Contacts of the helix formed by residues 383 - 393 (chain A) in PDB entry 1L2L
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 LYS 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A VAL* 3.7 8.1 - - - -
381A ILE* 3.7 9.5 - - - +
382A GLU* 1.3 89.7 - - + +
384A LEU* 1.3 65.3 + - - +
385A SER* 3.7 20.4 - - - +
386A ASP* 3.2 34.4 + - - +
387A ILE 4.1 0.5 + - - -
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 5.3 3.5 - - + +
18A VAL 5.0 0.2 - - - +
19A GLU* 3.0 47.3 - - + +
22A ILE* 3.9 27.8 - - + -
127A VAL* 3.6 22.9 + - - +
128A TYR* 4.4 23.3 - - + +
367A PHE* 4.7 11.9 - - + -
383A LYS* 1.3 73.6 - - - +
385A SER* 1.3 63.3 + - - +
387A ILE* 3.0 31.1 + - + +
388A ARG 4.5 0.2 + - - -
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Residues in contact with SER 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU* 4.4 16.1 + - - -
383A LYS* 3.7 16.9 - - - +
384A LEU* 1.3 80.7 - - - +
386A ASP* 1.3 70.7 + - - +
387A ILE 3.3 0.9 + - - -
388A ARG* 3.4 22.2 + - - +
389A GLU* 5.4 0.3 - - - +
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Residues in contact with ASP 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A THR* 3.7 13.9 - - + +
378A LYS* 3.6 24.3 + - + +
381A ILE* 5.4 0.4 - - + -
382A GLU* 4.4 3.9 + - - +
383A LYS* 3.3 41.1 + - - +
384A LEU 3.0 1.0 + - - -
385A SER* 1.3 82.2 + - - +
387A ILE* 1.3 62.8 + - - +
388A ARG 3.1 2.9 - - - -
389A GLU* 3.0 48.9 + - - +
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Residues in contact with ILE 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.8 17.9 - - + -
128A TYR* 4.9 4.5 - - + +
367A PHE* 4.3 18.8 - - + -
370A LEU* 3.4 32.8 - - + +
371A ALA* 3.7 22.0 - - + +
374A THR* 3.4 10.8 + - + +
381A ILE* 3.6 33.7 - - + -
384A LEU* 3.0 23.3 + - + +
386A ASP* 1.3 73.3 - - - +
388A ARG* 1.3 56.6 + - - +
389A GLU 2.9 5.6 - - - -
390A GLY* 2.9 21.5 + - - -
391A LEU* 3.9 4.3 - - - +
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Residues in contact with ARG 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLU* 5.2 2.0 + - - +
15A LEU* 3.2 25.2 - - + +
16A ASP* 2.8 31.3 + - - +
19A GLU* 4.8 14.1 + - - +
384A LEU 4.5 0.2 + - - -
385A SER* 3.4 16.0 + - - +
386A ASP 3.1 0.4 - - - -
387A ILE* 1.3 77.9 - - - +
389A GLU* 1.3 61.8 + - + +
390A GLY 3.1 0.2 - - - -
391A LEU* 3.2 49.8 + - + +
392A ALA* 4.5 0.7 + - - +
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Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A THR* 4.6 6.9 - - + +
377A MET* 5.2 6.6 - - - +
378A LYS* 4.2 26.2 + - - +
385A SER 5.4 0.4 - - - +
386A ASP* 3.0 47.2 - - - +
387A ILE 2.9 0.2 - - - -
388A ARG* 1.3 80.4 - - + +
390A GLY* 1.3 61.2 + - - +
391A LEU 3.2 1.0 + - - -
392A ALA* 3.5 15.0 + - - +
393A VAL* 4.0 8.8 - - - +
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Residues in contact with GLY 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A LEU* 3.6 23.0 - - - +
373A ALA* 4.5 7.5 - - - +
374A THR* 3.8 11.1 + - - -
377A MET* 5.9 0.2 - - - -
387A ILE 2.9 12.1 + - - -
389A GLU* 1.3 80.6 - - - +
391A LEU* 1.3 61.2 + - - +
392A ALA 3.3 0.2 - - - -
393A VAL* 3.2 30.2 + - - +
430A LYS* 5.8 0.3 - - - +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLU* 2.5 35.1 - - - +
11A TYR* 4.9 2.9 - - + +
12A GLU* 4.0 38.4 - - + +
15A LEU* 4.1 6.7 - - + -
370A LEU* 3.7 32.8 - - + -
387A ILE 3.9 0.2 - - - +
388A ARG* 3.3 61.2 - - + +
389A GLU 3.1 0.6 - - - -
390A GLY* 1.3 78.5 - - - +
392A ALA* 1.3 60.8 + - - +
393A VAL 3.4 3.8 + - - +
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Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A ARG 4.5 0.4 + - - -
389A GLU 3.5 9.2 + - - +
390A GLY 3.3 1.0 - - - -
391A LEU* 1.3 75.7 - - - +
393A VAL* 1.3 63.9 + - + +
394A PRO* 3.3 9.0 - - - +
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Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLU* 5.1 2.4 - - - +
373A ALA* 4.7 5.8 - - + -
377A MET* 3.5 37.7 - - + -
389A GLU 4.0 8.7 - - - +
390A GLY* 3.2 24.0 + - - +
391A LEU 4.0 4.5 - - - +
392A ALA* 1.3 77.9 - - + +
394A PRO* 1.3 78.7 - - + +
395A ILE* 3.7 3.5 + - - +
430A LYS* 3.7 44.5 - - + +
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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