Contacts of the helix formed by residues 18 - 30 (chain A) in PDB entry 1LFB
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 PRO 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A TRP 4.0 4.0 - - - +
17A GLY* 1.3 83.0 - - - +
19A ALA* 1.3 60.1 + - - +
21A GLN* 3.9 15.4 - - + +
22A GLN* 3.2 27.0 + - - +
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Residues in contact with ALA 19 (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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17A GLY 3.0 0.6 - - - -
18A PRO* 1.3 81.8 - - - +
20A SER* 1.3 63.1 + - - +
21A GLN 3.4 0.2 + - - -
22A GLN* 3.6 9.2 + - - +
23A ILE* 3.0 27.6 + - - +
49A ALA* 4.0 13.5 - - + +
50A GLU* 3.2 17.2 + - - +
53A GLN* 3.9 29.4 - - + +
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Residues in contact with SER 20 (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 LYS 5.3 0.2 + - - -
16A TRP* 3.9 22.5 - - - -
17A GLY 2.8 26.8 + - - -
19A ALA* 1.3 75.3 - - - +
21A GLN* 1.3 63.2 + - - +
23A ILE* 3.2 9.3 + - - +
24A LEU* 3.0 25.1 + - - +
46A CYS* 4.1 22.4 - - - +
50A GLU* 3.4 22.1 + - - +
69A VAL* 5.0 2.1 - - - +
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Residues in contact with GLN 21 (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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16A TRP* 4.0 27.1 - - + +
17A GLY 2.8 19.4 + - - +
18A PRO* 3.9 19.1 - - + +
19A ALA 3.3 0.4 - - - -
20A SER* 1.3 73.8 - - - +
22A GLN* 1.3 58.7 + - - +
24A LEU* 3.1 5.8 + - - +
25A PHE* 2.8 62.5 + - + -
77A TRP* 4.7 11.9 - - - +
81A ARG* 6.3 0.2 - - - -
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Residues in contact with GLN 22 (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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18A PRO 3.2 17.4 + - - +
19A ALA* 3.7 14.6 - - - +
21A GLN* 1.3 76.6 - - - +
23A ILE* 1.4 68.7 + - + +
25A PHE* 4.4 6.0 - - - +
26A GLN* 3.1 44.2 + - - +
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Residues in contact with ILE 23 (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 ALA 3.0 24.8 + - - +
20A SER* 3.2 7.5 + - - +
21A GLN 3.1 0.2 - - - -
22A GLN* 1.4 85.3 - - + +
24A LEU* 1.3 65.5 + - - +
26A GLN* 3.3 19.1 - - - +
27A ALA* 3.3 9.7 + - - +
42A LEU* 4.0 20.4 - - + +
45A GLU* 3.9 21.3 - - + +
46A CYS* 3.6 24.7 - - - -
49A ALA* 3.6 27.1 - - + -
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Residues in contact with LEU 24 (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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16A TRP* 3.6 36.3 - - + -
20A SER 3.0 14.9 + - - +
21A GLN* 3.5 4.9 - - - +
23A ILE* 1.3 75.4 - - + +
25A PHE* 1.3 62.5 + - - +
27A ALA* 3.1 15.8 + - - +
28A TYR 3.2 9.9 + - - -
42A LEU* 4.2 16.8 - - + -
46A CYS* 3.7 21.8 - - - -
74A VAL* 4.3 7.0 - - + -
77A TRP* 3.7 52.6 - - + +
78A PHE* 4.0 16.7 - - + -
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Residues in contact with PHE 25 (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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21A GLN* 2.8 62.2 + - + +
22A GLN* 4.4 4.9 - - - +
24A LEU* 1.3 68.7 - - - +
26A GLN* 1.3 62.9 + - - +
27A ALA 2.9 1.4 + - - -
28A TYR* 3.2 18.3 + + + +
29A GLU* 3.6 16.4 + - - +
77A TRP* 3.6 28.9 - + - -
81A ARG* 4.5 16.4 - - + -
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Residues in contact with GLN 26 (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 GLN* 3.1 42.1 + - - +
23A ILE* 3.3 9.6 - - - +
25A PHE* 1.3 74.6 - - - +
27A ALA* 1.3 60.7 + - - +
29A GLU* 3.5 18.6 - - - +
30A ARG* 4.4 9.9 + - - +
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Residues in contact with ALA 27 (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 ILE 3.3 8.7 + - - +
24A LEU 3.1 10.3 + - - +
25A PHE 2.9 1.4 + - - -
26A GLN* 1.3 76.8 - - - +
28A TYR* 1.3 65.0 + - - +
29A GLU 3.2 2.0 - - - -
30A ARG* 3.0 19.0 + - - +
31A GLN* 3.0 13.2 + - - +
42A LEU* 4.1 25.4 - - + -
78A PHE* 4.1 11.4 - - + -
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Residues in contact with TYR 28 (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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24A LEU 3.2 1.6 + - - -
25A PHE* 3.2 13.3 + + - +
27A ALA* 1.3 77.6 - - - +
29A GLU* 1.3 62.3 + - + +
30A ARG 3.2 0.4 - - - -
31A GLN 3.1 29.0 + - - -
32A LYS* 3.2 41.0 + - + +
77A TRP* 4.0 17.7 - + + -
78A PHE* 3.7 25.5 - + + -
81A ARG* 3.3 43.3 + - + -
82A ARG* 4.0 8.0 - - + -
85A GLU* 2.9 30.7 + - - -
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Residues in contact with GLU 29 (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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25A PHE* 3.7 10.4 - - - +
26A GLN* 3.5 20.4 - - - +
28A TYR* 1.3 81.6 - - + +
30A ARG* 1.3 79.4 + - - +
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Residues in contact with ARG 30 (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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26A GLN 4.6 9.2 - - - +
27A ALA* 3.0 9.5 + - - +
28A TYR 4.1 0.2 - - - -
29A GLU* 1.3 102.0 + - - +
31A GLN* 1.3 68.7 + - + +
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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