Contacts of the helix formed by residues 290 - 300 (chain B) in PDB entry 4LQL
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 GLY 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B GLN* 5.4 0.6 - - - +
287B GLN* 5.4 2.8 - - - +
288B LEU 3.1 2.6 + - - -
289B PRO* 1.3 74.1 - - - +
291B LEU* 1.3 54.6 + - - +
292B ALA* 3.0 3.0 - - - +
293B VAL* 2.6 26.7 + - - +
294B GLN* 2.7 24.1 + - - +
350B LEU* 3.6 29.8 - - - -
351B GLU* 4.7 1.3 - - - -
377B ALA 4.1 2.9 + - - -
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Residues in contact with LEU 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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233B LEU* 6.2 5.6 - - + -
237B TYR* 5.7 7.6 - - + -
253B VAL* 4.7 15.7 - - + +
256B GLN* 4.3 12.9 - - + +
257B LEU* 5.7 2.9 - - + +
290B GLY* 1.3 70.5 - - - +
292B ALA* 1.3 53.9 + - - +
294B GLN* 3.0 11.4 + - + +
295B LEU* 2.6 48.4 + - + +
362B ARG* 5.0 12.1 - - + -
377B ALA* 3.0 41.4 + - + +
378B ARG* 3.9 1.9 - - - +
379B LEU* 3.8 37.0 - - + +
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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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256B GLN* 3.1 28.2 + - + +
259B GLU* 3.4 14.4 - - + -
260B TYR* 3.2 27.5 - - - +
263B ILE* 6.0 2.0 - - + -
289B PRO* 4.7 10.1 - - + -
290B GLY 4.1 0.6 - - - +
291B LEU* 1.3 77.7 - - - +
293B VAL* 1.3 63.1 + - + +
295B LEU* 3.8 2.5 - - - +
296B LEU* 3.3 30.4 + - + +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B PHE* 3.9 25.6 - - + -
277B ASP* 4.9 2.5 - - - -
289B PRO* 4.0 24.5 - - + +
290B GLY 2.6 17.0 + - - +
292B ALA* 1.3 76.8 - - - +
294B GLN* 1.3 59.3 + - - -
296B LEU* 3.7 6.9 + - + +
297B MET* 3.3 28.3 + - + +
303B PHE* 3.5 43.0 - - + +
351B GLU* 3.5 23.1 - - + -
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Residues in contact with GLN 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLY 2.7 11.3 + - - +
291B LEU* 3.4 13.2 - - + +
293B VAL* 1.3 74.2 - - - +
295B LEU* 1.3 69.3 + - - +
297B MET* 3.6 8.8 + - + +
298B ILE 3.7 2.6 + - - -
350B LEU 3.2 12.9 + - - -
351B GLU* 4.1 2.9 - - - -
352B VAL* 2.8 55.6 + - - +
354B PRO* 3.3 27.2 - - + +
378B ARG* 3.6 7.1 - - - +
379B LEU* 2.6 50.1 + - + +
381B PHE* 3.9 5.5 - - - -
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Residues in contact with LEU 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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233B LEU* 5.4 13.0 - - + -
237B TYR* 5.6 7.6 - - + +
256B GLN 5.9 0.2 - - - +
260B TYR* 3.9 21.5 - - + -
291B LEU* 2.6 38.1 + - + +
292B ALA 3.8 5.8 - - - +
293B VAL 3.3 0.2 - - - -
294B GLN* 1.3 70.9 - - - +
296B LEU* 1.3 53.2 + - - +
297B MET 2.6 0.4 + - - -
298B ILE* 2.4 43.7 + - - +
299B ASP* 3.2 5.6 + - - -
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Residues in contact with LEU 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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260B TYR* 4.5 14.4 - - + +
263B ILE* 4.1 19.3 - - + -
264B LYS* 3.9 26.7 - - + +
267B LEU* 4.5 2.0 - - + -
275B PHE* 3.6 32.1 - - + -
292B ALA* 3.3 19.8 + - + +
293B VAL* 4.0 4.0 - - + +
295B LEU* 1.3 74.9 - - - +
297B MET* 1.3 55.5 + - - +
298B ILE 3.1 0.4 - - - -
299B ASP* 3.2 12.8 - - + +
300B GLY 2.8 23.0 + - - -
301B TYR* 3.0 54.8 + - + -
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Residues in contact with MET 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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293B VAL* 3.3 28.6 + - + +
294B GLN* 3.6 14.1 - - + +
295B LEU 2.6 3.8 + - - -
296B LEU* 1.3 74.6 - - - +
298B ILE* 1.3 59.3 + - - +
300B GLY* 3.0 19.6 + - - -
301B TYR 4.3 12.8 - - - +
303B PHE* 4.7 18.8 - - + +
319B LYS* 3.8 17.6 + - - +
329B LEU* 5.2 13.7 - - - -
351B GLU* 3.5 27.4 - - + +
352B VAL 3.5 2.7 - - - -
353B ASP* 3.3 53.3 - - - +
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Residues in contact with ILE 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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237B TYR* 5.8 4.0 - - - +
294B GLN 3.7 6.7 + - - +
295B LEU* 2.4 25.3 + - - +
297B MET* 1.3 75.5 - - - +
299B ASP* 1.3 58.2 + - - +
300B GLY* 3.5 0.9 + - - -
353B ASP* 4.9 3.4 - - - -
354B PRO* 3.7 33.9 - - + +
355B THR* 5.5 3.6 - - - -
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Residues in contact with ASP 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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260B TYR* 5.9 4.7 - - - -
264B LYS* 5.5 9.2 - - - -
295B LEU* 3.2 4.8 + - - -
296B LEU* 3.2 27.1 - - - +
298B ILE* 1.3 79.4 - - - +
300B GLY* 1.3 53.4 + - - -
301B TYR* 4.0 17.3 - - + -
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Residues in contact with GLY 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU 2.8 5.5 + - - -
297B MET 3.0 10.8 + - - -
298B ILE 4.4 0.9 - - - -
299B ASP* 1.3 77.9 - - - +
301B TYR* 1.3 68.5 + - - +
316B ARG* 4.3 17.4 + - - -
319B LYS* 3.7 16.0 - - - +
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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