Contacts of the helix formed by residues 15 - 26 (chain B) in PDB entry 5L08
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 ASP 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B GLN 3.6 3.9 + - - +
14B LEU* 1.3 73.0 - - - +
16B SER* 1.3 77.4 + - - +
17B GLU* 2.8 23.0 + - - +
18B ASP* 3.0 23.4 + - - +
19B LEU* 2.8 31.9 + - - +
71B ARG* 3.7 7.0 - - - +
133H LEU 4.8 9.6 - - - +
34I LYS* 5.6 2.7 - - - +
47I ARG* 5.3 6.7 + - - -
50I GLU* 5.7 2.4 - - - +
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Residues in contact with SER 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU 4.0 1.2 + - - -
15B ASP* 1.3 80.9 + - - +
17B GLU* 1.3 58.8 + - - +
19B LEU* 3.4 17.8 + - - +
20B ALA* 3.1 24.6 + - - +
134H ASP* 5.9 4.5 - - - +
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP* 2.8 15.9 + - + +
16B SER* 1.3 78.3 + - - +
18B ASP* 1.3 66.5 + - - +
20B ALA* 3.2 10.6 + - - +
21B SER* 3.2 19.1 + - - -
138B ASN* 3.6 11.1 + - - -
33I ARG* 2.9 33.2 + - - +
34I LYS* 4.9 13.5 - - - +
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Residues in contact with ASP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 5.0 3.1 - - + -
15B ASP* 3.0 21.0 + - - +
17B GLU* 1.3 74.4 - - - +
19B LEU* 1.3 61.2 + - - +
21B SER* 2.6 24.8 + - - -
22B LEU* 2.8 19.6 + - - +
69B ILE* 4.0 26.3 - - + +
71B ARG* 3.1 37.5 + - - +
106B TYR* 5.6 1.4 + - - -
34I LYS* 3.0 29.8 + - - -
50I GLU* 5.7 1.0 - - - +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLY 5.7 1.1 - - - +
14B LEU* 4.2 13.2 - - + +
15B ASP 2.8 20.3 + - - +
16B SER* 3.5 17.9 - - - +
18B ASP* 1.3 75.9 - - - +
20B ALA* 1.3 55.9 + - - +
22B LEU* 3.2 21.4 + - + +
23B LYS* 2.9 39.1 + - - +
38B ILE* 6.4 0.9 - - + -
39B LYS 4.5 5.6 - - - +
40B ASP* 3.9 13.7 - - + -
41B ALA* 3.7 45.3 - - + +
44B LEU* 4.7 8.5 - - + +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER 3.1 13.7 + - - +
17B GLU* 3.2 15.7 + - - +
19B LEU* 1.3 75.9 - - - +
21B SER* 1.3 61.3 + - - +
23B LYS* 3.3 16.7 + - - +
24B PHE* 3.3 17.7 + - - +
138B ASN* 4.4 17.7 - - + +
140B LEU* 5.1 0.9 - - - +
141B ASP* 5.5 5.5 - - - +
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU 3.2 6.3 + - - -
18B ASP* 2.6 25.4 + - - -
20B ALA* 1.3 76.6 - - - +
22B LEU* 1.3 59.4 + - - +
24B PHE* 3.2 5.4 + - - +
25B LEU* 3.0 31.4 + - - +
69B ILE* 3.3 16.7 - - - +
106B TYR* 3.8 25.1 + - - -
138B ASN* 5.1 2.4 - - - +
140B LEU* 4.0 17.9 - - - +
33I ARG* 6.1 2.7 - - - -
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 4.3 14.4 - - + -
18B ASP 2.8 19.5 + - - +
19B LEU* 3.2 30.3 + - + +
21B SER* 1.3 75.3 + - - +
23B LYS* 1.3 58.4 + - - +
25B LEU* 3.2 5.3 + - + +
26B SER* 2.8 31.1 + - - -
44B LEU* 4.1 21.5 - - + +
45B PHE* 6.1 1.3 - - + -
62B LEU* 6.2 3.4 - - + -
65B LEU* 3.7 41.9 - - + +
66B LEU* 6.2 0.7 - - + -
69B ILE* 3.8 35.2 - - + -
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 2.9 22.3 + - + +
20B ALA* 3.3 15.0 - - - +
22B LEU* 1.3 76.3 - - - +
24B PHE* 1.3 62.3 + - - +
26B SER* 2.6 25.6 + - - -
27B LEU* 3.5 8.0 + - - +
35B GLN* 3.5 47.0 + - + +
36B GLU* 4.0 10.8 + - - +
38B ILE* 2.8 39.6 + - + -
44B LEU* 5.2 9.4 - - + +
144B ILE* 6.3 0.2 - - - -
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Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ALA 3.3 4.4 + - - +
21B SER 3.2 9.9 + - - +
23B LYS* 1.3 79.5 - - - +
25B LEU* 1.3 71.4 + - + +
27B LEU* 3.0 44.5 + - + +
102B ARG* 3.5 54.1 - - + -
105B LEU* 3.5 33.2 - - + -
106B TYR* 4.2 3.4 - - + -
140B LEU* 3.7 62.8 - - + -
141B ASP* 6.1 0.4 - - - +
143B PHE* 4.3 7.0 - - + -
144B ILE* 4.6 6.3 - - + -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B SER 3.0 18.6 + - - +
22B LEU* 3.2 9.6 + - + +
24B PHE* 1.3 88.6 - - + +
26B SER* 1.3 60.2 + - - +
27B LEU 3.1 1.1 + - - -
28B ASP* 4.0 9.6 + - - +
29B TYR* 5.2 0.5 - - - -
61B PHE* 4.9 2.6 - - - -
65B LEU* 3.7 24.0 - - + -
68B ARG* 3.4 36.1 - - + +
69B ILE* 3.8 21.3 - - + -
98B ILE* 4.2 37.4 - - + +
102B ARG* 4.6 14.1 - - + +
103B VAL* 5.2 1.3 - - - +
106B TYR* 4.7 11.7 - - + -
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Residues in contact with SER 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU 2.8 13.3 + - - -
23B LYS* 2.6 24.1 + - - -
25B LEU* 1.3 73.1 - - - +
27B LEU* 1.3 54.6 + - - +
28B ASP 3.1 5.8 - - - -
29B TYR* 2.9 7.6 + - - +
30B ILE* 2.7 56.1 + - - +
35B GLN* 4.4 8.8 + - - +
44B LEU* 4.8 11.8 - - - +
48B LEU* 5.4 5.4 - - - -
61B PHE* 5.1 11.4 - - - -
65B LEU* 5.7 1.1 - - - -
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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