Contacts of the helix formed by residues 24 - 36 (chain R) 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 SER 24 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13700 G 2.7 41.1 + - - -
20520 U 5.1 10.3 + - - -
23R MET* 1.3 72.6 - - - +
25R PHE* 1.3 57.5 + - - +
26R LYS 3.1 2.9 + - - -
27R HIS* 2.9 44.4 + - - +
28R SER* 2.9 28.6 + - - -
83R LYS* 5.8 0.2 - - - +
84R ALA* 4.7 1.7 - - - +
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Residues in contact with PHE 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5230 C 3.2 30.3 - - - -
5240 A 3.6 16.8 - - - -
13700 G 4.6 2.0 + - - -
23R MET 3.2 4.0 + - - -
24R SER* 1.3 73.8 - - - +
26R LYS* 1.3 58.1 + - + +
28R SER* 3.2 3.1 + - - -
29R LYS* 3.0 51.8 + - + +
116R ALA* 3.5 12.8 - - + -
117R HIS* 3.3 20.6 - - - -
118R LYS* 3.1 48.9 - - + -
139R PRO* 4.5 9.0 - - + +
141R VAL* 3.8 19.3 - - + -
8806R CL 4.4 17.3 - - + -
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Residues in contact with LYS 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13670 A 5.4 7.7 + - - -
13680 U 4.2 3.8 + - - -
13690 A 2.9 30.5 + - - -
13700 G 2.9 55.4 + - + +
24R SER* 3.5 6.5 - - - +
25R PHE* 1.3 77.3 - - + +
27R HIS* 1.3 65.4 + - + +
29R LYS* 3.5 6.8 + - - +
30R ALA* 3.5 18.4 + - - +
59R PHE* 5.9 0.2 - - - -
62R HIS* 3.4 50.7 + - + +
8806R CL 3.8 27.1 - - + -
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Residues in contact with HIS 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13700 G 3.8 24.9 + + - +
20500 G 6.0 0.4 - - - -
20510 G 3.6 25.8 + - - -
20520 U 5.3 5.8 + - - -
20530 G 5.7 1.8 - - - -
24R SER* 2.9 34.2 + - - +
26R LYS* 1.3 78.8 - - + +
28R SER* 1.3 58.5 + - - +
30R ALA* 3.3 7.2 + - - +
31R ILE* 3.0 34.1 + - - +
59R PHE* 3.8 28.7 - + - -
79R ARG* 5.7 3.7 + - + -
81R PRO* 3.4 23.3 - - + +
84R ALA* 3.9 16.5 - - + +
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Residues in contact with SER 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23R MET* 3.7 25.6 - - - +
24R SER 2.9 17.4 + - - -
25R PHE* 3.3 12.6 - - - -
26R LYS 3.1 0.4 - - - -
27R HIS* 1.3 74.4 - - - +
29R LYS* 1.3 66.9 + - - +
30R ALA 3.0 0.3 + - - -
31R ILE 3.1 1.0 + - - -
32R ALA* 2.8 26.9 + - - +
84R ALA* 4.5 2.4 - - - +
88R PHE* 3.8 18.7 - - - -
116R ALA* 3.5 22.9 - - - -
141R VAL* 4.0 3.7 - - - +
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Residues in contact with LYS 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5230 C 3.7 4.9 + - - -
5240 A 2.6 46.1 + - - +
5250 G 4.7 12.3 + - - +
13670 A 5.5 3.0 + - - -
25R PHE* 3.0 53.5 + - + +
26R LYS* 3.9 4.9 - - - +
27R HIS 3.5 0.4 - - - -
28R SER* 1.3 74.0 - - - +
30R ALA* 1.3 57.2 + - - +
32R ALA* 3.7 4.3 - - - +
33R ARG* 2.9 43.3 + - - +
61R GLN* 3.3 12.0 + - + +
62R HIS* 2.8 39.8 + - + +
116R ALA* 4.1 5.1 - - + +
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Residues in contact with ALA 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26R LYS 3.5 9.9 + - - +
27R HIS 3.3 9.8 + - - +
28R SER 3.0 0.4 - - - -
29R LYS* 1.3 77.8 - - - +
31R ILE* 1.3 67.5 + - - +
33R ARG* 3.4 13.6 - - - +
34R GLU* 2.8 24.4 + - - +
57R VAL* 3.9 12.1 - - + -
58R PRO 3.8 20.9 - - - +
59R PHE* 4.1 15.7 - - + -
60R LYS 5.9 0.4 - - - +
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Residues in contact with ILE 31 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27R HIS 3.0 16.3 + - - +
28R SER 3.8 2.5 - - - +
30R ALA* 1.3 68.3 - - - +
32R ALA* 1.3 73.0 + - - +
34R GLU* 2.9 4.2 + - - -
35R ILE* 2.9 25.0 + - + +
47R LEU* 3.9 27.1 - - + -
57R VAL* 4.2 20.0 - - + -
81R PRO* 4.1 9.0 - - + -
84R ALA* 3.6 18.4 - - + +
85R SER* 3.2 43.1 - - - +
88R PHE* 3.9 24.5 - - + -
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Residues in contact with ALA 32 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5250 G 6.2 2.0 - - - -
28R SER 2.8 21.4 + - - +
29R LYS* 3.7 4.0 - - - +
31R ILE* 1.3 77.5 - - - +
33R ARG* 1.3 65.4 + - - +
35R ILE* 2.7 13.0 + - - +
36R LYS* 3.1 10.8 + - - +
88R PHE* 3.9 16.9 - - + -
114R VAL* 3.9 34.3 - - + +
115R ALA* 4.4 10.1 - - - -
116R ALA 4.5 4.5 - - - +
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Residues in contact with ARG 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120 U 5.0 12.2 + - - -
130 G 5.4 3.0 + - - -
5250 G 3.7 31.7 + - - +
29R LYS* 2.9 34.7 + - - +
30R ALA* 3.4 9.4 - - - +
32R ALA* 1.3 76.7 - - - +
34R GLU* 1.3 66.0 + - + +
35R ILE 3.6 0.2 + - - -
36R LYS* 3.9 17.4 + - - +
58R PRO* 5.6 3.6 - - - -
60R LYS* 4.7 22.4 - - - +
61R GLN* 4.1 40.4 - - - +
114R VAL 5.0 0.6 + - - -
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Residues in contact with GLU 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30R ALA 2.8 20.6 + - - +
31R ILE* 3.4 6.5 - - - +
32R ALA 2.8 4.2 + - - -
33R ARG* 1.3 78.7 - - + +
35R ILE* 1.3 58.9 + - + +
36R LYS 4.6 2.1 - - - +
38R LYS* 3.6 23.0 + - - +
46R TYR* 3.3 36.3 + - + +
57R VAL* 4.5 2.0 - - + -
58R PRO* 3.7 32.8 - - + +
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Residues in contact with ILE 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R ILE* 3.3 11.9 - - + +
32R ALA* 2.7 20.4 + - - +
34R GLU* 1.3 72.6 - - - +
36R LYS* 1.3 67.3 + - - +
37R GLY 3.2 0.5 + - - -
38R LYS* 3.0 31.3 + - + +
43R ALA* 4.6 5.6 - - + -
46R TYR* 4.0 15.0 - - + -
47R LEU* 3.8 28.0 - - + -
88R PHE* 4.1 25.8 - - + -
92R LEU* 4.6 17.0 - - + -
111R ILE* 3.4 27.3 - - + +
114R VAL* 4.5 10.5 - - + -
145R LEU* 5.2 1.8 - - + -
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Residues in contact with LYS 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5250 G 3.4 14.3 + - - +
5260 U 2.7 39.9 + - - +
32R ALA 3.1 10.2 + - - +
33R ARG* 4.1 13.0 - - - +
34R GLU 3.5 3.4 - - - +
35R ILE* 1.3 77.4 - - - +
37R GLY* 1.3 62.2 + - - +
38R LYS* 3.6 2.9 + - - +
111R ILE* 4.0 7.0 - - - +
112R LYS 3.8 16.9 + - - +
113R HIS* 5.2 7.2 - - - +
114R VAL* 3.5 35.0 - - + +
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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