Contacts of the helix formed by residues 22 - 39 (chain M) 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 LYS 22 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M LEU* 5.3 7.5 + - + +
19M PRO 5.2 2.3 + - - +
20M ARG 3.3 0.4 - - - -
21M GLU* 1.3 77.5 - - - +
23M ILE* 1.3 60.3 + - + +
24M PHE 3.4 0.7 - - - -
25M GLU* 3.4 9.4 + - - +
26M ALA* 3.0 22.7 + - - +
117M LYS* 5.6 7.1 - - + +
121M ALA* 6.2 4.3 - - + -
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Residues in contact with ILE 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M SER* 6.2 2.5 - - - -
19M PRO 5.0 7.1 + - - +
20M ARG* 3.3 8.7 + - - +
22M LYS* 1.3 76.6 - - + +
24M PHE* 1.3 60.5 + - - +
26M ALA* 3.6 12.9 - - + +
27M LEU* 2.9 29.6 + - - +
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Residues in contact with PHE 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M ARG 2.9 17.3 + - - +
21M GLU* 4.3 11.2 - - - +
23M ILE* 1.3 75.7 - - - +
25M GLU* 1.3 57.8 + - - +
27M LEU* 3.1 4.5 + - - +
28M GLU* 2.9 26.3 + - - +
49M ILE* 5.9 5.6 - - - +
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Residues in contact with GLU 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M GLU 4.8 5.1 + - - +
22M LYS* 3.4 11.8 + - - +
23M ILE 3.4 0.2 - - - -
24M PHE* 1.3 78.8 - - - +
26M ALA* 1.3 57.6 + - - +
28M GLU* 3.5 9.2 - - - +
29M SER* 3.0 31.4 + - - -
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Residues in contact with ALA 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M LYS 3.0 16.5 + - - +
23M ILE* 3.6 14.6 - - + +
24M PHE 3.2 0.2 - - - -
25M GLU* 1.3 77.3 - - - +
27M LEU* 1.3 50.2 + - - +
29M SER* 4.0 2.4 - - - -
30M ALA* 2.6 38.3 + - - +
113M VAL* 5.2 9.8 - - + +
114M ILE* 5.9 2.2 - - - -
117M LYS* 4.6 19.5 - - + -
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Residues in contact with LEU 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M ILE 2.9 17.4 + - - +
24M PHE* 3.8 4.3 - - - +
26M ALA* 1.3 74.4 - - - +
28M GLU* 1.3 61.0 + - - +
30M ALA* 3.7 6.7 - - - -
31M LEU* 3.0 31.6 + - + +
47M VAL* 5.5 3.2 - - - +
49M ILE* 5.1 14.6 - - + -
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Residues in contact with GLU 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M PHE 2.9 14.0 + - - +
25M GLU* 3.5 13.5 - - - +
27M LEU* 1.3 77.1 - - - +
29M SER* 1.3 57.6 + - - +
32M ALA* 2.8 34.3 + - - +
46M ARG* 5.9 2.6 - - + +
47M VAL* 5.6 16.5 + - - +
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Residues in contact with SER 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M GLU 3.0 15.7 + - - -
26M ALA* 4.7 2.2 - - - -
28M GLU* 1.3 75.8 - - - +
30M ALA* 1.3 63.1 + - - +
32M ALA* 4.1 5.2 - - - -
33M THR* 3.5 21.1 + - - -
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Residues in contact with ALA 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M ALA 2.6 25.2 + - - +
27M LEU* 3.8 5.4 - - - -
28M GLU 3.2 0.2 - - - -
29M SER* 1.3 80.5 - - - +
31M LEU* 1.3 63.0 + - - +
32M ALA 3.6 0.2 + - - -
33M THR* 3.6 8.5 + - - -
34M ALA* 3.7 10.4 + - - +
109M THR* 5.4 5.7 - - - +
110M ALA* 5.5 6.5 - - - +
113M VAL* 4.6 18.6 - - + -
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Residues in contact with LEU 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M LEU* 3.0 17.9 + - + +
30M ALA* 1.3 76.3 - - + +
32M ALA* 1.3 64.3 + - - +
33M THR 3.2 0.2 - - - -
34M ALA* 3.4 19.1 + - - +
35M THR* 3.9 7.6 + - - -
47M VAL* 5.3 12.1 - - + -
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Residues in contact with ALA 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M GLU 2.8 23.9 + - - +
29M SER* 4.3 4.5 - - - -
31M LEU* 1.3 79.4 - - - +
33M THR* 1.3 59.3 + - - +
35M THR* 4.1 7.4 + - - -
36M LYS* 4.2 7.6 + - - +
43M ILE 5.2 2.8 - - - +
44M ASP* 5.9 0.2 - - - -
45M VAL* 3.4 39.2 + - - +
46M ARG* 5.2 2.5 - - - -
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Residues in contact with THR 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M SER 3.5 19.2 + - - -
30M ALA* 3.6 4.7 + - - -
31M LEU 3.2 0.6 - - - -
32M ALA* 1.3 77.9 - - - +
34M ALA* 1.3 64.5 + - - +
35M THR 3.4 0.2 - - - -
36M LYS* 3.3 21.3 + - - +
37M LYS* 4.4 2.6 + - - +
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Residues in contact with ALA 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M ALA 3.7 9.6 + - - +
31M LEU* 3.4 13.4 + - - +
32M ALA 3.3 1.2 - - - -
33M THR* 1.3 79.8 - - - +
35M THR* 1.3 59.1 + - - +
36M LYS 3.2 0.9 + - - -
37M LYS* 3.8 10.7 + - - +
38M LYS* 4.3 7.3 + - - +
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Residues in contact with THR 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M LEU 3.9 7.9 + - - -
32M ALA 4.1 4.2 + - - -
33M THR 3.4 0.4 - - - -
34M ALA* 1.3 75.6 - - - +
36M LYS* 1.3 62.5 + - - +
37M LYS 3.3 1.7 + - - -
38M LYS* 4.2 7.5 - - - +
39M TYR* 3.9 19.8 + - - +
43M ILE* 4.7 11.2 - - - +
45M VAL* 5.3 12.3 - - - -
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Residues in contact with LYS 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M ALA 4.2 6.4 + - - +
33M THR* 3.3 19.6 + - - +
34M ALA 3.2 1.2 - - - -
35M THR* 1.3 78.5 - - - +
37M LYS* 1.3 58.8 + - + +
38M LYS 3.6 0.2 - - - -
39M TYR 3.3 17.1 - - - +
40M GLU* 4.8 2.4 - - - -
43M ILE* 4.4 14.7 + - - +
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Residues in contact with LYS 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M THR 4.4 2.7 + - - +
34M ALA 3.8 7.9 + - - +
35M THR 3.3 0.6 - - - -
36M LYS* 1.3 79.8 - - + +
38M LYS* 1.3 63.1 + - - +
39M TYR 3.4 3.5 + - - -
40M GLU* 4.7 8.4 - - - +
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Residues in contact with LYS 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M ALA 4.3 7.7 + - - +
35M THR* 4.0 8.3 + - - +
36M LYS 3.6 0.2 - - - -
37M LYS* 1.3 81.4 - - - +
39M TYR* 1.3 58.1 + - - +
40M GLU* 4.0 2.4 + - - +
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Residues in contact with TYR 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M THR 3.9 12.0 + - - +
36M LYS 3.3 15.8 - - - +
38M LYS* 1.3 76.6 - - + +
40M GLU* 1.3 59.4 + - - +
41M GLN 3.2 9.6 + - - -
42M GLU 4.8 0.2 + - - -
43M ILE* 4.7 20.3 + - + +
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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