Contacts of the helix formed by residues 19 - 31 (chain N) in PDB entry 4ADV
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 TYR 19 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1008A U 4.6 9.8 + - - -
15N LEU* 3.3 22.6 + - + +
17N ASP 2.8 2.7 - - - +
18N LYS* 1.3 88.9 - - + +
20N PHE* 1.3 64.6 + - + +
21N ALA 3.0 2.0 + - - -
22N LYS* 2.8 6.1 + - - +
23N ARG* 2.6 84.8 + - + +
50N LEU* 4.2 24.4 - - + +
51N PRO* 5.2 5.4 - - + -
54N SER* 3.6 16.2 - - - +
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Residues in contact with PHE 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1317A C 3.0 46.4 - - - -
15N LEU 4.4 1.0 + - - -
16N ALA 4.0 8.5 - - - +
19N TYR* 1.3 79.4 - - + +
21N ALA* 1.3 55.8 + - - +
22N LYS* 2.6 14.7 + - - -
23N ARG* 3.3 0.4 + - + -
24N ALA* 3.0 44.7 + - + +
25N GLU* 3.8 4.0 + - - +
27N LYS* 4.8 0.4 - - - -
48N GLN* 3.5 31.4 - - - -
50N LEU* 5.4 4.0 - - + -
51N PRO* 3.6 22.9 - - + -
54N SER* 3.0 37.2 + - - +
55N SER* 4.5 1.3 - - - -
56N PRO* 4.0 13.0 - - + -
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Residues in contact with ALA 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1257A A 5.9 7.7 - - - +
16N ALA 3.3 9.5 + - - +
17N ASP* 3.3 38.8 - - + +
19N TYR 3.0 2.8 + - - -
20N PHE* 1.3 74.5 - - - +
22N LYS* 1.3 58.8 + - + +
25N GLU* 3.6 14.6 - - - +
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Residues in contact with LYS 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N ASP 4.0 4.9 + - - +
18N LYS 5.9 0.9 - - - +
19N TYR 2.8 4.1 + - - +
20N PHE 2.6 4.7 + - - -
21N ALA* 1.3 76.1 - - + +
23N ARG* 1.3 61.5 + - - +
25N GLU* 2.6 37.1 - - - +
26N LEU* 4.4 1.7 + - - +
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Residues in contact with ARG 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008A U 2.7 32.9 + - - -
1009A U 4.2 15.8 + - - -
18N LYS 4.8 3.4 - - - +
19N TYR* 2.6 59.7 + - + +
22N LYS* 1.3 70.8 - - - +
24N ALA* 1.3 64.2 + - - +
25N GLU 3.0 2.0 - - - -
26N LEU* 2.9 32.6 + - + +
27N LYS* 3.8 2.4 + - - +
50N LEU* 3.6 33.6 - - + +
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Residues in contact with ALA 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20N PHE* 3.0 52.1 + - + +
23N ARG* 1.3 79.2 - - - +
25N GLU* 1.3 62.0 + - + +
26N LEU 3.0 0.3 + - - -
27N LYS* 2.9 35.4 + - - +
28N ALA* 2.8 21.5 + - - +
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Residues in contact with GLU 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N PHE 4.1 2.2 - - - +
21N ALA 3.6 11.1 - - - +
22N LYS* 2.6 50.8 - - - +
24N ALA* 1.3 78.4 - - - +
26N LEU* 1.3 60.5 + - - +
28N ALA* 3.3 15.7 + - - +
29N ILE* 3.0 20.1 - - - +
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Residues in contact with LEU 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22N LYS 4.4 1.3 + - - +
23N ARG* 2.9 23.2 + - + +
25N GLU* 1.3 77.6 - - - +
27N LYS* 1.3 60.2 + - - +
29N ILE* 3.0 33.4 - - + +
30N ILE* 3.1 27.4 - - + +
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Residues in contact with LYS 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1317A C 4.7 7.3 + - - -
20N PHE* 4.8 1.3 - - + -
23N ARG 3.8 1.1 + - - +
24N ALA* 2.9 40.8 + - - +
26N LEU* 1.3 76.7 - - + +
28N ALA* 1.3 73.4 + - - +
29N ILE 3.0 5.8 - - - -
30N ILE* 3.3 1.9 + - - -
31N SER* 2.8 42.2 + - - +
44N VAL* 3.5 30.9 - - + +
47N LEU* 6.1 1.8 - - + -
48N GLN* 3.2 47.8 - - + +
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Residues in contact with ALA 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N ALA 2.8 16.9 + - - +
25N GLU* 3.3 14.8 - - - +
26N LEU 3.1 0.2 - - - -
27N LYS* 1.3 95.3 - - - +
29N ILE* 1.3 56.6 + - - +
31N SER* 3.9 4.6 - - - +
32N ASP* 3.0 28.1 + - - +
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Residues in contact with ILE 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N GLU 3.0 14.8 - - - +
26N LEU* 3.0 30.1 - - + +
27N LYS 3.0 0.2 - - - -
28N ALA* 1.3 75.1 - - - +
30N ILE* 1.3 62.4 + - + +
32N ASP 2.7 30.1 + - - +
34N ASN* 2.9 41.0 - - + +
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Residues in contact with ILE 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N LEU* 3.1 34.1 - - + +
27N LYS* 4.0 7.6 - - - -
29N ILE* 1.3 79.8 - - + +
31N SER* 1.3 52.4 + - - +
32N ASP 2.6 20.5 + - - +
34N ASN* 5.6 0.7 - - - -
40N ARG 2.7 29.8 + - - +
41N TRP* 3.1 47.6 - - + +
44N VAL* 3.4 23.3 - - + -
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Residues in contact with SER 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27N LYS* 2.8 31.1 + - - +
28N ALA* 3.9 5.1 - - - +
30N ILE* 1.3 68.4 - - - +
32N ASP* 1.3 59.1 + - - +
40N ARG* 3.2 26.3 + - - +
41N TRP 5.1 0.3 + - - -
44N VAL* 3.7 14.6 + - - +
45N LEU* 4.1 18.0 + - - +
48N GLN* 5.6 2.5 - - - +
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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