Contacts of the helix formed by residues 36 - 46 (chain A) in PDB entry 2LUC
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 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A SER* 1.3 80.8 + - - +
37A THR* 1.3 54.8 + - - +
39A PHE* 3.4 1.6 - - - +
40A LEU* 2.8 59.1 + - + +
61A ASP* 2.6 46.1 + - - +
64A MET* 3.7 31.6 - - + -
65A LYS* 5.7 4.1 - - + +
73A GLY* 3.4 12.3 + - - +
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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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35A SER* 3.4 1.0 + - - -
36A LYS* 1.3 80.4 - - - +
38A GLU* 1.3 71.8 + - - +
40A LEU* 3.4 17.4 - - + +
41A SER* 2.9 42.0 + - - +
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Residues in contact with GLU 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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24A TYR* 3.3 31.1 - - + +
27A LYS* 3.7 23.9 - - + +
28A ASP* 4.0 15.9 - - + +
34A LEU* 3.3 15.5 - - + -
35A SER* 3.0 34.2 + - - +
37A THR* 1.3 91.2 - - - +
39A PHE* 1.3 57.6 + - - +
41A SER* 4.6 3.1 - - - -
42A PHE* 2.8 27.0 + - - +
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Residues in contact with PHE 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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34A LEU* 3.5 21.3 - - + +
35A SER 2.7 16.1 + - - +
36A LYS 3.4 4.7 - - - +
38A GLU* 1.3 77.7 - - - +
40A LEU* 1.3 57.3 + - + +
42A PHE* 3.7 9.0 - + - -
43A MET* 2.7 72.7 + - + +
60A LEU* 4.1 11.4 - - + -
63A MET* 3.8 15.5 - - + -
64A MET* 3.6 25.4 - - + -
67A LEU* 4.1 0.7 - - + -
75A LEU* 3.4 26.0 - - + -
80A PHE* 4.5 3.1 - + - -
83A LEU* 3.5 33.4 - - + -
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Residues in contact with LEU 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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36A LYS* 2.8 57.4 + - + +
37A THR* 3.4 20.9 - - + +
39A PHE* 1.3 79.9 - - + +
41A SER* 1.3 62.4 + - - +
43A MET 3.5 0.2 + - - -
44A ASN* 2.7 36.0 + - - +
57A PRO* 5.3 1.8 - - + +
60A LEU* 3.6 35.3 - - + +
61A ASP 5.0 0.4 - - - +
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Residues in contact with SER 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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24A TYR* 3.9 13.2 - - - -
27A LYS* 5.3 3.6 - - - -
37A THR* 2.9 23.4 + - - +
38A GLU* 3.8 6.2 - - - -
40A LEU* 1.3 72.4 - - - +
42A PHE* 1.3 58.8 + - - +
44A ASN* 3.3 4.8 + - - +
45A THR* 2.6 40.6 + - - +
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Residues in contact with PHE 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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20A VAL* 3.5 31.0 - - + -
24A TYR* 3.3 32.7 - + + -
34A LEU* 4.2 6.3 - - + -
38A GLU 2.8 21.8 + - - +
39A PHE* 3.4 24.5 - + - +
41A SER* 1.3 75.8 - - - +
43A MET* 1.3 62.6 + - - +
45A THR* 2.9 5.8 + - - -
46A GLU* 2.6 48.4 + - + +
47A LEU* 3.6 24.9 - - + -
80A PHE* 3.2 35.9 - + - -
10B THR* 3.7 12.8 - - + -
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Residues in contact with MET 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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39A PHE* 2.7 64.9 + - + +
42A PHE* 1.3 73.9 - - + +
44A ASN* 1.3 56.7 + - - +
47A LEU* 2.8 50.5 - - + -
50A PHE* 3.9 21.5 - - + -
51A THR* 2.7 33.2 + - - +
60A LEU* 3.3 27.4 - - + -
63A MET* 3.8 23.1 - - + -
83A LEU* 4.6 0.9 - - + -
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Residues in contact with ASN 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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40A LEU* 2.7 34.4 + - - +
41A SER* 3.9 4.9 - - - +
42A PHE 3.2 0.2 - - - -
43A MET* 1.3 76.5 - - - +
45A THR* 1.3 60.2 + - + +
48A ALA* 3.0 18.8 - - - +
51A THR* 3.5 15.9 - - - +
52A LYS* 2.8 36.5 + - - +
57A PRO* 4.8 10.4 - - - +
60A LEU* 3.1 18.4 - - - +
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Residues in contact with THR 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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24A TYR* 2.7 26.5 + - - +
41A SER* 2.6 25.4 + - - +
42A PHE 2.9 3.5 + - - -
44A ASN* 1.3 82.3 - - + +
46A GLU* 1.3 75.9 + - - +
47A LEU 3.2 1.6 + - - -
48A ALA* 3.7 11.4 + - - +
3B LYS* 5.7 1.7 + - - -
8B THR* 3.7 9.9 - - - +
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Residues in contact with GLU 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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20A VAL* 4.1 9.5 - - - +
23A LYS* 2.7 32.7 + - - -
24A TYR* 3.5 26.7 + - + -
42A PHE* 2.6 29.2 + - + +
45A THR* 1.3 86.0 + - - +
47A LEU* 1.3 64.8 + - - +
8B THR* 2.5 43.4 + - - +
9B GLU* 4.8 2.1 + - - +
10B THR* 3.8 15.5 - - + -
11B GLU* 3.3 2.6 - - - -
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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