Contacts of the helix formed by residues 277 - 292 (chain B) in PDB entry 5HQ0
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 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269B ALA* 4.6 0.9 - - - -
274B ASN 5.9 0.9 - - - +
276B TYR* 1.3 77.3 - - - +
278B LYS* 1.3 65.6 + - - +
279B HIS* 3.5 11.3 + - - +
280B GLN* 2.9 46.3 + - - +
281B ILE* 3.3 16.3 + - - +
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Residues in contact with LYS 278 (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* 5.7 6.6 - - + +
265B ILE* 3.5 46.4 - - + +
266B GLY* 4.3 10.7 - - - -
269B ALA* 4.3 11.8 - - + +
277B THR* 1.3 72.3 - - - +
279B HIS* 1.3 58.0 + - - +
281B ILE* 3.2 7.2 + - - -
282B ARG* 2.9 45.6 + - - +
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Residues in contact with HIS 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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277B THR* 3.1 10.2 + - - +
278B LYS* 1.3 81.0 - - - +
280B GLN* 1.3 61.4 + - - +
282B ARG* 3.3 29.1 + - - +
283B GLN* 3.0 61.7 + - + +
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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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242B MET* 4.5 14.6 - - - +
245B LEU* 3.8 22.0 - - + +
275B THR 4.1 3.2 + - - +
276B TYR* 3.1 24.6 - - - -
277B THR* 2.9 49.9 + - - +
279B HIS* 1.3 77.0 - - - +
281B ILE* 1.3 59.8 + - - +
283B GLN* 3.3 6.1 + - - +
284B MET* 2.9 30.0 + - - +
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Residues in contact with ILE 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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245B LEU* 3.5 19.5 - - + -
248B VAL* 4.4 7.9 - - + -
249B THR* 3.6 21.6 - - + +
252B PHE* 3.8 24.5 - - + -
265B ILE* 3.8 23.6 - - + +
268B PHE* 4.2 9.9 - - + +
269B ALA* 3.8 34.8 - - + +
272B THR* 5.9 0.7 - - + -
276B TYR* 5.1 3.8 - - + -
277B THR 3.7 12.6 - - - +
278B LYS* 3.2 6.2 + - - +
280B GLN* 1.3 72.4 - - - +
282B ARG* 1.3 57.3 + - - +
285B GLU* 2.8 35.4 + - - +
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Residues in contact with ARG 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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40A GLU 3.6 19.3 - - - -
41A GLU* 2.6 58.6 + - - +
43A GLY* 4.0 18.8 - - - +
252B PHE* 6.0 0.4 - - + -
265B ILE* 4.1 7.0 - - + +
278B LYS* 2.9 26.8 + - - +
279B HIS* 3.4 45.0 - - - +
281B ILE* 1.3 78.5 - - - +
283B GLN* 1.3 67.9 + - - +
285B GLU* 3.3 9.8 + - - +
286B MET* 3.3 23.8 + - - +
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Residues in contact with GLN 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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279B HIS* 3.0 51.8 + - + +
280B GLN* 3.9 5.4 - - - +
281B ILE 3.3 0.2 - - - -
282B ARG* 1.3 76.8 - - - +
284B MET* 1.3 66.2 + - - +
286B MET* 3.2 11.1 + - - +
287B LYS* 3.0 23.0 + - - +
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Residues in contact with MET 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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232B PHE* 4.7 2.0 - - - -
238B VAL* 6.0 0.2 - - + -
242B MET* 4.7 13.2 - - + -
245B LEU* 4.1 21.8 - - + +
246B VAL* 3.6 33.9 - - + -
249B THR* 3.6 22.9 - - - +
280B GLN 2.9 18.1 + - - +
283B GLN* 1.3 73.7 - - - +
285B GLU* 1.3 66.9 + - - +
287B LYS* 3.3 28.3 + - + +
288B ILE* 2.9 44.3 + - + +
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Residues in contact with GLU 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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43A GLY* 3.4 8.8 - - - -
44A VAL* 2.8 36.6 + - + +
49A ILE* 4.1 5.2 - - - +
249B THR* 3.3 13.4 - - + +
252B PHE* 3.9 9.9 - - + -
253B ILE* 3.8 18.9 - - + +
256B LYS* 2.7 32.5 + - - -
281B ILE 2.8 22.4 + - - +
282B ARG* 3.4 8.8 - - - +
284B MET* 1.3 73.4 - - - +
286B MET* 1.3 57.3 + - - +
288B ILE* 3.2 1.9 + - - +
289B LEU* 2.9 41.7 + - + +
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Residues in contact with MET 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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44A VAL* 3.9 13.2 - - + -
71A MET* 3.5 44.2 - - + +
282B ARG 3.3 11.8 + - - +
283B GLN* 3.2 13.1 + - - +
285B GLU* 1.3 75.3 - - + +
287B LYS* 1.3 64.3 + - - +
289B LEU* 4.7 1.6 - - + -
290B ARG* 3.0 69.5 + - - +
294B PHE* 4.0 17.7 - - + -
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Residues in contact with LYS 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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232B PHE* 4.1 25.0 - - + -
236B ASN* 4.6 14.3 - - - +
237B SER 5.3 6.3 + - - -
238B VAL* 6.4 0.9 - - - -
283B GLN 3.0 12.7 + - - +
284B MET* 3.5 27.6 - - + +
286B MET* 1.3 75.1 - - - +
288B ILE* 1.3 57.7 + - - +
290B ARG* 3.6 7.5 + - - +
291B ALA* 3.1 28.0 + - + +
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Residues in contact with ILE 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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228B ILE* 3.7 27.6 - - + -
232B PHE* 4.0 28.9 - - + -
246B VAL* 4.2 22.9 - - + +
249B THR* 4.0 12.8 - - + -
250B ALA* 4.6 4.3 - - + +
253B ILE* 3.8 13.9 - - + -
284B MET* 2.9 40.3 + - + +
285B GLU 3.6 3.1 - - - +
287B LYS* 1.3 73.8 - - - +
289B LEU* 1.3 68.5 + - + +
291B ALA* 3.4 0.5 + - - +
292B LEU* 3.1 33.3 + - + +
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Residues in contact with LEU 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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44A VAL* 4.0 18.8 - - + -
49A ILE* 4.5 13.7 - - + -
253B ILE* 4.0 28.9 - - + -
285B GLU* 2.9 38.6 + - + +
286B MET* 4.1 3.8 - - - +
288B ILE* 1.3 77.0 - - + +
290B ARG* 1.3 56.6 + - - +
292B LEU* 3.4 2.4 + - - -
293B ASN 3.0 7.8 + - - -
294B PHE* 2.8 69.2 + - + +
296B LEU* 4.1 22.0 - - + -
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Residues in contact with ARG 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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-2A LEU* 5.5 18.0 - - + +
71A MET* 3.5 27.3 + - - +
72A GLN* 5.9 0.6 - - - +
286B MET* 3.0 55.5 + - + +
287B LYS* 3.8 5.6 - - - +
289B LEU* 1.3 74.0 - - - +
291B ALA* 1.3 60.2 + - - +
293B ASN* 3.0 25.6 + - - +
294B PHE* 4.5 12.7 - - + -
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Residues in contact with ALA 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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232B PHE* 3.6 31.9 - - + -
236B ASN* 3.7 17.2 - - - +
287B LYS* 3.1 16.2 + - + +
288B ILE 3.7 0.9 - - - +
290B ARG* 1.3 79.4 - - - +
292B LEU* 1.3 60.8 + - + +
293B ASN* 3.3 7.8 + - - -
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Residues in contact with LEU 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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228B ILE* 4.0 25.6 - - + -
231B ARG* 4.3 25.6 - - + +
232B PHE* 3.7 36.8 - - + +
288B ILE* 3.1 23.9 + - + +
289B LEU* 4.1 3.8 - - - +
291B ALA* 1.3 78.2 - - + +
293B ASN* 1.3 70.3 + - - +
294B PHE 4.5 0.2 - - - +
295B GLY* 3.1 23.2 + - - +
296B LEU* 3.9 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