Contacts of the helix formed by residues 287 - 301 (chain B) in PDB entry 2ABQ
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 287 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B ARG* 5.4 4.5 - - - -
49B LEU* 4.7 0.4 - - - -
285B PHE 4.3 6.3 - - - +
286B CYS* 1.3 77.2 - - - +
288B ARG* 1.3 64.9 + - - +
289B GLU* 3.0 21.4 + - - +
290B GLU* 2.8 51.4 + - - +
291B VAL* 3.1 15.3 - - - +
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Residues in contact with ARG 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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48B ARG 4.1 16.7 + - - +
49B LEU* 3.4 35.7 + - - +
51B HIS* 4.3 1.4 + - - -
261B GLU* 3.1 39.2 + - - -
263B LYS* 5.2 1.8 - - - +
271B PHE* 2.8 44.5 - - - -
287B THR* 1.3 71.6 - - - +
289B GLU* 1.3 76.8 + - - +
291B VAL* 3.0 18.4 + - - +
292B GLU* 3.1 46.4 + - - +
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Residues in contact with GLU 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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287B THR* 3.0 27.1 + - - +
288B ARG* 1.3 88.4 + - - +
290B GLU* 1.3 62.5 + - + +
292B GLU* 3.5 14.6 + - - +
293B ARG* 3.4 20.4 + - - +
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Residues in contact with GLU 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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278B ALA* 3.3 33.5 - - + +
281B PHE* 6.0 0.3 - - - +
282B SER* 3.4 13.4 + - - -
285B PHE 4.7 0.5 - - - +
286B CYS* 3.9 2.8 - - - -
287B THR* 2.8 54.3 + - - +
289B GLU* 1.3 76.0 - - + +
291B VAL* 1.3 66.9 + - - +
293B ARG* 3.3 17.1 + - - +
294B LEU* 3.3 24.3 + - + +
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Residues in contact with VAL 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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49B LEU* 4.0 19.3 - - + -
271B PHE* 3.4 29.2 - - + +
274B ALA* 3.3 31.7 - - + +
275B ALA* 3.3 24.7 - - + +
278B ALA* 4.6 0.9 - - + -
286B CYS* 4.3 8.1 - - + -
287B THR 3.1 20.0 - - - +
288B ARG* 3.0 6.0 + - - +
290B GLU* 1.3 74.5 - - - +
292B GLU* 1.3 55.2 + - - +
293B ARG 3.0 0.5 + - - -
294B LEU* 3.2 2.4 + - - -
295B GLN* 2.7 35.7 + - - +
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Residues in contact with GLU 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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271B PHE* 4.4 9.4 - - + -
288B ARG* 3.1 52.6 + - - +
289B GLU* 3.5 16.9 - - - +
291B VAL* 1.3 75.3 - - - +
293B ARG* 1.3 63.7 + - - +
295B GLN* 3.1 24.7 - - - +
296B GLN* 3.3 20.9 + - - +
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Residues in contact with ARG 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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281B PHE* 6.2 0.4 - - - -
289B GLU 3.4 10.7 + - - +
290B GLU* 3.3 18.1 + - - +
291B VAL 3.1 0.8 - - - -
292B GLU* 1.3 79.1 - - - +
294B LEU* 1.3 102.4 + - - +
296B GLN* 3.1 27.7 + - - +
297B GLN* 3.4 5.3 + - - +
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Residues in contact with LEU 294 (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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237B PRO* 4.0 30.7 - - + -
274B ALA* 4.4 8.3 - - + +
278B ALA* 4.3 22.9 - - + +
281B PHE* 4.1 18.6 - - + -
290B GLU* 3.3 10.3 + - + +
291B VAL 3.2 4.5 + - - +
293B ARG* 1.3 120.7 - - - +
295B GLN* 1.3 65.3 + - - +
297B GLN* 3.0 23.1 + - + +
298B LEU* 2.9 27.6 + - - +
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Residues in contact with GLN 295 (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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263B LYS* 4.1 13.7 - - - +
267B ASP 5.1 4.0 + - - -
270B PRO* 2.9 27.7 - - - +
271B PHE* 4.1 26.8 - - + +
274B ALA* 3.8 15.4 - - + +
291B VAL 2.7 19.6 + - - +
292B GLU* 3.1 17.3 - - - +
294B LEU* 1.3 77.4 - - - +
296B GLN* 1.3 60.6 + - + +
298B LEU* 3.2 3.4 + - - +
299B GLN* 2.7 40.2 + - - +
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Residues in contact with GLN 296 (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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292B GLU* 3.4 24.6 + - - +
293B ARG* 3.1 12.2 + - - +
295B GLN* 1.3 77.9 - - + +
297B GLN* 1.3 56.1 - - - +
299B GLN* 2.9 28.6 - - - +
300B ARG* 2.4 37.8 + - - +
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Residues in contact with GLN 297 (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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237B PRO* 3.3 43.2 + - - +
293B ARG* 3.4 4.5 + - - +
294B LEU* 3.0 25.3 + - + +
296B GLN* 1.3 78.2 - - - +
298B LEU* 1.3 62.5 + - + +
300B ARG* 2.8 37.0 - - - +
301B THR* 3.9 2.3 + - - +
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Residues in contact with LEU 298 (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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234B VAL* 3.9 11.9 - - + -
235B ASN 2.9 22.4 - - - +
236B VAL 4.0 0.2 - - - -
237B PRO* 3.5 36.1 - - + -
270B PRO* 4.3 10.1 - - + +
273B VAL* 3.4 39.3 - - + -
274B ALA* 4.1 9.9 - - - +
294B LEU 2.9 17.4 + - - +
295B GLN* 3.7 5.2 - - - +
297B GLN* 1.3 78.8 - - + +
299B GLN* 1.3 67.3 + - - +
301B THR* 2.8 32.8 + - + +
302B ILE* 4.0 3.2 - - - +
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Residues in contact with GLN 299 (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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270B PRO* 4.8 7.0 - - - -
295B GLN* 2.7 30.0 + - - +
296B GLN* 2.9 28.7 + - - +
298B LEU* 1.3 70.5 - - - +
300B ARG* 1.3 76.5 + - - +
302B ILE* 2.9 26.3 - - - +
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Residues in contact with ARG 300 (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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296B GLN* 2.4 35.5 + - - +
297B GLN* 2.8 27.6 - - - +
299B GLN* 1.3 106.7 + - - +
301B THR* 1.3 56.5 + - - +
302B ILE* 2.7 21.1 + - - +
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Residues in contact with THR 301 (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 HIS* 4.4 2.6 - - - -
234B VAL* 3.7 11.7 - - + +
235B ASN* 3.2 51.7 + - + +
297B GLN 4.4 2.2 - - - +
298B LEU* 2.8 39.2 + - + +
300B ARG* 1.3 78.6 - - - +
302B ILE* 1.3 67.6 + - - +
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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