ARG* 2.9 47.1 + - - +
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Residues in contact with HIS 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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278B THR* 3.2 9.1 - - + +
279B LYS* 1.3 76.8 - - - +
281B GLN* 1.3 63.0 + - - +
283B ARG* 3.2 30.6 + - + +
284B GLN* 2.9 63.2 + - + +
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Residues in contact with GLN 281 (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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243B MET* 5.5 9.1 - - - +
246B LEU* 3.8 21.6 - - + +
276B THR 4.4 2.0 + - - +
277B TYR* 3.2 22.7 - - - -
278B THR* 2.6 42.4 + - - +
280B HIS* 1.3 82.9 - - + +
282B ILE* 1.3 55.6 + - - +
284B GLN* 3.4 9.7 + - + +
285B MET* 3.0 30.0 + - - +
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Residues in contact with ILE 282 (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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246B LEU* 3.8 16.2 - - + -
249B VAL* 4.2 9.9 - - + -
250B THR* 3.5 25.0 - - + +
253B PHE* 3.8 30.3 - - + -
266B ILE* 3.9 13.0 - - + +
269B PHE* 3.9 13.7 - - + -
270B ALA* 3.6 36.1 - - + +
273B THR* 5.7 0.4 - - + -
277B TYR* 4.9 4.3 - - + -
278B THR 3.0 17.1 + - - +
279B LYS* 3.1 8.4 + - - +
281B GLN* 1.3 75.1 - - - +
283B ARG* 1.3 51.4 + - - +
285B MET 3.2 1.4 + - - -
286B GLU* 2.8 31.9 + - - +
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Residues in contact with ARG 283 (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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40A GLU 3.6 8.5 + - - -
41A GLU* 2.6 63.4 + - - -
43A GLY* 3.5 21.1 - - - +
266B ILE* 3.2 21.2 - - + +
279B LYS* 2.9 27.9 + - - +
280B HIS* 3.2 34.7 + - + +
282B ILE* 1.3 71.7 - - - +
284B GLN* 1.3 66.4 + - - +
286B GLU* 3.4 10.6 + - - +
287B MET* 3.2 27.2 + - - +
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Residues in contact with GLN 284 (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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280B HIS* 2.9 49.5 + - + +
281B GLN* 3.6 10.5 - - - +
283B ARG* 1.3 73.6 - - - +
285B MET* 1.3 61.6 + - - +
287B MET* 3.3 8.6 + - - +
288B LYS* 2.9 28.2 + - - +
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Residues in contact with MET 285 (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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233B PHE* 4.5 3.1 - - - -
243B MET* 4.9 12.1 - - + -
246B LEU* 3.6 26.7 - - + -
247B VAL* 3.8 28.5 - - + -
250B THR* 3.7 20.9 - - - +
281B GLN 3.0 17.0 + - - +
282B ILE 3.7 0.2 - - - +
284B GLN* 1.3 75.6 - - - +
286B GLU* 1.3 60.4 + - - +
288B LYS* 3.2 34.2 + - - +
289B ILE* 2.8 49.3 + - + +
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Residues in contact with GLU 286 (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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43A GLY* 3.4 7.8 - - - -
44A VAL* 2.7 38.7 + - + +
49A ILE* 4.1 2.8 - - - +
250B THR* 3.3 13.8 - - + +
253B PHE* 3.9 9.3 - - + -
254B ILE* 3.7 19.4 - - + +
257B LYS* 2.4 34.7 + - - -
282B ILE 2.8 14.1 + - - +
283B ARG* 3.6 11.4 - - - +
284B GLN 3.2 0.2 - - - -
285B MET* 1.3 75.4 - - - +
287B MET* 1.3 53.1 + - - +
289B ILE* 3.2 2.6 + - - +
290B LEU* 2.7 55.2 + - + +
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Residues in contact with MET 287 (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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44A VAL* 3.9 11.9 - - + -
71A MET* 3.3 55.9 - - + +
283B ARG 3.2 12.6 + - - +
284B GLN* 3.5 11.2 - - - +
286B GLU* 1.3 82.1 - - + +
288B LYS* 1.3 55.9 + - - +
290B LEU* 4.1 3.1 - - - +
291B ARG* 3.0 83.9 + - + +
295B PHE* 5.1 3.4 - - + -
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Residues in contact with LYS 288 (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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233B PHE* 4.1 26.8 - - + -
237B ASN* 5.3 5.2 - - - +
238B SER 4.6 12.5 + - - -
239B VAL* 5.9 0.8 - - - +
284B GLN 2.9 15.7 + - - +
285B MET* 3.6 28.6 - - - +
287B MET* 1.3 77.2 - - - +
289B ILE* 1.3 56.5 + - - +
291B ARG* 3.9 6.6 - - - +
292B ALA* 3.0 29.6 + - - +
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Residues in contact with ILE 289 (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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229B ILE* 3.7 28.9 - - + -
233B PHE* 3.8 34.3 - - + -
247B VAL* 3.9 26.7 - - + +
250B THR* 4.2 9.6 - - + -
251B ALA 4.5 4.5 - - - +
254B ILE* 3.9 12.6 - - + -
285B MET* 2.8 41.5 + - + +
286B GLU 3.8 2.5 - - - +
288B LYS* 1.3 70.8 - - - +
290B LEU* 1.3 68.2 + - + +
292B ALA* 3.3 1.4 + - - +
293B LEU* 3.0 32.6 + - + +
297B LEU* 5.8 0.2 - - + -
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Residues in contact with LEU 290 (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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44A VAL* 3.6 27.6 - - + -
49A ILE* 4.4 11.4 - - + -
254B ILE* 4.1 28.3 - - + -
286B GLU* 2.7 43.8 + - + +
287B MET* 4.1 4.5 - - - +
289B ILE* 1.3 73.7 - - - +
291B ARG* 1.3 60.9 + - - +
293B LEU* 3.4 1.4 + - - -
294B ASN 3.2 2.8 + - - -
295B PHE* 2.8 67.7 + - + +
297B LEU* 4.4 18.8 - - + -
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Residues in contact with ARG 291 (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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-2A LEU* 4.0 34.2 - - + +
-1A GLY 5.7 2.8 + - - -
71A MET* 3.6 26.9 + - - +
72A GLN* 5.4 2.6 - - - +
287B MET* 3.0 59.0 + - + +
288B LYS* 3.9 5.2 - - - +
290B LEU* 1.3 75.2 - - - +
292B ALA* 1.4 53.6 + - - +
294B ASN* 2.7 27.7 + - - +
295B PHE* 4.5 4.0 - - + -
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Residues in contact with ALA 292 (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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233B PHE* 3.6 20.2 - - + -
236B ASN* 6.0 1.2 - - - +
237B ASN* 3.5 30.2 - - - +
288B LYS 3.0 19.9 + - - +
289B ILE 3.3 0.9 + - - +
291B ARG* 1.4 75.3 - - - +
293B LEU* 1.3 62.4 + - + +
294B ASN* 3.3 1.8 + - - +
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Residues in contact with LEU 293 (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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56A LYS* 4.4 1.4 - - - -
229B ILE* 4.2 18.8 - - + +
232B ARG* 4.2 20.0 - - + +
233B PHE* 3.8 33.7 - - + +
237B ASN* 5.5 0.2 - - - +
289B ILE* 3.0 31.9 + - + +
290B LEU* 4.0 2.9 - - - +
292B ALA* 1.3 81.7 - - + +
294B ASN* 1.3 68.6 + - - +
295B PHE 4.3 2.5 - - - +
296B GLY* 3.0 25.8 + - - +
297B LEU* 3.8 25.4 - - + -
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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