Contacts of the helix formed by residues 43 - 59 (chain Z) 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 GLY 43 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17710 U 3.1 20.2 + - - -
18850 A 3.3 13.3 - - - -
18860 A 3.9 4.7 - - - -
41Z ARG 3.0 7.9 + - - -
42Z TYR* 1.3 82.4 - - - +
44Z ARG* 1.3 70.1 - - - +
45Z VAL 3.8 0.7 - - - -
46Z SER 3.7 1.0 + - - -
47Z ARG* 3.1 25.8 + - - +
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Residues in contact with ARG 44 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17710 U 3.1 66.5 + - - +
17720 C 4.9 4.9 + - - +
18860 A 3.1 21.8 + - - +
18870 U 4.2 27.8 + - - -
43Z GLY* 1.3 73.7 - - - +
45Z VAL* 1.3 58.4 + - + +
47Z ARG* 2.9 8.2 + - - +
48Z ARG* 2.6 40.1 + - + +
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Residues in contact with VAL 45 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18860 A 3.4 14.6 + - - +
18870 U 2.8 32.5 - - - +
168A PRO* 6.3 0.7 - - + -
43Z GLY 3.8 0.4 - - - -
44Z ARG* 1.3 78.3 - - + +
46Z SER* 1.3 66.2 + - - +
48Z ARG* 4.1 11.4 - - - +
49Z ARG* 3.1 58.5 + - + +
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Residues in contact with SER 46 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18470 A 4.1 15.6 + - - -
18480 G 4.6 8.0 - - - -
18850 A 4.3 6.2 + - - -
18860 A 5.2 3.5 - - - -
168A PRO* 3.6 22.7 - - - +
170A VAL* 4.3 9.2 - - - +
42Z TYR* 3.6 32.5 + - - +
43Z GLY 3.7 1.2 + - - -
44Z ARG 3.1 1.4 + - - -
45Z VAL* 1.3 82.8 - - - +
47Z ARG* 1.3 58.8 + - - +
50Z VAL* 2.8 28.2 + - - +
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Residues in contact with ARG 47 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17710 U 2.7 47.5 + - - +
17720 C 3.4 12.6 + - - +
17730 G 3.3 13.1 + - - -
35Z SER* 2.6 48.2 + - - +
38Z PHE* 3.7 14.8 - - + -
39Z GLY 3.8 14.3 + - - -
40Z ALA 4.1 2.2 - - - -
41Z ARG 2.7 42.4 + - - +
42Z TYR* 5.0 2.0 - - + -
43Z GLY* 3.1 40.9 - - - +
44Z ARG* 2.9 10.9 + - - +
46Z SER* 1.3 74.7 - - - +
48Z ARG* 1.3 62.1 + - - +
49Z ARG 3.6 0.2 - - - -
50Z VAL* 3.9 7.4 - - - -
51Z ALA* 3.3 9.5 + - - +
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Residues in contact with ARG 48 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Z ARG* 2.6 26.9 + - - +
45Z VAL* 3.1 10.7 + - - +
47Z ARG* 1.3 72.3 - - - +
49Z ARG* 1.3 64.5 + - - +
50Z VAL 3.2 0.2 - - - -
51Z ALA* 3.1 9.6 - - + +
52Z GLU* 2.9 48.7 + - + +
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Residues in contact with ARG 49 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18490 G 5.3 8.1 + - - -
166A ASP* 4.2 20.0 + - - +
168A PRO* 4.5 12.9 - - + +
45Z VAL* 3.1 40.4 + - + +
48Z ARG* 1.3 77.5 - - + +
50Z VAL* 1.3 58.9 + - - +
52Z GLU* 3.1 13.0 + - - +
53Z ILE* 2.6 52.6 + - + +
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Residues in contact with VAL 50 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LYS* 4.3 15.9 - - - -
168A PRO* 4.2 9.4 - - + -
170A VAL* 3.8 22.9 - - + -
34Z SER 5.5 0.7 - - - +
35Z SER* 4.2 4.3 - - - +
37Z ARG* 3.9 4.9 - - - +
38Z PHE* 3.7 20.6 - - + -
46Z SER 2.8 27.5 + - - +
47Z ARG* 3.9 7.4 - - - +
48Z ARG 3.2 0.4 - - - -
49Z ARG* 1.3 76.3 - - - +
51Z ALA* 1.3 64.1 + - - +
53Z ILE* 4.6 3.6 - - - -
54Z GLU* 2.9 56.1 + - + +
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Residues in contact with ALA 51 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Z SER* 4.3 22.6 + - - +
35Z SER* 4.0 7.6 - - - +
47Z ARG 3.3 12.9 + - - +
48Z ARG* 3.1 13.4 + - + +
49Z ARG 3.1 0.2 - - - -
50Z VAL* 1.3 78.5 - - - +
52Z GLU* 1.3 53.2 + - + +
54Z GLU* 3.9 0.9 - - - +
55Z SER* 2.6 40.5 + - - -
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Residues in contact with GLU 52 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Z ARG* 2.9 47.2 + - + +
49Z ARG* 3.6 14.7 - - - +
51Z ALA* 1.3 74.5 - - + +
53Z ILE* 1.3 55.1 + - + +
55Z SER* 2.7 11.3 + - - -
56Z GLU* 2.7 37.3 + - - +
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Residues in contact with ILE 53 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASP* 3.4 35.7 - - + +
167A LYS* 3.4 28.9 - - + +
49Z ARG* 2.6 34.2 + - + +
50Z VAL* 4.1 2.9 - - - +
52Z GLU* 1.3 73.5 - - + +
54Z GLU* 1.3 58.8 + - + +
56Z GLU* 3.5 7.3 + - - +
57Z MET* 2.8 28.7 + - + +
93Z TYR* 3.6 39.4 - - + +
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Residues in contact with GLU 54 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16510 C 3.6 14.7 + - - -
167A LYS* 3.5 23.6 + - - -
34Z SER* 4.5 12.0 - - - +
37Z ARG* 2.7 33.6 + - - -
50Z VAL* 2.9 34.2 + - + +
51Z ALA* 4.1 1.6 - - - +
53Z ILE* 1.3 73.8 - - + +
55Z SER* 1.3 57.1 + - - +
57Z MET* 3.2 21.7 - - + +
58Z ASN* 2.7 48.5 + - - +
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Residues in contact with SER 55 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7980 G 5.4 4.0 + - - -
34Z SER* 5.1 7.1 + - - -
51Z ALA 2.6 27.4 + - - -
52Z GLU* 2.7 9.3 + - - -
54Z GLU* 1.3 71.7 - - - +
56Z GLU* 1.3 60.8 + - - -
58Z ASN* 3.5 7.6 + - - +
59Z GLU* 3.2 21.8 + - - +
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Residues in contact with GLU 56 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Z GLU 2.7 19.2 + - - +
53Z ILE* 3.8 6.8 - - - +
55Z SER* 1.3 72.5 - - - +
57Z MET* 1.3 63.6 + - - +
59Z GLU* 3.2 32.2 - - - +
61Z HIS* 3.1 23.3 - - + -
94Z LYS* 2.6 50.2 + - + +
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Residues in contact with MET 57 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16510 C 4.4 10.5 - - - +
16520 C 5.9 0.2 - - - +
167A LYS* 5.2 2.5 - - - +
53Z ILE* 2.8 21.3 + - + +
54Z GLU* 3.2 45.1 - - + +
56Z GLU* 1.3 77.8 - - - +
58Z ASN* 1.3 65.8 + - - +
61Z HIS* 2.8 22.3 + - - -
72Z ASP* 6.2 0.2 - - - -
73Z ARG* 3.9 38.7 + - + +
79Z TRP* 3.9 12.4 - - + -
93Z TYR* 3.3 41.3 - - + +
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Residues in contact with ASN 58 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7970 A 4.0 17.8 + - - +
7980 G 5.4 11.7 - - - -
16500 C 4.3 14.0 + - - -
34Z SER* 5.2 2.2 + - - -
54Z GLU* 2.7 38.9 + - - +
55Z SER* 4.1 6.0 - - - +
57Z MET* 1.3 81.2 - - - +
59Z GLU* 1.3 71.7 + - - +
60Z ASP* 4.5 3.3 - - - +
72Z ASP* 5.0 4.9 - - - +
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Residues in contact with GLU 59 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Z SER 3.2 13.2 + - - +
56Z GLU* 3.2 40.5 + - - +
58Z ASN* 1.3 89.3 - - - +
60Z ASP* 1.3 66.2 + - - +
61Z HIS* 3.2 27.4 + - + -
71Z VAL 4.1 3.5 - - - +
72Z ASP* 4.9 1.6 - - - +
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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