Contacts of the helix formed by residues 40 - 63 (chain Z) in PDB entry 5GAG
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 40 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A C 3.0 47.7 + - - +
94A A 4.3 6.0 - - - -
95A A 3.3 18.6 + - - -
37Z LEU* 4.6 2.9 - - - -
38Z GLN 3.2 7.8 + - - -
39Z GLN* 1.3 69.6 - - - +
41Z HIS* 1.3 67.1 + - - +
42Z LEU 2.9 5.2 - - - -
43Z LEU* 2.9 33.4 + - - +
44Z LYS 3.8 1.4 + - - -
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Residues in contact with HIS 41 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A C 5.8 0.7 - - - -
95A A 3.4 16.1 + - + +
96A C 3.3 50.7 + - - +
97A C 5.1 1.8 + - - -
39Z GLN* 3.2 43.3 + - + +
40Z SER* 1.3 83.9 + - - +
42Z LEU* 1.3 82.4 + - + +
44Z LYS* 3.3 9.5 + - - +
45Z GLN* 3.0 55.0 + - + +
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Residues in contact with LEU 42 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Z LEU* 3.5 32.1 - - + -
37Z LEU* 4.3 4.5 - - + -
39Z GLN* 3.3 40.4 - - + +
41Z HIS* 1.3 94.1 + - + +
43Z LEU* 1.3 66.7 + - + +
45Z GLN* 3.0 31.1 + - - +
46Z VAL* 3.1 20.2 + - + +
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Residues in contact with LEU 43 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A C 3.4 40.8 - - - +
25Z GLN* 5.5 1.5 - - + +
28Z LEU* 3.6 36.3 - - + +
29Z ARG* 4.6 9.6 - - + +
32Z ALA* 4.6 14.8 - - + -
37Z LEU* 4.1 11.7 - - + -
40Z SER* 2.9 18.3 + - - +
42Z LEU* 1.3 74.1 - - - +
44Z LYS* 1.3 64.1 + - - +
46Z VAL* 2.9 16.5 + - - +
47Z ARG* 3.0 19.5 + - - +
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Residues in contact with LYS 44 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A G 4.8 1.6 - - - -
61A C 3.4 26.9 - - - +
74A A 5.9 3.2 - - - -
75A G 5.5 2.8 + - - -
87A U 2.6 39.6 + - - +
40Z SER 3.8 1.2 + - - +
41Z HIS* 3.3 11.4 + - - +
43Z LEU* 1.3 78.9 - - - +
45Z GLN* 1.3 63.6 + - - +
47Z ARG* 3.4 31.9 - - - +
48Z ARG* 3.2 52.0 + - - +
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Residues in contact with GLN 45 (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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96A C 4.9 1.0 + - - -
97A C 5.1 10.5 + - - -
41Z HIS* 3.0 47.2 + - + +
42Z LEU* 3.0 31.1 + - - +
44Z LYS* 1.3 77.8 - - - +
46Z VAL* 1.3 64.7 + - + +
48Z ARG* 3.2 6.4 + - - +
49Z ASP* 2.8 37.1 + - - +
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Residues in contact with VAL 46 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Z LEU* 3.5 28.5 - - + +
24Z GLU* 4.8 5.8 - - + +
25Z GLN* 3.6 33.9 - - + +
28Z LEU* 4.0 18.4 - - + -
42Z LEU* 3.2 20.4 - - + +
43Z LEU* 2.9 4.9 + - - +
45Z GLN* 1.3 78.8 - - + +
47Z ARG* 1.3 63.6 + - - +
49Z ASP* 2.9 20.5 + - - +
50Z VAL* 2.9 15.3 + - + +
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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
----------------------------------------------------------
59A U 5.5 2.1 + - - -
60A G 3.9 25.0 + - - -
61A C 3.0 25.8 + - - -
73A A 3.7 38.3 + - - +
74A A 3.7 11.5 + - - -
25Z GLN* 4.1 26.6 - - + +
43Z LEU* 3.0 9.4 + - - +
44Z LYS* 3.4 36.8 - - - +
46Z VAL* 1.3 81.2 - - - +
48Z ARG* 1.3 78.9 + - - +
50Z VAL* 3.3 18.7 - - - +
51Z ALA* 3.5 3.1 + - - +
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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
----------------------------------------------------------
73A A 4.6 3.7 + - - -
74A A 3.0 35.6 + - - -
75A G 2.9 53.7 + - - +
76A C 3.4 30.2 + - - +
44Z LYS* 3.2 46.8 + - - +
45Z GLN* 3.2 5.2 + - - +
47Z ARG* 1.3 91.2 - - - +
49Z ASP* 1.3 63.7 + - - +
51Z ALA* 2.9 24.0 + - - +
52Z ARG* 3.2 20.4 + - - +
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Residues in contact with ASP 49 (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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2Z LYS* 2.7 32.9 + - - +
6Z LEU* 5.4 1.0 - - + +
21Z LEU* 3.6 19.5 - - + +
45Z GLN* 2.8 30.8 + - - +
46Z VAL* 2.9 11.3 + - - +
48Z ARG* 1.3 73.2 - - - +
50Z VAL* 1.3 67.5 + - - +
52Z ARG* 2.9 31.4 + - - +
53Z VAL* 3.1 14.6 + - - +
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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
----------------------------------------------------------
72A U 4.4 11.9 - - - +
73A A 5.9 0.2 - - - +
18Z LEU* 4.2 10.1 - - + -
21Z LEU* 3.4 22.2 - - + +
22Z LEU* 3.8 26.7 - - + -
25Z GLN* 4.4 9.4 - - - +
46Z VAL* 2.9 20.8 + - + +
47Z ARG* 3.3 11.0 - - - +
49Z ASP* 1.3 75.4 - - - +
51Z ALA* 1.3 64.3 + - - +
53Z VAL* 3.0 16.5 + - - +
54Z LYS* 3.0 33.0 + - + +
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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
----------------------------------------------------------
72A U 3.6 40.8 - - - +
73A A 4.6 1.8 - - - +
75A G 5.5 2.0 - - - +
76A C 3.8 20.0 - - - +
47Z ARG 3.5 2.7 + - - +
48Z ARG* 2.9 15.7 + - - +
50Z VAL* 1.3 75.5 - - - +
52Z ARG* 1.3 68.5 - - - +
54Z LYS* 3.0 3.2 + - - +
55Z THR* 2.7 28.2 + - - -
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Residues in contact with ARG 52 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A C 3.2 31.3 + - - +
77A G 2.5 39.8 + - - +
2Z LYS* 3.6 16.8 - - - +
3Z ALA* 3.7 28.0 - - + +
6Z LEU* 4.2 14.1 - - + -
48Z ARG* 3.2 33.0 + - - +
49Z ASP* 2.9 34.2 + - - +
51Z ALA* 1.3 81.7 - - - +
53Z VAL* 1.3 63.3 + - - +
55Z THR* 3.0 10.2 + - - -
56Z LEU* 3.0 20.7 + - + +
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Residues in contact with VAL 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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6Z LEU* 4.7 14.6 - - + -
14Z LEU* 4.0 19.2 - - + +
17Z GLU* 5.0 10.1 - - + -
18Z LEU* 4.0 34.1 - - + -
21Z LEU* 3.9 18.6 - - + -
49Z ASP 3.4 12.6 - - - +
50Z VAL 3.0 8.0 + - - +
52Z ARG* 1.3 76.2 - - - +
54Z LYS* 1.3 64.0 + - - +
56Z LEU* 2.9 20.2 + - - +
57Z LEU* 3.0 23.3 + - + +
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Residues in contact with LYS 54 (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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72A U 3.3 70.1 + - + +
5U GLU* 2.8 32.1 + - - -
18Z LEU* 3.9 25.4 - - + +
22Z LEU* 5.9 0.4 - - - +
50Z VAL* 3.0 24.3 + - + +
51Z ALA 3.0 4.2 + - - +
53Z VAL* 1.3 78.6 - - - +
55Z THR* 1.3 59.5 + - - +
57Z LEU* 3.0 12.1 + - + +
58Z ASN* 2.8 30.8 + - - +
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Residues in contact with THR 55 (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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72A U 3.6 22.6 + - - +
76A C 3.1 35.5 + - - +
77A G 4.3 9.0 - - - +
110A G 4.0 11.0 - - - +
111A A 3.8 18.6 - - - +
51Z ALA 2.7 20.0 + - - -
52Z ARG 3.5 6.1 - - - -
54Z LYS* 1.3 77.7 - - - +
56Z LEU* 1.3 64.2 + - - +
58Z ASN* 3.9 2.9 - - - +
59Z GLU* 3.4 24.9 + - - +
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Residues in contact with LEU 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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77A G 4.8 10.8 - - - -
3Z ALA* 4.4 6.5 - - - +
6Z LEU* 3.5 49.1 - - + +
7Z ARG* 3.7 35.4 - - + +
14Z LEU* 3.8 13.0 - - + -
52Z ARG* 3.0 17.0 + - + +
53Z VAL* 2.9 8.8 + - - +
55Z THR* 1.3 78.2 - - - +
57Z LEU* 1.3 65.2 + - - +
59Z GLU* 3.0 31.3 + - - +
60Z LYS* 3.0 23.5 + - - +
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Residues in contact with LEU 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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11Z VAL* 4.0 14.6 - - + +
14Z LEU* 3.5 31.9 - - + -
15Z ASN* 3.6 35.7 - - - +
18Z LEU* 3.8 22.7 - - + -
53Z VAL* 3.0 21.3 + - + +
54Z LYS* 3.3 11.0 - - + +
56Z LEU* 1.3 73.2 - - - +
58Z ASN* 1.3 64.1 + - - +
60Z LYS* 3.0 18.5 + - + +
61Z ALA* 3.0 13.8 + - - +
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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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72A U 3.7 24.2 + - - +
111A A 3.3 27.1 + - - +
112A U 3.7 15.0 + - - -
54Z LYS 2.8 14.7 + - - +
55Z THR 3.9 5.6 - - - +
57Z LEU* 1.3 76.6 - - - +
59Z GLU* 1.3 57.3 + - - +
61Z ALA* 2.9 23.6 + - - +
62Z GLY* 2.9 13.5 + - - -
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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
----------------------------------------------------------
77A G 3.8 15.0 + - - -
111A A 6.4 2.9 - - - -
7Z ARG* 3.8 22.0 + - - +
55Z THR* 3.4 17.1 + - - +
56Z LEU* 3.0 28.0 + - + +
58Z ASN* 1.3 79.1 - - - +
60Z LYS* 1.3 63.8 + - + +
62Z GLY* 4.2 2.5 - - - +
63Z ALA* 3.1 26.6 + - - +
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Residues in contact with LYS 60 (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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6Z LEU 4.9 1.8 - - - -
7Z ARG* 3.4 27.7 + - - +
9Z LYS 3.7 20.6 + - - +
10Z SER* 5.0 1.0 - - - +
11Z VAL* 4.2 28.3 - - + +
14Z LEU* 4.0 23.8 - - + -
56Z LEU* 3.0 18.7 + - - +
57Z LEU* 3.0 13.0 + - + +
59Z GLU* 1.3 83.9 - - + +
61Z ALA* 1.3 58.0 + - - +
63Z ALA* 3.7 17.4 - - - +
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Residues in contact with ALA 61 (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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57Z LEU 3.0 10.1 + - - +
58Z ASN* 2.9 14.0 + - - +
60Z LYS* 1.3 78.4 - - - +
62Z GLY* 1.3 62.3 + - - +
63Z ALA* 4.8 1.0 - - - +
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Residues in contact with GLY 62 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Z ASN 2.9 13.2 + - - -
59Z GLU* 4.8 0.9 - - - -
61Z ALA* 1.3 78.8 - - - +
63Z ALA* 1.3 60.2 + - - +
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Residues in contact with ALA 63 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59Z GLU* 3.1 24.2 + - - +
60Z LYS* 3.7 18.1 - - - +
61Z ALA 4.9 1.2 - - - +
62Z GLY* 1.3 77.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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