Contacts of the helix formed by residues 290 - 301 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288E LEU 3.6 2.4 + - - -
289E PRO* 1.3 74.6 - - - +
291E LEU* 1.3 70.6 + - - +
292E ALA* 3.0 4.4 - - - +
293E VAL* 2.9 16.2 + - - +
294E GLN* 2.9 17.2 + - - +
350E LEU* 3.5 27.8 - - - -
351E GLU* 4.2 7.3 - - - +
377E ALA 4.8 1.5 + - - -
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Residues in contact with LEU 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E VAL* 5.7 4.5 - - + +
256E GLN* 3.3 31.6 - - + +
257E LEU* 5.4 8.5 - - + -
287E GLN* 5.3 1.3 - - - +
290E GLY* 1.3 75.0 - - - +
292E ALA* 1.3 62.5 + - + +
294E GLN* 2.6 22.8 + - - +
295E LEU* 2.4 39.9 + - + +
362E ARG* 5.0 9.4 - - + -
377E ALA* 3.4 29.8 + - + +
378E ARG* 3.6 30.0 - - - +
379E LEU* 4.3 8.5 - - + +
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Residues in contact with ALA 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E GLN 3.7 15.5 - - - +
259E GLU* 4.3 7.2 - - + -
260E TYR* 3.5 40.6 - - + +
289E PRO* 4.7 6.3 - - + -
290E GLY 3.0 6.4 - - - +
291E LEU* 1.3 82.7 - - + +
293E VAL* 1.3 61.2 + - - +
295E LEU* 3.4 5.9 + - - +
296E LEU* 3.2 28.5 + - - +
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Residues in contact with VAL 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E PHE* 3.6 29.4 - - + -
277E ASP* 5.6 2.0 - - - -
289E PRO* 4.3 21.1 - - + +
290E GLY 2.9 10.1 + - - +
292E ALA* 1.3 78.4 - - - +
294E GLN* 1.3 49.0 + - - +
296E LEU* 2.7 6.6 + - - +
297E MET* 2.4 62.5 + - + +
303E PHE* 3.6 32.3 - - + -
351E GLU* 3.8 14.8 - - + +
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Residues in contact with GLN 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290E GLY 2.9 9.3 + - - +
291E LEU* 2.6 20.4 + - - +
293E VAL* 1.3 73.3 - - - +
295E LEU* 1.3 53.2 + - - -
296E LEU 3.1 0.2 - - - -
297E MET* 3.2 27.5 + - + -
298E ILE* 3.3 7.4 + - - +
299E ASP 4.7 0.2 + - - -
350E LEU 3.1 23.8 + - - -
351E GLU* 4.3 0.4 - - - -
352E VAL* 2.9 35.9 + - - +
354E PRO* 3.2 27.3 - - + +
379E LEU* 3.2 40.0 + - + +
381E PHE* 3.4 17.5 - - - -
422E ALA* 5.2 1.8 - - - +
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Residues in contact with LEU 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E LEU* 5.5 11.9 - - + -
237E TYR* 5.6 9.9 - - + +
260E TYR* 3.8 29.7 - - + -
291E LEU* 2.4 31.1 + - + +
292E ALA* 3.5 7.2 - - - +
293E VAL 3.1 0.2 - - - -
294E GLN* 1.3 67.3 - - - +
296E LEU* 1.3 58.2 + - - +
299E ASP* 3.6 18.4 - - - -
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Residues in contact with LEU 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E TYR* 4.1 9.2 - - + +
263E ILE* 4.0 24.0 - - + -
264E LYS* 4.1 27.1 - - + -
267E LEU* 4.5 6.7 - - + -
275E PHE* 4.1 27.8 - - + -
292E ALA* 3.2 16.7 + - + +
293E VAL* 2.7 9.4 + - + +
295E LEU* 1.3 82.1 - - - +
297E MET* 1.3 62.4 + - + +
298E ILE 3.7 0.7 - - - -
299E ASP* 3.2 7.5 - - - +
300E GLY 3.1 21.1 + - - -
301E TYR* 3.4 45.0 - - + +
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Residues in contact with MET 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E PHE* 5.7 0.4 - - + -
293E VAL* 2.4 46.0 + - + +
294E GLN* 3.2 23.7 + - + -
296E LEU* 1.3 72.7 - - + +
298E ILE* 1.3 63.0 + - - +
299E ASP 3.3 5.4 + - - -
300E GLY* 3.9 2.3 + - - -
301E TYR 4.2 14.5 + - - +
303E PHE* 4.4 20.0 - - + +
315E THR* 5.5 3.1 - - - -
319E LYS* 4.3 10.4 - - - +
329E LEU* 5.2 11.0 - - - -
351E GLU* 3.5 29.8 - - + +
352E VAL 3.6 0.7 - - - +
353E ASP* 3.4 52.0 - - - +
354E PRO* 3.9 1.1 - - + -
355E THR* 4.1 0.9 + - - -
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Residues in contact with ILE 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E TYR* 6.2 0.2 - - - +
294E GLN 3.3 5.6 + - - +
297E MET* 1.3 74.6 - - - +
299E ASP* 1.3 68.4 + - - +
354E PRO* 3.1 43.4 - - + +
355E THR* 3.3 24.2 + - - +
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Residues in contact with ASP 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E GLN 4.7 0.4 + - - -
295E LEU* 3.6 27.1 - - - -
296E LEU* 3.2 11.4 + - - +
297E MET 3.1 1.5 - - - +
298E ILE* 1.3 83.9 - - - +
300E GLY* 1.3 59.3 + - - +
301E TYR* 4.3 9.0 - - + -
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Residues in contact with GLY 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E ASP* 4.4 3.5 - - - +
296E LEU 3.1 2.6 + - - -
297E MET 4.4 2.5 - - - -
299E ASP* 1.3 81.0 - - - +
301E TYR* 1.3 74.4 + - - +
316E ARG* 3.8 24.7 + - - -
319E LYS* 5.9 3.1 - - - -
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Residues in contact with TYR 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E LYS* 4.0 10.5 - - + +
267E LEU* 3.3 43.4 - - + +
268E ASP* 3.1 28.8 - - - -
273E ASP* 3.2 20.4 - - + +
275E PHE* 4.9 4.3 - - + -
296E LEU* 3.4 52.0 + - + +
297E MET* 4.2 18.0 + - + +
299E ASP* 4.6 6.1 - - + -
300E GLY* 1.3 96.1 - - - +
302E GLY* 1.3 65.5 + - - +
303E PHE 3.6 2.1 + - - -
315E THR* 4.9 1.0 + - - -
316E ARG* 4.5 4.4 - - - +
319E LYS* 4.8 13.2 - - - +
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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
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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