Contacts of the helix formed by residues 18 - 31 (chain A) in PDB entry 3L6D
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 GLY 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLY* 3.5 3.6 - - - -
17A LEU* 1.3 76.5 - - - +
19A ALA* 1.3 59.3 + - - -
20A MSE 3.5 2.2 - - - -
21A GLY 4.2 2.3 - - - +
22A THR* 2.6 33.0 + - - -
44A LYS* 5.3 3.8 - - - -
72A VAL 5.1 2.0 + - - -
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Residues in contact with ALA 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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18A GLY* 1.3 72.8 - - - +
20A MSE 1.3 55.1 + - - +
22A THR* 3.8 2.5 - - - -
23A ILE* 2.7 42.9 + - + +
44A LYS* 6.2 0.9 - - - +
131A PRO* 5.2 9.9 - - + -
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Residues in contact with MSE 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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18A GLY 3.5 0.2 - - - -
19A ALA* 1.3 76.1 - - - +
21A GLY* 1.3 60.2 + - - +
23A ILE* 3.4 4.5 + - - +
24A MSE 2.9 52.4 + - + +
72A VAL* 3.8 21.3 - - + -
100A TYR* 5.8 1.3 - - + -
127A ILE* 4.6 11.9 - - + -
129A ALA 4.0 14.4 - - - +
131A PRO* 3.6 36.3 - - + -
134A VAL* 3.5 27.8 - - + -
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Residues in contact with GLY 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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14A VAL* 3.9 5.9 - - - +
16A GLY 3.2 25.6 - - - -
17A LEU* 4.5 1.3 - - - -
18A GLY 3.6 4.4 + - - +
19A ALA 3.4 0.4 - - - -
20A MSE 1.3 74.9 - - - +
22A THR* 1.3 59.8 + - - +
24A MSE 3.3 2.6 + - - +
25A ALA* 2.9 32.1 + - - +
72A VAL* 3.7 23.0 + - - +
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Residues in contact with THR 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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17A LEU* 2.9 21.0 + - - +
18A GLY 2.6 29.2 + - - -
19A ALA* 3.8 4.0 - - - -
21A GLY* 1.3 73.5 - - - +
23A ILE* 1.3 58.9 + - + +
25A ALA* 3.3 2.6 + - - +
26A GLN* 2.8 53.9 + - + +
44A LYS* 3.2 33.8 - - + +
47A ALA* 6.5 1.1 - - + -
48A LEU* 4.0 17.4 - - + +
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Residues in contact with ILE 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 ALA* 2.7 32.2 + - + +
20A MSE 3.8 4.5 - - - +
22A THR* 1.3 75.7 - - + +
24A MSE 1.3 61.2 - - - +
26A GLN* 3.6 20.3 - - + +
27A VAL* 2.8 42.7 + - + +
131A PRO* 3.5 43.7 - - + +
132A ARG* 5.6 0.2 - - - -
134A VAL* 4.2 8.5 - - + +
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Residues in contact with MSE 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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14A VAL* 5.3 4.3 - - + -
20A MSE 2.9 42.4 + - + +
21A GLY* 3.8 3.8 - - - +
23A ILE* 1.3 76.6 - - - +
25A ALA* 1.3 63.5 + - - +
27A VAL 3.5 0.2 + - - -
28A LEU* 3.0 33.7 + - + +
70A ILE* 4.1 7.9 - - + -
72A VAL* 3.8 27.4 - - - -
100A TYR* 3.7 38.8 - - + -
127A ILE* 4.3 17.3 - - + -
134A VAL* 4.0 10.1 - - + -
160A LEU* 3.8 34.1 - - + +
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Residues in contact with ALA 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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14A VAL* 4.2 23.6 - - + +
17A LEU* 4.6 0.4 - - + -
21A GLY 2.9 16.9 + - - +
22A THR 3.7 3.8 - - - +
24A MSE 1.3 77.4 - - - +
26A GLN* 1.3 55.5 + - - +
28A LEU* 3.3 4.5 + - - +
29A LEU* 2.9 34.7 + - + +
35A VAL* 4.4 5.0 - - + +
37A ILE* 4.3 12.8 - - + -
48A LEU* 4.0 23.3 - - + -
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Residues in contact with GLN 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 THR* 2.8 34.7 + - - +
23A ILE* 3.2 29.9 + - + +
25A ALA* 1.3 72.0 - - - +
27A VAL* 1.3 63.0 + - + +
29A LEU* 3.3 6.0 + - - +
30A LYS* 3.0 27.4 + - - +
47A ALA* 5.3 8.8 - - - +
48A LEU* 3.4 20.4 - - + +
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Residues in contact with VAL 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 ILE* 2.8 31.6 + - + +
24A MSE 3.9 3.4 - - - +
26A GLN* 1.3 72.5 - - + +
28A LEU* 1.3 59.3 + - - +
30A LYS* 3.3 22.0 + - + +
31A GLN* 3.0 52.5 + - - +
134A VAL* 3.5 29.8 - - + +
135A GLY* 3.7 9.6 - - - +
159A GLY 3.6 12.8 - - - +
160A LEU* 4.7 4.3 - - + -
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Residues in contact with LEU 28 (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 VAL* 4.0 20.0 - - + -
14A VAL* 4.6 6.3 - - + -
24A MSE 3.0 25.3 + - - +
25A ALA 3.7 3.1 - - - +
27A VAL* 1.3 72.7 - - - +
29A LEU* 1.3 66.4 + - - +
31A GLN* 3.2 23.1 + - - +
33A LYS* 2.9 51.8 + - + +
35A VAL* 3.9 7.9 - - + -
70A ILE* 4.0 19.7 - - + -
156A LEU* 4.1 19.1 - - + +
159A GLY* 4.5 1.3 - - - -
160A LEU* 3.8 22.4 - - + -
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Residues in contact with LEU 29 (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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25A ALA* 2.9 20.8 + - + +
26A GLN* 3.6 4.7 - - - +
28A LEU* 1.3 75.0 - - - +
30A LYS* 1.3 59.9 + - - +
32A GLY* 2.8 22.0 + - - -
33A LYS 3.8 17.2 + - - +
34A ARG* 5.3 0.4 - - - -
35A VAL* 3.8 19.3 - - + +
48A LEU* 4.0 18.4 - - + +
51A ALA* 4.0 24.5 - - + +
52A GLY* 3.9 9.6 - - - +
53A ALA* 3.8 39.0 - - + +
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Residues in contact with LYS 30 (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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26A GLN* 3.0 19.0 + - - +
27A VAL* 3.3 21.1 + - + +
29A LEU* 1.3 76.6 - - - +
31A GLN* 1.3 60.6 + - + +
32A GLY* 3.2 4.7 + - - -
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Residues in contact with GLN 31 (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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27A VAL* 3.0 29.3 + - + +
28A LEU* 3.7 13.1 - - - +
29A LEU 3.2 0.6 - - - -
30A LYS* 1.3 77.6 - - + +
32A GLY* 1.3 59.1 + - - +
33A LYS* 3.0 32.7 + - - +
135A GLY* 4.4 3.4 + - - -
137A ARG* 4.0 9.7 - - - +
159A GLY* 2.8 38.4 + - - +
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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