Contacts of the helix formed by residues 13 - 27 (chain A) in PDB entry 2LK2
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 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A MET 4.6 0.7 - - - +
12A LEU* 1.3 90.0 - - + +
14A LYS* 1.3 65.0 + - - +
15A GLU* 4.3 8.5 - - + +
16A SER* 2.5 36.9 + - - +
17A VAL* 2.9 7.4 + - - +
46A HIS* 4.5 22.0 - - + +
47A LEU* 5.0 6.3 - - + -
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Residues in contact with LYS 14 (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 LEU 3.7 0.9 + - - +
13A PRO* 1.3 72.9 - - - +
15A GLU* 1.3 63.1 + - - +
17A VAL* 3.6 8.7 - - - +
18A GLN* 2.9 25.1 + - - +
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Residues in contact with GLU 15 (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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13A PRO* 3.2 5.9 - - + +
14A LYS* 1.3 80.1 - - - +
16A SER* 1.3 63.1 + - - +
18A GLN* 3.4 5.7 + - - +
19A ILE* 3.2 38.9 + - + +
46A HIS* 6.1 1.8 - - + -
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Residues in contact with SER 16 (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 LEU* 3.3 6.4 - - - +
13A PRO* 2.5 47.0 + - - +
15A GLU* 1.3 80.5 - - - +
17A VAL* 1.3 56.9 + - - +
19A ILE* 3.9 6.4 - - - +
20A LEU* 2.8 49.0 + - - +
45A THR* 4.7 7.9 - - - -
46A HIS* 4.5 12.9 - - - -
47A LEU* 4.3 11.7 - - - -
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Residues in contact with VAL 17 (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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11A MET* 5.6 9.0 - - + -
12A LEU* 3.6 22.9 - - + +
13A PRO 2.9 17.1 + - - +
14A LYS* 3.2 8.3 + - - +
16A SER* 1.3 86.1 + - - +
18A GLN* 1.3 55.7 + - - +
20A LEU* 4.3 5.2 - - - -
21A ARG* 2.6 55.1 + - + +
55A TRP* 4.9 17.9 - - + +
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Residues in contact with GLN 18 (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 LYS 2.9 16.5 + - - +
15A GLU* 3.6 7.2 - - - +
17A VAL* 1.3 79.1 - - - +
19A ILE* 1.3 60.4 + - + +
21A ARG* 3.0 34.2 + - - +
22A ASP* 2.8 61.5 + - - +
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Residues in contact with ILE 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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15A GLU* 3.2 33.2 + - + +
16A SER* 3.9 5.4 - - - +
18A GLN* 1.3 78.5 - - + +
20A LEU* 1.3 64.7 + - - +
22A ASP* 3.3 9.8 + - - +
23A TRP* 3.2 21.5 + - - +
44A GLN* 2.8 54.0 - - + +
45A THR* 4.5 12.6 - - + -
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Residues in contact with LEU 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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12A LEU* 3.8 27.4 - - + -
16A SER* 2.8 39.7 + - - +
17A VAL 3.9 1.6 - - - +
19A ILE* 1.3 73.1 - - - +
21A ARG* 1.3 64.3 + - - +
23A TRP* 3.4 7.4 + - - +
24A LEU* 3.2 20.8 + - - +
41A LEU* 4.1 33.8 - - + +
45A THR* 3.7 23.8 - - + +
47A LEU* 4.5 4.3 - - + -
52A VAL* 4.4 13.9 - - + -
55A TRP* 3.4 33.1 - - + -
56A PHE* 6.2 0.2 - - - -
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Residues in contact with ARG 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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17A VAL* 2.6 36.8 + - + +
18A GLN* 3.0 43.1 + - - +
20A LEU* 1.3 71.7 - - - +
22A ASP* 1.3 57.4 + - - +
24A LEU* 3.2 6.4 + - + +
25A TYR* 2.7 43.1 + - + +
55A TRP* 4.3 6.0 - - + -
63A LEU* 4.7 25.8 - - + -
67A MET* 6.0 7.4 - - + -
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Residues in contact with ASP 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 GLN* 2.8 54.3 + - - +
19A ILE* 3.6 9.7 - - - +
20A LEU 3.3 0.2 - - - -
21A ARG* 1.3 80.5 + - - +
23A TRP* 1.3 62.3 + - - +
25A TYR* 3.7 6.1 - - - +
26A GLU* 2.9 40.6 + - - +
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Residues in contact with TRP 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 ILE 3.2 7.7 + - - +
20A LEU 3.6 5.4 - - - +
21A ARG 3.2 0.2 - - - -
22A ASP* 1.3 80.0 - - - +
24A LEU* 1.3 62.2 + - - +
26A GLU* 3.3 8.5 + - - -
27A HIS* 2.8 72.5 + + + +
30A ASN* 5.3 1.3 - - - -
37A GLU* 3.8 35.6 - - + +
40A LEU* 3.9 37.9 - - + -
41A LEU* 3.5 41.6 - - + +
44A GLN* 5.2 4.7 - - - +
56A PHE* 5.1 6.5 - + - -
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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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20A LEU 3.2 9.9 + - - +
21A ARG* 3.2 9.5 + - + +
23A TRP* 1.3 84.2 - - - +
25A TYR* 1.3 59.5 + - - +
27A HIS 3.0 3.2 - - - +
28A ARG* 2.8 36.4 + - + +
31A ALA* 3.4 33.2 - - + -
55A TRP* 5.6 3.1 - - + -
56A PHE* 4.1 20.4 - - + -
59A ALA* 5.5 0.4 - - + -
60A ARG* 4.0 16.6 - - + +
63A LEU* 3.5 44.2 - - + -
64A LEU* 4.0 13.2 - - + -
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Residues in contact with TYR 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 ARG* 2.7 27.9 + - + +
22A ASP* 3.7 8.5 - - - +
24A LEU* 1.3 73.8 - - - +
26A GLU* 1.3 73.6 + - + +
28A ARG* 3.3 52.8 + - - +
67A MET* 3.9 31.4 - - + -
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Residues in contact with GLU 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 ASP* 2.9 31.3 + - - +
23A TRP* 4.6 8.3 - - - -
25A TYR* 1.3 87.6 - - + +
27A HIS* 1.3 84.8 + - + +
28A ARG 3.6 1.4 + - - -
29A TYR* 5.2 7.4 - - - -
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Residues in contact with HIS 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 TRP* 2.8 65.4 + + + +
24A LEU* 3.0 7.5 - - - +
26A GLU* 1.3 95.2 - - + +
28A ARG* 1.3 63.8 + - - +
29A TYR* 3.3 4.0 - - - +
30A ASN* 3.2 35.9 - - - +
31A ALA* 3.4 19.8 + - - +
37A GLU* 6.1 0.2 - - + -
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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