Contacts of the strand formed by residues 32 - 43 (chain A) in PDB entry 1LKF
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 ILE 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ALA 4.5 0.2 - - - +
26A ASP* 3.6 2.3 - - - +
27A SER* 2.9 34.9 + - - +
30A PHE* 3.6 29.4 - - + +
31A LYS* 1.3 77.8 - - - +
33A SER* 1.3 63.5 + - - +
34A GLN 4.3 0.2 - - - -
58A ASN 3.3 9.6 - - - +
59A ILE* 4.2 13.9 - - + -
245A TYR* 3.5 47.3 - - + +
246A GLN* 4.9 0.2 - - - -
247A ARG* 3.9 11.7 - - + +
272A ARG 4.1 15.3 - - - +
274A PHE* 4.1 25.5 - - + -
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Residues in contact with SER 33 (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 THR* 5.4 0.9 - - - +
25A ALA 4.1 0.2 - - - -
26A ASP* 3.2 20.2 + - - -
31A LYS 4.3 0.4 - - - -
32A ILE* 1.3 75.8 - - - +
34A GLN* 1.3 61.8 + - - +
35A ILE* 4.1 17.0 - - - +
57A GLY* 3.3 5.0 - - - -
58A ASN* 2.7 52.5 + - - +
245A TYR* 3.4 5.6 - - - -
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Residues in contact with GLN 34 (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 ALA 3.8 0.5 - - - +
24A THR* 3.3 8.7 - - - +
25A ALA* 2.9 40.7 + - - +
33A SER* 1.3 72.9 + - - +
35A ILE* 1.3 64.4 + - - +
36A LEU* 3.9 16.6 - - + +
243A VAL* 3.0 30.8 + - - +
245A TYR* 3.5 33.0 + - + -
274A PHE* 3.5 28.2 - - + +
276A SER* 2.6 36.0 + - - -
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Residues in contact with ILE 35 (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* 3.8 22.4 - - + -
23A ALA 3.6 2.5 - - - -
24A THR* 4.2 12.6 - - + +
33A SER* 4.1 10.3 - - - +
34A GLN* 1.3 77.6 - - - +
36A LEU* 1.3 60.6 + - - +
37A THR* 4.1 5.7 + - - +
54A LYS 3.5 2.8 - - - +
55A ALA* 3.5 1.6 - - - -
56A THR* 2.8 53.8 + - - +
57A GLY* 3.8 20.6 - - - -
245A TYR* 4.2 0.2 + - - -
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Residues in contact with LEU 36 (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* 3.3 3.3 - - - -
23A ALA* 2.8 41.1 + - + +
34A GLN* 3.9 16.6 - - + +
35A ILE* 1.3 82.6 - - - +
37A THR* 1.3 61.6 + - - +
38A PHE* 3.6 23.2 - - + -
53A LEU* 3.9 6.7 - - + -
54A LYS 3.5 1.8 - - - -
55A ALA* 3.7 24.7 - - + -
243A VAL* 3.8 35.9 - - + -
245A TYR* 4.0 5.6 - - - +
278A TYR* 3.6 35.0 - - + +
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Residues in contact with THR 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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20A LYS* 3.9 30.5 - - + +
21A THR 3.7 2.0 - - - -
22A THR* 3.4 25.8 + - - +
35A ILE* 4.6 6.6 + - - +
36A LEU* 1.3 72.5 - - - +
38A PHE* 1.3 61.7 + - - +
39A ASN* 3.6 12.7 + - - +
52A VAL 3.4 6.2 - - - +
53A LEU* 3.4 2.0 - - - +
54A LYS* 2.9 50.9 + - + +
56A THR* 5.6 1.0 + - - +
140A GLU* 5.6 3.1 - - - +
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Residues in contact with PHE 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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19A TYR 3.4 1.9 - - - +
20A LYS* 3.3 5.5 - - - -
21A THR* 2.9 48.0 + - + +
23A ALA* 4.3 6.5 - - + -
36A LEU* 3.6 37.7 - - + -
37A THR* 1.3 72.5 - - - +
39A ASN* 1.3 61.9 + - - +
40A PHE* 3.8 7.8 + + + -
51A LEU* 3.8 25.6 - - + -
52A VAL 3.9 2.2 - - - -
53A LEU* 3.7 27.1 - - + -
241A ILE* 4.5 12.8 - - + -
243A VAL* 5.7 0.2 - - + -
278A TYR* 4.6 6.1 - + - -
280A ILE* 4.3 17.3 - - + -
287A VAL* 3.7 40.8 - - + -
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Residues in contact with ASN 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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18A LEU* 6.3 1.8 - - + -
19A TYR 3.4 4.9 - - - +
20A LYS* 3.1 32.7 - - - +
37A THR* 3.6 18.8 + - - +
38A PHE* 1.3 72.0 - - - +
40A PHE* 1.3 64.0 + - - +
41A ILE* 3.8 5.0 + - + +
50A THR 3.8 0.2 - - - +
51A LEU* 3.4 4.4 - - - +
52A VAL* 2.8 57.2 + - + +
54A LYS* 4.8 3.4 - - - +
138A PHE* 3.5 41.0 - - + -
140A GLU* 4.5 9.6 + - - +
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Residues in contact with PHE 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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17A THR 3.6 1.6 - - - +
18A LEU* 3.4 6.6 - - - +
19A TYR* 2.7 51.2 + - + +
21A THR* 4.2 6.1 - - + -
38A PHE* 3.9 21.3 - - + -
39A ASN* 1.3 72.3 - - - +
41A ILE* 1.3 61.5 + - - +
42A LYS* 4.0 3.6 - - - -
50A THR 3.6 2.7 - - - -
51A LEU* 4.0 18.6 - - + -
280A ILE* 3.5 34.3 - - + -
281A ASP 4.2 0.7 - - - -
282A TRP* 4.2 29.2 - + - -
285A HIS* 3.5 52.9 - - + +
286A LYS 4.1 6.1 - - - -
287A VAL* 4.4 5.4 - - + -
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Residues in contact with ILE 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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16A VAL* 4.1 9.6 - - + -
17A THR 3.9 2.2 - - - -
18A LEU* 3.9 22.0 - - + -
39A ASN 4.1 7.0 - - - +
40A PHE* 1.3 77.8 - - - +
42A LYS* 1.3 68.4 + - - +
43A ASP* 3.7 2.6 + - + +
48A LYS 4.8 0.9 - - - +
49A ASP* 4.2 2.4 - - - -
50A THR* 2.7 40.8 + - + +
52A VAL* 3.8 26.7 - - + -
116A TYR* 3.8 53.7 + - + +
138A PHE* 4.0 17.5 - - + -
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Residues in contact with LYS 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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15A LYS 3.3 2.5 - - - +
16A VAL* 3.1 6.1 - - - -
17A THR* 3.0 38.3 + - - +
19A TYR* 3.6 26.0 - - + +
40A PHE* 5.5 3.3 - - - -
41A ILE* 1.3 73.7 - - - +
43A ASP* 1.3 59.1 + - - +
44A LYS* 4.1 2.2 - - + -
49A ASP* 3.0 45.3 + - + +
282A TRP* 2.9 23.0 + - - +
283A GLU* 4.9 2.1 - - - +
285A HIS* 3.1 27.8 - - + -
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Residues in contact with ASP 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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15A LYS* 3.3 8.3 - - - +
16A VAL* 3.4 23.7 - - + +
41A ILE* 3.7 4.2 + - + +
42A LYS* 1.3 73.4 - - - +
44A LYS* 1.3 64.0 + - - +
45A SER* 2.9 23.4 + - - -
46A TYR* 3.0 26.5 + - + +
48A LYS 4.8 6.7 + - - +
49A ASP* 5.4 1.2 + - - -
116A TYR* 2.8 31.9 + - + +
118A PHE* 4.8 0.9 - - - -
119A GLY* 2.9 25.7 + - - -
233A GLN* 5.0 2.3 + - - -
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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