Contacts of the helix formed by residues 15 - 26 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E GLN 5.8 0.3 - - - +
33E ARG* 3.6 18.7 + - - +
36E GLU* 4.9 9.4 - - - +
148E LYS* 4.8 9.9 - - - +
13G GLN 3.6 2.6 + - - +
14G LEU* 1.3 76.1 - - - +
16G SER* 1.3 63.6 + - - +
17G GLU* 2.8 33.0 + - + +
18G ASP* 3.0 25.1 + - - +
19G LEU* 2.8 35.9 + - - +
71G ARG* 5.1 0.2 - - - +
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Residues in contact with SER 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ARG* 3.5 32.2 + - - +
15G ASP* 1.3 82.2 + - - +
17G GLU* 1.3 59.0 + - - +
19G LEU* 3.8 12.4 - - - +
20G ALA* 2.9 29.6 + - - +
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Residues in contact with GLU 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LYS* 5.2 7.5 + - - +
15G ASP* 2.8 16.8 + - + +
16G SER* 1.3 78.2 + - - +
18G ASP* 1.3 62.2 + - - +
20G ALA* 3.6 8.1 - - - +
21G SER* 2.9 41.6 + - - +
109G SER* 6.0 1.6 - - - -
138G ASN* 2.9 32.5 + - - +
140G LEU* 5.6 1.7 - - - +
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Residues in contact with ASP 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E LYS* 4.1 7.9 + - - -
14G LEU* 4.1 13.9 - - + -
15G ASP* 3.0 26.9 + - - +
17G GLU* 1.3 81.3 - - - +
19G LEU* 1.3 57.2 + - - +
21G SER* 3.3 8.4 + - - -
22G LEU* 2.9 33.1 + - - +
69G ILE* 4.1 14.3 - - + +
71G ARG* 2.7 44.6 + - - +
106G TYR* 5.3 2.3 + - - -
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ARG* 6.0 2.2 - - + +
11G GLY 5.1 4.0 - - - +
14G LEU* 3.8 35.2 - - + +
15G ASP 2.8 23.1 + - - +
16G SER* 3.8 12.6 - - - +
18G ASP* 1.3 69.0 - - - +
20G ALA* 1.3 59.4 + - - +
22G LEU* 3.2 13.2 + - + +
23G LYS* 2.8 40.2 + - - +
38G ILE* 6.1 2.7 - - + -
39G LYS 4.1 8.7 - - - +
40G ASP* 3.9 24.9 - - + -
41G ALA* 3.8 24.2 - - + +
44G LEU* 5.3 5.3 - - + +
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Residues in contact with ALA 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G SER 2.9 19.4 + - - +
17G GLU* 3.6 14.6 - - - +
19G LEU* 1.3 76.0 - - - +
21G SER* 1.3 62.0 + - - +
23G LYS* 3.3 15.3 + - + +
24G PHE* 3.0 21.7 + - - +
138G ASN* 5.7 4.9 - - + +
140G LEU* 4.9 2.4 - - + +
141G ASP* 5.9 2.9 - - - +
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Residues in contact with SER 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G GLU* 2.9 33.3 + - - +
18G ASP* 3.4 8.0 - - - -
20G ALA* 1.3 77.0 - - - +
22G LEU* 1.3 57.0 + - - +
24G PHE* 3.2 4.7 + - - +
25G LEU* 2.9 32.6 + - - +
69G ILE* 4.2 7.0 - - - -
106G TYR* 3.3 35.8 - - - -
109G SER* 5.3 0.2 + - - -
140G LEU* 4.2 15.7 - - - +
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Residues in contact with LEU 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 4.0 23.8 - - + -
18G ASP 2.9 18.5 + - - +
19G LEU* 3.4 17.3 - - + +
21G SER* 1.3 71.8 - - - +
23G LYS* 1.3 56.6 + - - +
25G LEU* 3.2 5.9 + - + +
26G SER* 2.7 37.2 + - - -
41G ALA* 6.0 0.2 - - + -
44G LEU* 4.1 21.3 - - + -
45G PHE* 6.3 1.3 - - + -
62G LEU* 6.1 2.5 - - + -
65G LEU* 3.7 41.7 - - + +
66G LEU* 4.8 4.0 - - + -
69G ILE* 3.7 34.5 - - + -
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Residues in contact with LYS 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G LEU* 2.8 24.7 + - - +
20G ALA* 3.3 15.7 - - + +
22G LEU* 1.3 75.3 - - - +
24G PHE* 1.3 62.9 + - - +
26G SER* 2.7 14.3 + - - +
27G LEU* 3.2 0.5 + - - +
35G GLN* 2.6 61.6 + - + +
36G GLU* 4.4 5.1 + - - +
38G ILE* 2.8 48.0 + - + -
39G LYS* 5.6 1.0 - - - +
44G LEU* 5.3 4.5 - - + +
144G ILE* 6.0 1.3 - - + -
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Residues in contact with PHE 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ALA 3.0 12.8 + - - +
21G SER 3.2 8.5 + - - +
23G LYS* 1.3 74.5 - - - +
25G LEU* 1.3 66.7 + - + +
27G LEU* 3.0 48.4 - - + +
102G ARG* 3.5 49.3 - - - -
105G LEU* 3.6 34.1 - - + -
106G TYR* 4.9 1.1 - - + -
140G LEU* 3.6 57.0 - - + -
143G PHE* 3.9 11.0 - + + -
144G ILE* 4.0 11.6 - - + +
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Residues in contact with LEU 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G SER 2.9 17.4 + - - +
22G LEU* 3.2 10.0 + - + +
24G PHE* 1.3 77.8 - - + +
26G SER* 1.3 58.2 + - - +
27G LEU 3.2 1.8 + - - -
28G ASP* 4.1 4.0 + - - +
65G LEU* 4.3 11.9 - - + +
68G ARG* 4.0 20.0 - - + -
69G ILE* 3.6 30.1 - - + -
98G ILE* 3.4 48.5 - - + +
102G ARG* 3.7 34.6 - - + +
103G VAL* 4.0 7.4 - - + +
106G TYR* 4.3 13.9 - - + -
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Residues in contact with SER 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G LEU 2.7 17.7 + - - -
23G LYS* 2.7 22.5 + - - -
25G LEU* 1.3 70.6 - - - +
27G LEU* 1.3 54.0 + - - +
28G ASP 3.0 5.8 - - - -
29G TYR* 2.9 13.4 + - - +
30G ILE* 2.7 41.9 + - - +
35G GLN* 2.9 13.9 + - - +
44G LEU* 4.3 19.2 - - - +
48G LEU* 5.7 1.1 - - - -
61G PHE* 5.1 10.1 - - - -
65G LEU* 5.5 3.4 - - - -
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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