Contacts of the helix formed by residues 14 - 32 (chain E) in PDB entry 5MS0
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 14 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ALA* 3.6 18.4 - - - +
13E PHE* 1.3 79.1 - - + +
15E HIS* 1.3 63.8 + - - +
16E ARG* 3.4 7.2 - - + +
17E LEU* 3.9 14.1 + - + +
18E ILE* 3.7 8.1 + - - +
70E HIS* 5.1 2.3 - - - +
254M MET* 6.5 0.9 - - + -
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Residues in contact with HIS 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E PHE 4.2 0.8 + - - -
14E ASP* 1.3 72.9 - - - +
16E ARG* 1.3 61.4 + - - +
18E ILE* 4.0 3.4 - - - +
19E ASP* 2.9 31.2 + - - +
70E HIS* 5.1 11.9 - - + +
116L ALA* 4.5 25.4 - - + -
117L GLU 5.6 1.1 - - - +
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Residues in contact with ARG 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ASP* 3.4 4.1 - - + +
15E HIS* 1.3 79.9 - - - +
17E LEU* 1.3 56.0 + - - +
19E ASP* 4.2 3.8 - - - +
20E GLN* 2.9 32.6 + - - +
214M PRO* 5.0 11.2 - - + +
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Residues in contact with LEU 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ALA* 5.5 2.5 - - + -
14E ASP* 3.9 18.3 + - + +
15E HIS 3.3 0.2 - - - -
16E ARG* 1.3 80.7 - - - +
18E ILE* 1.3 55.8 + - - +
20E GLN* 4.0 4.9 - - - +
21E ALA* 2.9 29.6 + - - +
93E ALA* 5.7 7.6 - - + -
94E ALA 5.4 6.7 - - - +
95E GLY 6.1 1.1 - - - +
96E VAL* 5.3 10.1 - - + -
212M GLU 5.9 2.9 - - - +
214M PRO* 5.7 3.8 - - - -
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Residues in contact with ILE 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU* 6.0 6.3 - - + -
11E LYS 5.8 0.2 - - - -
12E ALA* 3.7 26.0 - - + -
14E ASP 3.7 6.7 + - - +
15E HIS* 3.4 5.2 + - - +
16E ARG 3.3 0.2 - - - -
17E LEU* 1.3 77.7 - - - +
19E ASP* 1.3 62.0 + - - +
21E ALA* 4.0 4.2 - - - +
22E THR* 2.9 30.8 + - - -
70E HIS* 5.5 7.2 - - + +
71E LEU* 6.2 2.2 - - - +
72E ARG* 6.1 5.4 - - + +
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Residues in contact with ASP 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E HIS 2.9 18.6 + - - +
16E ARG* 4.2 4.0 - - - +
18E ILE* 1.3 74.7 - - - +
20E GLN* 1.3 64.2 + - - +
22E THR* 4.0 3.5 - - - -
23E ALA* 3.0 24.9 + - - +
79L GLN* 4.8 18.8 - - + +
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Residues in contact with GLN 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ARG 2.9 21.5 + - - +
17E LEU* 4.0 5.4 - - - +
19E ASP* 1.3 76.1 - - - +
21E ALA* 1.3 57.4 + - - +
23E ALA* 3.2 8.0 + - - +
24E GLU* 2.9 27.8 + - - +
214M PRO* 4.7 15.5 - - + -
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Residues in contact with ALA 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LEU 2.9 22.1 + - - +
18E ILE* 4.0 5.8 - - - +
20E GLN* 1.3 77.3 - - - +
22E THR* 1.3 58.1 + - - +
24E GLU* 3.2 9.4 + - - +
25E ILE* 2.9 27.7 + - - +
93E ALA* 6.3 3.8 - - + +
96E VAL* 5.7 6.7 - - + -
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Residues in contact with THR 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ILE 2.9 18.9 + - - -
19E ASP* 4.2 3.6 - - - -
21E ALA* 1.3 73.2 - - - +
23E ALA* 1.3 60.5 + - - +
25E ILE* 4.1 5.5 - - - +
26E VAL* 3.0 31.5 + - - +
39E PRO* 5.3 13.5 - - - -
72E ARG* 5.5 10.1 - - - -
22L LEU* 5.7 2.8 - - - +
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Residues in contact with ALA 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ASP 3.0 19.4 + - - +
20E GLN* 3.4 7.9 - - - +
22E THR* 1.3 77.9 - - - +
24E GLU* 1.3 56.3 + - - +
26E VAL* 4.2 3.5 - - - +
27E GLU* 3.0 31.9 + - - +
22L LEU* 6.0 4.3 - - - -
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Residues in contact with GLU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E GLN 2.9 13.6 + - - +
21E ALA* 3.2 13.4 + - - +
23E ALA* 1.3 78.3 - - - +
25E ILE* 1.3 56.3 + - - +
27E GLU* 3.5 3.3 + - - +
28E THR* 2.9 29.3 + - - -
54N PRO* 3.9 23.4 - - + +
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Residues in contact with ILE 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ALA 2.9 14.8 + - - +
22E THR* 4.1 6.3 - - - +
24E GLU* 1.3 74.0 - - - +
26E VAL* 1.3 61.9 + - - +
28E THR* 3.3 6.9 + - - -
29E ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E THR 3.0 18.0 + - - +
23E ALA* 4.2 4.0 - - - +
25E ILE* 1.3 75.4 - - - +
27E GLU* 1.3 57.7 + - - +
29E ALA* 3.3 5.9 + - - +
30E LYS* 2.9 30.1 + - - +
36E VAL* 5.5 8.1 - - + -
22L LEU* 4.2 25.4 - - + +
23L SER* 5.1 5.8 - - - -
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Residues in contact with GLU 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ALA 3.0 21.4 + - - +
24E GLU* 3.8 5.2 - - - +
26E VAL* 1.3 77.3 - - - +
28E THR* 1.3 55.7 + - - +
30E LYS* 3.4 5.8 + - - +
31E ARG* 3.0 30.3 + - - +
54N PRO* 5.1 7.0 - - + -
55N ILE* 6.0 1.7 - - - +
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Residues in contact with THR 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E GLU 2.9 18.4 + - - -
25E ILE* 3.5 7.4 - - - -
27E GLU* 1.3 76.8 - - - +
29E ALA* 1.3 57.6 + - - +
31E ARG* 3.2 4.7 + - - +
32E THR* 2.9 32.9 + - - -
86E ALA* 6.0 7.2 - - - -
87E LEU* 6.2 3.8 - - - -
54N PRO* 4.7 16.1 - - - +
55N ILE* 6.2 2.2 - - - +
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Residues in contact with ALA 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ILE 2.9 17.2 + - - +
26E VAL* 3.9 6.1 - - - +
28E THR* 1.3 75.9 - - - +
30E LYS* 1.3 61.9 + - - +
32E THR* 3.9 3.9 + - - +
33E GLY 3.9 1.4 + - - -
34E ALA* 3.1 36.5 + - + +
35E GLN 5.0 11.0 - - - +
36E VAL* 5.2 9.9 - - + -
76E ILE* 5.5 8.5 - - + -
83E THR* 6.5 0.7 - - - -
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Residues in contact with LYS 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E VAL 2.9 17.7 + - - +
27E GLU* 3.8 7.2 - - - +
29E ALA* 1.3 79.6 - - - +
31E ARG* 1.3 62.5 + - - +
32E THR 3.7 0.2 + - - -
33E GLY* 3.7 8.0 + - - -
34E ALA 4.4 6.0 - - - +
23L SER 5.7 4.5 - - - +
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Residues in contact with ARG 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E GLU 3.0 18.0 + - - +
28E THR* 3.2 5.6 + - - +
30E LYS* 1.3 74.0 - - - +
32E THR* 1.3 56.0 + - - +
33E GLY* 3.1 10.2 + - - -
55N ILE* 5.3 13.5 - - + -
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Residues in contact with THR 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E THR 2.9 17.0 + - - -
29E ALA* 3.9 4.2 + - - -
30E LYS 3.5 0.2 - - - -
31E ARG* 1.3 73.8 - - - +
33E GLY* 1.3 59.4 + - - +
34E ALA* 3.4 5.2 + - - +
80E THR* 5.6 5.9 + - - -
82E LYS* 4.7 14.1 - - - +
83E THR* 4.2 31.8 + - - -
86E ALA* 5.0 6.7 - - - -
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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