Contacts of the helix formed by residues 12 - 27 (chain A) in PDB entry 2LQ9
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 CYS 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A THR* 1.3 85.3 - - - +
13A GLY* 1.3 52.3 + - - +
14A GLY 2.9 2.9 - - - -
15A CYS* 2.3 51.3 + - + +
16A ALA* 2.3 32.3 + - + +
58A THR* 3.8 22.0 - - + +
60A ALA* 5.8 0.2 - - - +
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Residues in contact with GLY 13 (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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10A MET* 2.8 44.2 - - - +
11A THR 3.4 1.6 + - - -
12A CYS* 1.3 76.1 - - - +
14A GLY* 1.3 55.1 + - - +
16A ALA* 4.3 0.9 - - - -
17A GLU* 2.9 31.9 + - - +
35A LEU* 5.3 5.4 - - - +
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Residues in contact with GLY 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 CYS 2.4 9.8 + - - -
13A GLY* 1.3 71.0 - - - +
15A CYS* 1.3 58.2 + - - -
17A GLU* 3.1 22.6 - - - +
18A ALA* 3.7 5.2 + - - +
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Residues in contact with CYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A CYS* 2.3 34.0 + - + -
14A GLY* 1.3 67.1 - - - +
16A ALA* 1.3 55.4 + - - +
17A GLU 3.0 1.8 - - - -
18A ALA* 2.9 11.2 + - - +
19A VAL* 2.7 36.3 + - - +
58A THR* 3.7 12.3 - - + -
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Residues in contact with ALA 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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10A MET* 4.1 15.3 - - + -
11A THR 4.6 2.2 - - - +
12A CYS* 2.3 51.2 + - + +
13A GLY 3.8 1.8 - - - +
15A CYS* 1.3 66.4 - - - +
17A GLU* 1.3 60.3 + - - +
19A VAL* 3.3 6.1 + - - +
20A SER* 3.3 18.4 + - - -
58A THR* 3.6 20.0 - - - +
60A ALA* 5.3 5.6 - - + -
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Residues in contact with GLU 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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10A MET* 5.7 0.2 - - - +
13A GLY* 2.9 20.7 + - - +
14A GLY* 3.1 13.3 - - - +
15A CYS 3.0 0.6 - - - -
16A ALA* 1.3 75.9 - - - +
18A ALA* 1.3 75.4 + - - +
20A SER* 2.5 31.4 + - - +
21A ARG* 3.8 13.2 + - - +
33A ILE* 5.3 12.8 - - + -
35A LEU* 5.4 11.0 - - + -
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY 3.9 6.3 - - - +
15A CYS* 2.9 14.8 + - - +
17A GLU* 1.3 93.4 + - - +
19A VAL* 1.3 66.2 + - - +
21A ARG* 3.1 26.4 + - + +
22A VAL* 3.9 6.6 + - - +
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Residues in contact with VAL 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 CYS* 2.7 8.3 + - - +
16A ALA 3.3 9.0 - - - +
18A ALA* 1.3 77.7 - - - +
20A SER* 1.3 60.5 + - - +
22A VAL* 2.6 38.5 + - + +
54A THR* 2.8 33.7 - - + +
55A LEU* 4.9 2.2 - - + -
57A LYS* 3.7 24.5 - - + -
58A THR* 3.1 40.4 - - + +
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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
----------------------------------------------------------
16A ALA 3.3 6.3 + - - -
17A GLU* 2.5 23.1 + - - -
19A VAL* 1.3 81.6 - - - +
21A ARG* 1.3 60.1 + - - +
23A LEU* 2.9 29.8 + - - +
24A ASN* 4.1 2.9 + - - -
31A TYR* 4.7 8.0 - - - -
33A ILE* 2.9 37.5 - - - +
40A VAL* 6.2 2.0 - - - -
54A THR* 3.7 11.9 - - - -
55A LEU* 6.4 0.7 - - - -
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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 GLU* 4.0 20.6 - - - +
18A ALA* 3.2 19.3 - - - +
19A VAL 3.1 0.6 - - - -
20A SER* 1.3 84.6 + - - +
22A VAL* 1.3 62.5 + - + +
23A LEU 3.0 1.0 + - - -
24A ASN* 3.2 30.7 + - - +
25A LYS 4.6 0.2 + - - -
31A TYR* 4.7 15.5 + - + +
33A ILE* 6.1 0.2 - - + -
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Residues in contact with VAL 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 ALA 4.0 9.4 - - - +
19A VAL* 2.6 31.2 + - + +
21A ARG* 1.3 75.0 - - + +
23A LEU* 1.3 65.0 + - - +
24A ASN 3.1 0.2 - - - -
25A LYS* 3.0 24.8 + - + +
26A LEU* 3.6 4.7 + - - +
54A THR* 4.0 12.6 - - + +
57A LYS* 4.6 18.8 - - + +
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Residues in contact with LEU 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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20A SER* 2.9 18.6 + - - +
22A VAL* 1.3 81.6 - - - +
24A ASN* 1.3 56.4 + - - +
26A LEU 3.0 2.5 + - - +
27A GLY* 2.5 40.4 + - - -
28A GLY 4.6 1.8 - - - +
29A VAL 4.9 3.1 - - - +
31A TYR* 4.5 18.8 - - + -
40A VAL* 6.1 3.4 - - + -
42A ILE* 3.4 35.7 - - + -
50A THR* 3.3 21.8 - - - +
51A LEU* 4.3 5.6 - - - -
54A THR* 3.2 38.8 - - + +
55A LEU* 4.9 5.2 - - + -
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Residues in contact with ASN 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 SER 4.4 0.6 + - - -
21A ARG* 3.2 26.6 + - - +
22A VAL 3.1 0.4 - - - -
23A LEU* 1.3 80.3 - - - +
25A LYS* 1.3 59.9 + - - +
28A GLY* 2.4 39.2 + - - +
29A VAL 4.4 4.6 - - - +
31A TYR* 3.2 48.1 + - - -
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Residues in contact with LYS 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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22A VAL* 3.0 15.0 + - + +
24A ASN* 1.3 81.5 - - - +
26A LEU* 1.3 69.6 + - + +
27A GLY 4.7 0.5 - - - -
28A GLY 4.7 0.2 + - - -
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Residues in contact with LEU 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 VAL 3.6 3.4 + - - +
23A LEU 3.0 7.7 + - - +
25A LYS* 1.3 86.6 - - + +
27A GLY* 1.3 60.4 + - - +
49A ASP* 3.8 16.6 - - - +
50A THR* 3.7 29.2 - - - +
53A ALA* 4.3 19.3 - - + -
54A THR* 4.5 8.1 - - - +
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Residues in contact with GLY 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 LEU* 2.5 18.6 + - - -
24A ASN 3.4 0.2 - - - -
25A LYS 4.7 0.9 - - - -
26A LEU* 1.3 76.0 - - - +
28A GLY* 1.3 63.9 + - - -
29A VAL* 3.1 21.2 + - - +
44A SER* 5.3 1.1 - - - -
50A THR* 3.7 20.5 + - - -
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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