Contacts of the helix formed by residues 17 - 32 (chain M) in PDB entry 3CME
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 17 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11M ALA 5.3 1.0 - - - +
14M ASN* 3.1 33.8 + - + +
15M PRO 3.6 0.6 - - - -
16M GLY* 1.3 86.7 - - - +
18M GLY* 1.3 69.0 + - - +
19M GLN 3.8 0.3 + - - -
20M LEU* 3.9 6.4 + - - +
21M ALA* 3.6 8.3 + - - +
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Residues in contact with GLY 18 (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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17M ASP* 1.3 73.5 - - - +
19M GLN* 1.3 67.5 + - - +
21M ALA* 3.0 19.3 + - - +
22M GLU* 3.5 3.6 + - - +
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Residues in contact with GLN 19 (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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2F VAL* 3.4 33.9 + - + +
3F TYR* 3.5 19.6 - - - +
61F MET* 2.9 52.9 + - - +
64F PRO* 6.0 1.0 - - - +
18M GLY* 1.3 68.2 - - - -
20M LEU* 1.3 53.9 + - - +
22M GLU* 2.7 14.2 + - - +
23M LEU* 2.5 36.1 + - - +
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Residues in contact with LEU 20 (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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58F GLU* 2.9 30.1 - - + +
61F MET* 4.3 8.9 - - + -
11M ALA* 3.9 10.3 - - + +
12M TRP* 3.5 46.9 - - + +
15M PRO* 3.5 26.2 - - + +
17M ASP 3.9 8.0 + - - +
18M GLY 3.3 0.6 - - - -
19M GLN* 1.3 77.5 - - - +
21M ALA* 1.3 56.6 + - - +
23M LEU* 3.8 9.2 - - + -
24M GLN* 2.7 45.9 + - + +
27M ARG* 3.8 13.5 - - - +
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Residues in contact with ALA 21 (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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15M PRO 3.8 11.6 + - - -
16M GLY* 3.5 28.9 - - - +
17M ASP* 3.6 5.3 + - - +
18M GLY 3.0 17.3 + - - +
20M LEU* 1.3 78.6 - - - +
22M GLU* 1.3 59.7 + - - +
24M GLN* 4.1 2.8 - - - +
25M TRP* 3.3 19.2 + - - +
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Residues in contact with GLU 22 (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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2F VAL* 2.9 33.4 - - - +
18M GLY 3.5 1.5 + - - +
19M GLN* 2.7 19.1 + - - +
21M ALA* 1.3 72.4 - - - +
23M LEU* 1.3 65.5 + - - +
24M GLN 3.1 1.8 - - - -
25M TRP* 3.1 11.0 + - + +
26M GLN* 3.0 52.3 + - + +
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Residues in contact with LEU 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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2F VAL* 4.4 12.0 - - + +
57F GLU* 3.6 40.2 - - + +
58F GLU* 3.2 14.6 - - - +
61F MET* 3.9 19.7 - - - -
19M GLN 2.5 24.5 + - - +
20M LEU* 3.6 10.3 - - + +
22M GLU* 1.3 73.7 - - - +
24M GLN* 1.3 56.2 + - - +
26M GLN* 3.5 12.2 + - + +
27M ARG* 3.0 77.6 + - + +
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Residues in contact with GLN 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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12M TRP* 3.7 10.5 - - + -
15M PRO* 4.4 11.9 - - + +
20M LEU* 2.7 33.6 + - + +
21M ALA 4.1 3.1 - - - +
23M LEU* 1.3 72.4 - - - +
25M TRP* 1.3 64.5 + - - +
26M GLN 3.2 0.2 + - - -
27M ARG* 2.5 55.1 + - - +
28M GLN* 3.2 48.4 + - - +
31M TRP* 4.3 5.4 - - - -
120M VAL 3.1 24.6 - - - +
121M GLY* 4.2 3.3 - - - -
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Residues in contact with TRP 25 (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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21330 U 4.0 26.8 + - - -
21340 G 5.7 3.9 + - - -
22430 C 3.5 45.3 + + - -
22440 A 3.3 44.7 + - - -
22580 A 5.5 0.8 + - - -
21M ALA 3.3 13.1 + - - +
22M GLU* 3.1 14.0 + - + +
24M GLN* 1.3 80.1 - - - +
26M GLN* 1.3 77.8 + - + +
28M GLN* 4.9 5.2 - - - +
29M GLN* 3.1 46.7 + - - +
32M ARG* 5.3 1.8 + - - +
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Residues in contact with GLN 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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1F PRO* 5.8 1.6 - - - +
2F VAL* 3.6 19.6 - - - +
57F GLU* 4.7 4.0 - - - +
22M GLU* 3.0 43.5 + - + +
23M LEU* 3.8 10.0 - - + +
25M TRP* 1.3 90.2 - - + +
27M ARG* 1.3 67.6 + - + +
29M GLN* 3.3 26.0 - - - +
30M GLU* 4.1 9.1 + - - +
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Residues in contact with ARG 27 (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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55F GLN* 5.7 2.8 - - - +
56F PRO* 4.2 5.1 - - - +
57F GLU 4.6 0.4 - - - +
58F GLU* 2.3 47.6 + - - -
12M TRP* 3.3 17.0 - - - -
20M LEU* 3.8 1.2 - - - +
23M LEU* 3.0 48.5 + - + +
24M GLN* 2.5 42.3 + - - +
26M GLN* 1.3 76.4 - - - +
28M GLN* 1.3 53.7 + - + +
30M GLU* 2.5 42.4 + - - +
31M TRP* 3.1 34.4 + - + +
44M THR* 3.5 14.9 - - - +
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Residues in contact with GLN 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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21320 C 5.6 0.5 - - - +
21330 U 5.4 2.9 + - - -
24M GLN* 3.2 38.3 + - - +
25M TRP* 4.9 3.0 - - - +
27M ARG* 1.3 79.2 - - + +
29M GLN* 1.3 63.5 + - - +
31M TRP* 3.5 18.4 - - + -
32M ARG* 2.8 61.9 + - - +
120M VAL 4.9 0.4 + - - -
121M GLY* 4.8 0.2 - - - -
122M GLN 3.7 24.0 + - - +
123M ASP* 3.9 5.7 - - - +
128M TRP* 3.5 28.6 - - + -
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Residues in contact with GLN 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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22440 A 3.3 38.7 + - - +
22450 C 3.9 18.4 + - - +
25M TRP* 3.1 56.3 + - - +
26M GLN* 3.3 13.0 - - - +
27M ARG 2.8 2.8 + - - -
28M GLN* 1.3 76.3 - - - +
30M GLU* 1.3 56.0 + - + +
32M ARG* 3.8 8.1 + - - +
33M ASN* 2.8 29.6 + - - -
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Residues in contact with GLU 30 (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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26M GLN* 4.4 9.9 - - - +
27M ARG* 2.5 20.6 + - - +
29M GLN* 1.3 71.4 - - + +
31M TRP* 1.3 60.8 + - + +
32M ARG 3.2 1.8 - - - -
33M ASN* 2.9 22.7 + - - +
34M GLU* 2.8 29.4 + - - +
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Residues in contact with TRP 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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24M GLN* 4.3 15.0 - - - -
27M ARG* 3.1 34.1 + - + +
28M GLN* 3.0 22.8 + - + +
30M GLU* 1.3 75.6 - - + +
32M ARG* 1.3 57.4 + - - +
33M ASN 2.9 4.7 - - - -
34M GLU* 2.9 37.5 + - - +
35M GLY 4.8 1.7 - - - +
44M THR* 4.4 9.6 - - + -
64M ARG* 2.9 48.1 - - - +
120M VAL* 3.3 50.9 - - + -
128M TRP* 3.4 47.4 + + + +
130M GLU* 4.6 0.7 - - - -
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Residues in contact with ARG 32 (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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21320 C 5.0 5.6 + - - -
21330 U 5.3 3.8 + - - -
22440 A 3.0 24.6 + - - -
22450 C 2.7 46.8 + - - +
25M TRP* 5.3 2.6 + - - +
28M GLN* 2.8 53.3 + - - +
29M GLN* 4.0 12.4 - - - +
31M TRP* 1.3 75.1 - - - +
33M ASN* 1.3 63.5 + - - +
34M GLU 3.4 3.5 - - - +
123M ASP* 3.4 24.2 + - - +
126M GLN* 3.9 14.4 - - - +
128M TRP* 3.7 17.7 - - + -
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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