Contacts of the helix formed by residues 16 - 27 (chain J) in PDB entry 6CNB
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 16 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188C ASP* 4.0 14.5 - - + +
190C ASP* 2.9 35.7 + - + +
191C ILE* 3.9 7.7 - - + +
192C LEU* 5.0 1.9 - - - +
13J VAL* 3.1 23.1 - - - +
14J VAL 3.2 2.6 - - - +
15J GLY* 1.3 73.5 - - - +
17J LYS* 1.3 112.7 + - + +
18J TRP 3.0 7.1 + - - -
19J GLU* 3.4 16.6 + - - +
20J SER* 4.2 3.1 + - - -
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Residues in contact with LYS 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ASP* 4.9 2.2 + - - -
12J LYS* 4.5 17.1 - - - +
13J VAL* 3.6 15.8 + - - +
14J VAL* 3.2 6.0 + - - +
16J ASP* 1.3 109.5 + - - +
18J TRP* 1.3 54.4 + - - +
19J GLU 3.3 0.4 - - - -
20J SER* 3.2 10.2 + - - -
21J TYR* 2.4 39.6 + - - +
39J LEU* 3.4 46.0 - - + +
40J GLY* 5.2 1.6 - - - -
41J LEU* 3.5 17.9 - - + -
50J ILE* 4.1 6.3 - - + -
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Residues in contact with TRP 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C LEU* 4.6 13.7 - - + -
195C LYS* 4.8 3.5 - - - +
3J VAL* 3.6 42.4 - - + +
14J VAL 3.8 0.8 + - - -
15J GLY 4.3 1.8 - - - +
16J ASP 3.0 1.0 + - - -
17J LYS* 1.3 76.3 - - - +
19J GLU* 1.3 69.0 + - - +
21J TYR* 3.4 24.8 - + - +
22J LEU* 3.0 45.0 + - + +
49J MET 4.8 0.9 - - - -
50J ILE* 3.3 44.8 - - + +
52J THR 4.4 0.7 - - - -
53J HIS* 3.8 23.8 - + - -
54J VAL* 5.7 0.2 - - - -
55J ASP* 4.0 36.6 + - + -
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Residues in contact with GLU 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C LYS* 6.2 0.3 - - - +
161C HIS* 4.2 26.6 + - - -
163C TYR* 5.1 11.1 + - + +
192C LEU* 4.5 20.1 - - + +
195C LYS* 5.6 2.1 + - - -
15J GLY 5.0 0.4 + - - -
16J ASP 3.4 9.9 + - - +
17J LYS 3.3 0.4 - - - -
18J TRP* 1.3 87.1 - - - +
20J SER* 1.3 67.0 + - - +
22J LEU* 3.1 3.0 + - - +
23J ASN* 2.9 33.2 + - + +
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Residues in contact with SER 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J ASP 4.2 2.0 + - - -
17J LYS* 3.2 16.2 + - - -
19J GLU* 1.3 79.3 - - - +
21J TYR* 1.3 57.9 + - - +
23J ASN* 4.0 8.2 + - - +
24J LEU* 2.9 33.3 + - - +
39J LEU* 4.0 10.5 - - - +
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Residues in contact with TYR 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J LYS 2.4 32.9 + - - +
18J TRP* 3.4 35.2 - + - +
20J SER* 1.3 67.7 - - - +
22J LEU* 1.3 83.0 + - + +
24J LEU* 2.8 16.2 + - + +
25J LEU* 2.9 26.6 + - + +
32J GLU* 2.3 32.6 + - - -
35J ALA* 4.7 9.0 - - + -
36J LEU* 3.3 30.8 - - + +
39J LEU* 3.5 18.3 - - + +
50J ILE* 3.6 28.7 - - + -
51J LEU* 5.1 5.6 + - - +
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Residues in contact with LEU 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J TRP* 3.0 40.4 + - + +
19J GLU* 4.0 3.1 - - - +
21J TYR* 1.3 89.0 - - + +
23J ASN* 1.3 66.6 + - - +
25J LEU* 2.9 15.9 + - + +
26J GLN* 2.9 36.5 + - + +
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Residues in contact with ASN 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J GLU* 2.9 24.7 + - + +
20J SER* 4.0 7.9 + - - +
22J LEU* 1.3 82.5 - - - +
24J LEU* 1.3 63.2 + - - +
25J LEU 3.1 1.2 + - - -
26J GLN* 3.3 6.9 + - - +
27J GLU* 3.1 32.6 + - - +
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Residues in contact with LEU 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J SER* 2.9 21.5 + - - +
21J TYR* 2.8 11.1 + - + +
23J ASN* 1.3 75.2 - - - +
25J LEU* 1.3 56.7 + - - +
27J GLU* 2.7 18.4 - - - +
28J ASP* 2.9 16.5 - - - +
30J LEU* 4.8 4.8 - - + +
35J ALA* 3.8 34.8 - - + +
38J ARG* 4.5 33.4 - - + +
39J LEU* 4.8 17.7 - - + -
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Residues in contact with LEU 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J TYR* 2.9 28.3 + - + +
22J LEU* 2.9 11.8 + - + +
24J LEU* 1.3 79.2 - - + +
26J GLN* 1.3 93.1 + - - +
27J GLU 3.3 3.1 - - - +
28J ASP 4.3 1.1 - - - -
29J GLU* 3.4 19.6 - - - +
30J LEU 4.2 17.7 - - - +
32J GLU* 3.0 35.7 - - - +
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Residues in contact with GLN 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J LEU* 2.9 39.0 + - + +
23J ASN* 4.3 2.7 - - - +
25J LEU* 1.3 100.1 - - - +
27J GLU* 1.3 63.9 + - - +
29J GLU* 3.4 24.0 - - - +
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Residues in contact with GLU 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J ASN* 3.1 29.2 + - - +
24J LEU* 2.7 32.1 - - - +
26J GLN* 1.3 79.2 - - - +
28J ASP* 1.3 84.8 + - - +
29J GLU* 5.1 1.1 - - - -
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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