Contacts of the helix formed by residues 287 - 304 (chain B) in PDB entry 1LFD
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B ASN* 1.3 73.0 + - - +
288B LYS* 1.3 63.6 + - - +
290B PHE* 3.1 7.7 + - + +
291B GLU* 3.0 39.7 + - + +
324B THR* 3.2 31.6 + - - +
325B VAL* 3.8 12.1 - - + -
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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
----------------------------------------------------------
286B ASN* 3.2 10.8 + - - +
287B THR* 1.3 79.3 - - - +
289B SER* 1.3 57.5 + - - +
291B GLU* 3.1 26.0 + - - +
292B ASP* 2.8 56.9 + - - +
56C ASP* 4.6 27.1 + - - +
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ALA* 4.0 8.4 + - - +
214B VAL* 3.4 22.4 - - - -
281B VAL 5.0 0.5 - - - +
282B PHE* 3.6 10.3 - - - +
283B ALA 3.2 19.9 + - - -
286B ASN* 2.7 42.7 + - - +
288B LYS* 1.3 79.1 - - - +
290B PHE* 1.3 62.1 + - - +
292B ASP* 3.6 11.6 - - - +
293B ILE* 3.1 20.3 + - - +
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Residues in contact with PHE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 3.5 41.7 - + + -
286B ASN 3.3 0.4 + - - -
287B THR* 3.1 14.0 + - + +
289B SER* 1.3 80.3 + - - +
291B GLU* 1.3 62.9 + - + +
293B ILE* 3.1 13.7 - - + +
294B HIS* 3.0 33.4 + + - -
313B LEU* 4.8 0.2 - - + -
325B VAL* 3.8 22.7 - - + -
329B GLN* 3.7 48.7 - - + -
330B ALA* 3.8 19.3 - - + -
333B LEU* 3.8 24.0 - - + -
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B THR* 3.0 31.9 + - + +
288B LYS* 3.1 29.8 + - - +
290B PHE* 1.3 81.7 - - + +
292B ASP* 1.3 64.4 + - - +
294B HIS* 3.3 29.6 + - + +
295B GLN* 4.3 5.8 + - - +
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Residues in contact with ASP 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ALA* 3.4 26.8 - - + +
288B LYS* 2.8 52.5 + - - +
289B SER* 3.6 6.7 - - - +
290B PHE 3.3 0.2 - - - -
291B GLU* 1.3 71.7 - - - +
293B ILE* 1.3 57.7 + - - +
294B HIS 3.0 5.2 - - - -
295B GLN* 2.8 37.9 + - + +
296B TYR* 3.4 17.0 + - + -
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Residues in contact with ILE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL 4.4 0.2 - - - +
210B GLY* 4.2 13.2 - - - -
211B ALA 5.4 0.2 - - - +
280B CYS* 3.7 36.1 - - + +
281B VAL 3.4 27.1 - - - +
282B PHE* 4.6 3.4 - - + -
289B SER 3.1 11.4 + - - +
290B PHE* 3.1 25.8 - - + +
291B GLU 3.2 0.6 - - - -
292B ASP* 1.3 75.7 - - + +
294B HIS* 1.3 66.0 + - - +
296B TYR* 3.5 11.5 + - + +
297B ARG* 3.3 21.8 + - - +
313B LEU* 3.9 25.1 - - + -
333B LEU* 3.9 11.7 - - + -
337B TYR* 4.6 2.6 + - + -
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Residues in contact with HIS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B PHE* 3.0 35.4 + + - -
291B GLU* 3.3 19.2 + - - +
292B ASP 2.9 0.6 + - - -
293B ILE* 1.3 79.8 - - - +
295B GLN* 1.3 70.8 + - - +
297B ARG* 3.3 4.2 + - - +
298B GLU* 3.1 27.8 + - - +
333B LEU* 3.6 31.2 - - + +
337B TYR* 3.4 20.8 + - - +
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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
----------------------------------------------------------
291B GLU 4.3 2.9 - - - +
292B ASP* 2.8 27.7 + - + +
294B HIS* 1.3 83.8 - - - +
296B TYR* 1.3 60.5 + - + +
298B GLU* 3.1 27.7 + - - +
299B GLN* 3.0 33.7 + - - +
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Residues in contact with TYR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 3.8 33.4 - - + -
210B GLY* 3.4 41.2 + - - -
211B ALA* 3.8 4.7 - - - -
258B THR* 5.7 0.4 - - - -
259B ALA 4.0 7.2 + - - -
260B GLY 4.0 8.3 + - - -
268B ARG* 3.5 35.0 + - - -
271B TYR* 4.1 13.9 - - - -
272B MET* 4.1 14.1 - - + -
280B CYS* 5.0 1.6 - - - -
292B ASP* 3.4 21.5 + - + -
293B ILE* 3.9 18.2 - - + +
294B HIS 3.3 0.8 - - - -
295B GLN* 1.3 78.9 - - + +
297B ARG* 1.3 59.0 + - - +
299B GLN* 3.2 8.3 + - - +
300B ILE* 2.9 37.2 + - + +
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Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B CYS* 5.2 3.3 - - - -
293B ILE 3.3 10.7 + - - +
294B HIS 3.5 9.4 - - - +
295B GLN 3.3 0.2 - - - -
296B TYR* 1.3 79.0 - - - +
298B GLU* 1.3 63.7 + - - +
300B ILE* 3.4 3.1 + - - +
301B LYS* 3.1 66.1 + - - +
307B ASP 5.9 0.4 + - - -
311B MET* 3.6 39.0 - - - +
336B SER 5.4 1.4 + - - -
337B TYR* 3.3 73.5 + - + +
339B ILE* 5.5 0.9 - - + +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B HIS* 3.1 10.6 + - - +
295B GLN* 3.1 46.2 + - - +
297B ARG* 1.3 81.2 - - - +
299B GLN* 1.3 58.6 + - + +
301B LYS* 3.5 17.4 + - - +
302B ARG* 3.0 49.5 + - - +
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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
----------------------------------------------------------
265B SER 4.9 0.7 - - - +
268B ARG* 3.4 49.2 + - - +
269B ASP* 4.2 9.3 - - - +
272B MET* 3.6 22.9 - - + +
295B GLN* 3.0 21.6 + - - +
296B TYR* 3.6 9.1 - - - +
298B GLU* 1.3 75.7 - - - +
300B ILE* 1.3 59.1 + - - +
302B ARG* 3.2 23.7 + - - +
303B VAL* 2.9 42.0 + - + +
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Residues in contact with ILE 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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209B VAL* 4.4 7.9 - - + -
272B MET* 3.7 28.9 - - + -
278B PHE* 3.6 55.0 - - + -
280B CYS* 4.3 12.8 - - - -
296B TYR 2.9 26.4 + - - +
297B ARG 3.7 4.9 - - - +
299B GLN* 1.3 76.3 - - - +
301B LYS* 1.3 57.2 + - - +
303B VAL* 4.1 0.2 - - - +
304B LYS* 3.0 34.8 + - + +
309B VAL* 3.8 18.2 - - + -
311B MET* 4.4 11.0 - - + -
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Residues in contact with LYS 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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297B ARG* 3.1 60.1 + - - +
298B GLU* 3.8 16.8 - - - +
300B ILE* 1.3 76.7 - - - +
302B ARG* 1.3 54.2 + - - +
305B ASP* 2.7 34.2 + - - +
306B SER 3.3 23.1 + - - +
307B ASP* 4.8 19.3 + - - +
309B VAL* 4.6 6.1 - - + +
311B MET* 4.4 9.2 - - + -
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Residues in contact with ARG 302 (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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298B GLU* 3.0 39.2 + - - +
299B GLN* 3.2 31.1 + - - +
301B LYS* 1.3 79.6 - - - +
303B VAL* 1.3 68.5 + - - +
305B ASP* 3.4 11.1 + - - +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ASP* 3.5 49.1 - - - +
272B MET* 3.9 24.9 - - + -
273B ARG* 3.5 31.7 + - + +
299B GLN* 2.9 29.4 + - + +
300B ILE 4.1 2.0 - - - +
302B ARG* 1.3 79.4 - - + +
304B LYS* 1.3 60.6 + - - +
305B ASP* 3.6 2.3 + - - +
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B MET 2.7 30.4 + - - +
273B ARG* 2.8 22.6 + - - +
275B GLY 2.7 26.3 + - - -
276B GLU* 5.3 3.4 - - - +
278B PHE* 3.9 6.5 - - + -
300B ILE* 3.0 17.4 + - + +
303B VAL* 1.3 73.7 - - + +
305B ASP* 1.3 72.3 + - - +
306B SER* 4.3 7.1 - - - +
309B VAL* 3.7 39.0 - - + -
310B PRO* 6.1 0.2 - - - -
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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
------------------------------------------------------------
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