Contacts of the helix formed by residues 9 - 26 (chain A) in PDB entry 2LE4
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 ASN 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A MET* 1.3 90.0 - - + +
10A ALA* 1.3 68.4 + - - +
11A PHE* 3.8 8.0 + - - +
12A MET* 3.0 32.0 + - - +
13A VAL* 3.0 15.7 + - - +
54A ILE* 6.1 1.3 - - - -
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Residues in contact with ALA 10 (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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9A ASN* 1.3 76.7 - - + +
11A PHE* 1.3 64.8 + - - +
13A VAL* 3.1 6.0 + - - +
14A TRP 2.9 22.0 + - - -
42A TRP* 4.2 9.0 - - + -
50A LYS* 6.6 0.2 - - + -
53A PHE* 3.4 45.0 - - + -
54A ILE* 4.7 13.3 - - + +
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Residues in contact with PHE 11 (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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9A ASN* 3.2 9.0 + - - +
10A ALA* 1.3 77.5 - - - +
12A MET* 1.3 82.3 + - + +
14A TRP* 3.6 2.9 + - - +
15A SER* 2.7 44.7 + - - -
39A GLY* 5.8 6.5 - - - -
42A TRP* 3.1 61.8 + + + -
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Residues in contact with MET 12 (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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8A MET* 3.6 38.8 - - + -
9A ASN* 3.0 28.0 + - - +
10A ALA 3.3 0.4 - - - -
11A PHE* 1.3 92.6 - - + +
13A VAL* 1.3 60.3 + - - +
15A SER* 3.0 8.9 + - - -
16A ARG* 2.8 45.8 + - + +
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Residues in contact with VAL 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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8A MET* 3.0 33.6 - - + +
9A ASN 3.0 9.1 + - - +
10A ALA 3.1 7.1 + - - +
12A MET* 1.3 76.2 - - - +
14A TRP* 1.3 53.8 + - - +
16A ARG* 3.2 1.5 + - - -
17A GLY* 2.7 34.1 + - - -
53A PHE* 3.2 22.7 - - - +
56A GLU* 3.5 16.6 - - + -
57A ALA* 3.3 32.1 - - + +
60A LEU* 3.7 16.9 - - + +
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Residues in contact with TRP 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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10A ALA 2.9 7.8 + - - +
13A VAL* 1.3 78.3 - - - +
15A SER* 1.3 60.1 + - - +
17A GLY* 5.1 0.2 - - - -
18A GLN* 3.0 69.1 + - + +
22A MET* 6.1 1.1 - - + -
38A LEU* 3.4 53.4 - - + +
41A GLU* 3.5 26.7 - - + -
42A TRP* 3.4 24.7 - + - +
45A LEU* 5.8 5.6 - - + -
49A GLU* 4.9 18.6 + - + +
52A PRO* 5.4 5.1 - - + +
53A PHE* 3.2 51.9 - + + -
56A GLU* 5.5 5.2 - - + -
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Residues in contact with SER 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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11A PHE* 2.7 34.6 + - - -
12A MET* 3.0 12.3 + - - -
14A TRP* 1.3 77.6 - - - +
16A ARG* 1.3 84.6 + - - +
19A ARG* 3.0 29.5 + - - +
38A LEU* 3.6 18.5 - - - +
42A TRP* 5.2 2.6 + - - -
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Residues in contact with ARG 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 MET* 2.8 30.4 + - + +
13A VAL* 3.9 3.8 - - - +
15A SER* 1.3 103.7 + - - +
17A GLY* 1.3 60.4 + - - +
19A ARG* 3.4 9.7 + - - +
20A ARG* 2.9 30.0 + - - +
60A LEU* 5.0 12.8 - - + -
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Residues in contact with GLY 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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13A VAL 2.7 20.1 + - - -
16A ARG* 1.3 73.0 - - - +
18A GLN* 1.3 56.5 + - - +
20A ARG* 3.1 8.4 + - - +
21A LYS* 2.8 35.8 + - - +
56A GLU* 4.0 21.8 - - - +
60A LEU* 5.1 9.1 - - - +
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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 TRP* 3.0 68.2 + - + +
17A GLY* 1.3 74.7 - - - +
19A ARG* 1.3 57.4 + - - +
21A LYS* 3.6 31.0 - - - +
22A MET* 2.9 66.2 + - + +
38A LEU* 3.9 7.4 - - + -
49A GLU* 5.6 2.0 + - - -
56A GLU* 4.7 4.6 + - + +
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Residues in contact with ARG 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 SER 3.0 22.0 + - - +
16A ARG* 3.7 11.0 - - - +
17A GLY 3.2 0.4 - - - -
18A GLN* 1.3 77.9 - - - +
20A ARG* 1.3 59.8 + - - +
22A MET* 5.1 0.4 - - - -
23A ALA* 2.9 36.4 + - - +
30A HIS* 2.8 36.7 + - - +
31A ASN* 5.2 2.0 - - - +
34A ILE* 4.2 26.6 - - + +
38A LEU* 4.6 0.8 - - - +
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Residues in contact with ARG 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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16A ARG 2.9 14.3 + - - +
17A GLY* 3.1 9.6 + - - +
19A ARG* 1.3 80.1 - - - +
21A LYS* 1.3 89.3 + - - +
23A ALA* 3.8 1.8 - - - +
24A GLN* 3.2 53.1 + - + +
25A GLU* 4.8 4.6 + - - +
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Residues in contact with LYS 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 GLY 2.8 26.5 + - - +
18A GLN* 3.5 36.2 - - - +
20A ARG* 1.3 93.4 - - - +
22A MET* 1.3 63.4 + - + +
24A GLN* 3.4 1.6 + - - +
25A GLU* 3.1 48.8 + - - +
56A GLU* 2.8 30.3 + - - +
59A ARG* 4.1 7.6 - - - +
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Residues in contact with MET 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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14A TRP* 6.1 0.9 - - + -
18A GLN* 2.9 49.9 + - + +
19A ARG 4.7 0.2 - - - +
21A LYS* 1.3 77.4 - - + +
23A ALA* 1.3 59.1 + - - +
25A GLU* 4.6 1.6 - - - -
26A ASN* 2.6 62.2 + - - +
29A MET* 4.1 4.5 - - - +
34A ILE* 3.7 22.7 - - + -
37A ARG* 5.9 0.7 - - + -
38A LEU* 3.6 31.2 - - + -
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Residues in contact with ALA 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 ARG* 2.9 29.9 + - - +
20A ARG* 3.4 3.6 + - - +
22A MET* 1.3 76.6 - - - +
24A GLN* 1.3 69.7 + - - +
26A ASN 4.1 0.2 - - - -
27A PRO* 3.2 25.6 - - - +
29A MET 3.3 19.0 + - - +
30A HIS* 3.9 17.4 - - + +
34A ILE* 5.9 0.2 - - - +
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Residues in contact with GLN 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 ARG* 3.2 43.1 + - + +
21A LYS 3.9 3.4 - - - +
22A MET 3.1 0.4 - - - -
23A ALA* 1.3 90.4 + - - +
25A GLU* 1.3 62.5 + - + +
27A PRO* 4.4 8.9 - - - +
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Residues in contact with GLU 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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20A ARG* 4.8 4.5 + - - +
21A LYS* 3.1 38.1 + - - +
22A MET* 4.2 1.1 - - - +
24A GLN* 1.3 84.8 - - + +
26A ASN* 1.3 65.4 + - - +
27A PRO* 3.5 7.1 - - - +
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Residues in contact with ASN 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 MET* 2.6 54.1 + - - +
25A GLU* 1.3 78.8 - - - +
27A PRO* 1.3 69.6 - - - +
28A LYS* 3.2 6.5 - - + -
29A MET* 3.0 48.7 + - + +
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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