Contacts of the helix formed by residues 36 - 48 (chain A) in PDB entry 1L4E
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 LEU 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LYS* 3.9 18.2 - - + -
35A SER* 1.3 82.9 + - - +
37A GLY* 1.3 66.4 + - - +
38A ARG 3.2 0.7 + - - -
39A LEU* 3.0 33.2 + - + +
40A GLU* 3.0 22.6 + - + +
334A MET* 3.5 20.2 - - + -
338A MET* 3.2 35.2 - - + -
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Residues in contact with GLY 37 (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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34A GLY* 3.1 17.0 + - - -
35A SER 3.2 3.0 + - - -
36A LEU* 1.3 75.0 - - - +
38A ARG* 1.3 57.4 + - - -
40A GLU* 2.8 24.2 + - - +
41A THR* 3.3 14.7 + - - +
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Residues in contact with ARG 38 (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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36A LEU 3.2 1.2 + - - -
37A GLY* 1.3 71.2 - - - -
39A LEU* 1.3 57.1 + - - +
41A THR* 3.1 16.8 + - + +
42A LEU* 2.9 29.8 + - - +
287A PRO* 5.3 1.4 - - - +
306A GLU* 2.7 45.2 + - - +
307A PRO 2.9 19.8 + - - -
308A TYR* 3.5 38.5 + - + +
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Residues in contact with LEU 39 (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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36A LEU* 3.0 30.7 + - + +
38A ARG* 1.3 78.5 - - - +
40A GLU* 1.3 62.4 + - - +
42A LEU* 4.4 3.4 - - + -
43A ALA* 3.2 18.4 + - - +
327A ILE* 3.8 35.7 - - + +
330A ALA* 4.3 18.6 - - + +
331A ALA* 3.6 29.9 - - + +
334A MET* 3.9 16.4 - - + +
338A MET* 6.1 0.2 - - + -
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Residues in contact with GLU 40 (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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23A GLN* 4.6 7.6 + - - +
26A ILE* 3.4 24.7 - - + +
27A ASP* 4.5 4.7 - - - +
31A LYS* 2.8 28.4 + - - -
34A GLY* 3.3 27.8 + - - -
36A LEU* 3.0 36.6 + - + -
37A GLY 2.8 10.7 + - - +
39A LEU* 1.3 75.4 - - - +
41A THR* 1.3 67.7 + - + +
43A ALA* 3.2 4.5 + - - +
44A VAL* 3.1 27.4 + - + +
334A MET* 4.2 11.4 - - - -
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Residues in contact with THR 41 (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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23A GLN* 6.0 0.9 - - - +
37A GLY 3.3 11.8 + - - +
38A ARG* 3.1 27.4 + - + +
40A GLU* 1.3 77.6 - - + +
42A LEU* 1.3 56.5 + - - +
44A VAL* 3.4 7.9 + - - +
45A GLN* 2.9 29.2 + - - +
308A TYR* 5.6 0.3 + - - -
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Residues in contact with LEU 42 (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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38A ARG 2.9 18.6 + - - +
39A LEU* 3.8 7.2 - - + +
41A THR* 1.3 78.4 + - - +
43A ALA* 1.3 62.4 + - - +
45A GLN* 3.2 20.2 + - - +
46A LEU* 3.0 36.2 + - + +
286A ILE* 4.2 25.1 - - + -
308A TYR* 3.8 27.1 - - + +
327A ILE* 4.1 17.5 - - + +
328A VAL* 4.0 23.1 - - + -
331A ALA* 3.9 19.3 - - + -
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Residues in contact with ALA 43 (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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22A THR* 4.2 1.1 - - - -
26A ILE* 3.7 17.0 - - + -
39A LEU 3.2 12.0 + - - +
40A GLU 3.2 8.8 + - - +
42A LEU* 1.3 78.6 - - - +
44A VAL* 1.3 62.8 + - - +
46A LEU* 3.4 10.1 + - - +
47A ALA* 3.0 18.0 + - - +
56A PRO* 3.2 25.8 - - + +
331A ALA* 4.0 11.4 - - + +
334A MET* 3.8 12.1 - - + -
335A PHE* 4.6 1.8 - - + -
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Residues in contact with VAL 44 (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 MET* 3.6 41.9 - - + +
22A THR* 3.7 12.3 - - + -
23A GLN* 3.5 30.1 - - + +
26A ILE* 3.7 17.7 - - + -
40A GLU 3.1 15.9 + - - +
41A THR* 3.8 9.0 - - - +
43A ALA* 1.3 71.9 - - - +
45A GLN* 1.3 68.4 + - - +
47A ALA* 3.1 11.6 + - - +
48A GLY 3.2 8.0 + - - -
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Residues in contact with GLN 45 (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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14A PRO* 6.0 0.3 - - - +
19A MET* 4.3 12.5 - - + +
41A THR 2.9 14.1 + - - +
42A LEU* 3.4 23.7 - - - +
44A VAL* 1.3 76.5 - - - +
46A LEU* 1.3 61.9 + - - +
48A GLY* 3.1 12.1 + - - -
49A MET* 3.3 30.2 + - + +
282A ARG* 5.5 2.2 - - - +
283A PRO* 3.0 27.2 + - + +
285A LEU 3.3 22.3 + - - +
286A ILE* 3.8 10.3 - - - +
308A TYR* 4.7 4.3 + - - -
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Residues in contact with LEU 46 (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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42A LEU* 3.0 30.3 + - + +
43A ALA* 3.6 12.3 - - - +
44A VAL 3.2 0.2 - - - -
45A GLN* 1.3 78.0 - - - +
47A ALA* 1.3 62.7 + - - +
49A MET* 3.0 19.8 + - + +
52A LEU* 3.3 37.1 - - + +
56A PRO* 4.1 8.5 - - + -
57A GLN 5.2 1.8 - - - +
259A PRO* 4.1 13.5 - - + -
286A ILE* 4.0 25.6 - - + -
328A VAL* 3.9 28.3 - - + +
331A ALA* 4.7 1.6 - - + -
332A CYS* 4.1 19.5 - - - -
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Residues in contact with ALA 47 (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 ASP* 4.7 0.9 - - - +
18A ALA* 3.4 25.6 - - - +
19A MET* 4.4 0.4 - - - -
22A THR* 2.7 33.7 - - + +
43A ALA 3.0 13.5 + - - +
44A VAL 3.1 9.8 + - - +
46A LEU* 1.3 76.6 - - - +
48A GLY* 1.3 60.9 + - - +
49A MET 3.5 2.1 + - - +
54A GLY* 3.8 14.5 + - - +
55A THR 4.2 12.5 + - - +
56A PRO* 4.2 7.8 - - + +
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Residues in contact with GLY 48 (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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14A PRO* 3.3 8.0 - - - +
15A ASP* 2.8 32.2 + - - +
19A MET* 3.4 26.6 - - - +
44A VAL 3.2 5.3 + - - -
45A GLN 3.1 7.7 + - - -
46A LEU 3.1 1.4 - - - -
47A ALA* 1.3 77.4 - - - +
49A MET* 1.3 59.8 + - - +
50A PRO* 3.2 9.4 - - - +
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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