Contacts of the helix formed by residues 3 - 31 (chain E) in PDB entry 3CRP
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 VAL 3 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4E LYS* 1.3 57.1 + - - +
5E GLN* 3.3 5.5 - - - +
6E LEU* 3.3 21.6 + - + +
7E GLU* 2.8 54.3 + - + +
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Residues in contact with LYS 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E VAL* 1.3 77.8 - - - +
5E GLN* 1.3 53.5 + - + +
7E GLU* 3.1 16.4 + - + +
8E ASP* 2.8 51.1 + - - +
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Residues in contact with GLN 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E VAL 3.3 3.2 - - - +
4E LYS* 1.3 75.3 - - + +
6E LEU* 1.3 65.5 + - - +
8E ASP* 3.2 12.0 + - - +
9E ALA* 3.0 23.4 + - - +
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Residues in contact with LEU 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E VAL* 3.3 23.5 + - + +
5E GLN* 1.3 78.2 - - - +
7E GLU* 1.3 63.8 + - + +
9E ALA* 3.2 10.8 + - + +
10E VAL* 3.0 33.4 + - + +
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Residues in contact with GLU 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E VAL* 2.8 42.0 + - + +
4E LYS* 3.1 17.2 + - + +
6E LEU* 1.3 73.4 - - + +
8E ASP* 1.3 58.3 + - - +
10E VAL* 3.3 9.1 + - - +
11E GLU* 3.0 29.1 + - - +
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Residues in contact with ASP 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E LYS* 2.8 34.2 + - - +
5E GLN* 3.2 14.3 + - - +
7E GLU* 1.3 72.6 - - - +
9E ALA* 1.3 59.9 + - - +
11E GLU* 3.3 8.2 + - - +
12E GLU* 3.1 30.4 + - - +
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Residues in contact with ALA 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E GLN 3.0 12.6 + - - +
6E LEU* 3.2 15.2 + - + +
8E ASP* 1.3 74.8 - - - +
10E VAL* 1.3 65.0 + - + +
12E GLU* 3.2 10.1 + - - +
13E LEU* 3.0 32.3 + - + +
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Residues in contact with VAL 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LEU* 3.0 27.4 + - + +
7E GLU* 3.3 9.8 + - - +
9E ALA* 1.3 74.1 - - + +
11E GLU* 1.3 61.1 + - - +
13E LEU* 3.1 14.2 + - + +
14E LEU* 2.8 47.2 + - + +
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Residues in contact with GLU 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.7 35.2 + - + +
7E GLU 3.0 14.9 + - - +
8E ASP* 3.7 10.5 - - - +
9E ALA 3.3 0.2 - - - -
10E VAL* 1.3 78.4 - - - +
12E GLU* 1.3 61.3 + - - +
14E LEU* 3.3 22.3 + - - +
15E SER* 3.1 22.2 + - - +
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Residues in contact with GLU 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ASP 3.1 18.6 + - - +
9E ALA* 3.6 10.1 - - - +
10E VAL 3.2 0.4 - - - -
11E GLU* 1.3 75.3 - - - +
13E LEU* 1.3 61.0 + - + +
15E SER* 3.0 12.7 + - - -
16E ALA* 2.9 25.8 + - - +
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Residues in contact with LEU 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ALA* 3.0 20.7 + - + +
10E VAL* 3.1 14.8 + - + +
12E GLU* 1.3 77.0 - - + +
14E LEU* 1.3 61.1 + - + +
16E ALA* 3.2 11.6 + - + +
17E ASN* 2.9 29.8 + - - +
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Residues in contact with LEU 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.8 16.5 - - + +
10E VAL* 2.8 32.4 + - + +
11E GLU* 3.6 29.2 - - - +
13E LEU* 1.3 78.1 - - + +
15E SER* 1.3 58.7 + - - +
17E ASN* 3.4 14.4 + - + +
18E TYR* 3.0 28.4 + - - +
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Residues in contact with SER 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.1 28.2 - - - +
4B LYS* 3.2 24.8 + - - +
11E GLU* 3.1 10.3 + - - +
12E GLU* 3.0 16.0 + - - -
14E LEU* 1.3 72.6 - - - +
16E ALA* 1.3 67.2 + - - +
18E TYR* 3.4 3.1 + - - +
19E HIS* 3.0 31.7 + - - -
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Residues in contact with ALA 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E GLU 2.9 13.2 + - - +
13E LEU* 3.6 18.4 - - + +
15E SER* 1.3 78.9 - - - +
17E ASN* 1.3 57.6 + - - +
19E HIS* 3.4 5.7 + - - +
20E LEU* 2.9 30.8 + - - +
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Residues in contact with ASN 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS* 4.9 5.7 - - - +
13E LEU 2.9 17.5 + - - +
14E LEU* 3.7 15.3 + - + +
16E ALA* 1.3 73.9 - - - +
18E TYR* 1.3 66.5 + - - +
20E LEU* 3.7 12.2 - - - +
21E GLU* 2.9 52.7 + - - +
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Residues in contact with TYR 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.6 8.1 - - + -
4B LYS* 4.2 15.9 - - + -
5B GLN* 3.8 39.0 - - + +
8B ASP* 2.7 41.2 + - - +
26C ARG* 3.4 21.8 - - + +
29C LYS* 4.2 22.8 - - + +
14E LEU 3.0 17.2 + - - +
15E SER* 3.6 4.0 - - - +
17E ASN* 1.3 77.0 - - - +
19E HIS* 1.3 80.3 + + - +
21E GLU* 3.4 3.4 + - - +
22E ASN* 3.0 55.9 + - - +
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Residues in contact with HIS 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LYS* 3.1 28.9 + - - -
8B ASP* 4.3 7.4 - - - -
26C ARG* 5.3 2.8 + - - -
15E SER* 3.0 28.1 + - - +
16E ALA* 3.8 4.9 - - - +
18E TYR* 1.3 97.9 - + - +
20E LEU* 1.3 66.1 + - - +
22E ASN* 3.3 12.4 + - - +
23E ALA* 3.0 23.6 + - - +
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Residues in contact with LEU 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ALA 2.9 18.8 + - - +
17E ASN* 3.7 14.4 - - - +
19E HIS* 1.3 76.6 - - - +
21E GLU* 1.3 61.6 + - + +
23E ALA* 3.3 7.7 + - + +
24E VAL* 3.0 42.6 + - + +
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Residues in contact with GLU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LYS* 3.1 36.7 + - - -
17E ASN* 2.9 41.1 + - - +
18E TYR* 4.0 2.7 - - - +
20E LEU* 1.3 77.9 - - + +
22E ASN* 1.3 67.1 + - - +
24E VAL* 3.4 8.0 + - + +
25E ALA* 3.0 24.4 + - - +
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Residues in contact with ASN 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA* 5.6 3.1 - - - +
26C ARG* 3.2 42.4 + - - +
29C LYS* 5.3 5.4 - - - +
18E TYR* 3.0 54.1 + - - +
19E HIS* 3.4 13.6 + - - +
21E GLU* 1.3 76.8 - - - +
23E ALA* 1.3 57.0 + - - +
25E ALA* 3.2 7.9 + - - +
26E ARG* 3.0 38.9 + - - +
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Residues in contact with ALA 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E HIS 3.0 11.0 + - - +
20E LEU* 3.6 12.8 - - + +
22E ASN* 1.3 77.4 - - - +
24E VAL* 1.3 60.1 + - + +
26E ARG* 3.2 13.4 + - - +
27E LEU* 2.9 43.6 + - + +
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Residues in contact with VAL 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E LEU* 3.0 33.3 + - + +
21E GLU* 3.8 7.9 - - + +
22E ASN 3.3 0.4 - - - -
23E ALA* 1.3 77.3 - - + +
25E ALA* 1.3 57.0 + - - +
27E LEU* 3.3 9.6 + - + +
28E LYS* 2.9 59.5 + - + +
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Residues in contact with ALA 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA* 6.3 2.9 - - + -
21E GLU 3.0 15.1 + - - +
22E ASN* 3.2 10.7 + - - +
24E VAL* 1.3 76.7 - - - +
26E ARG* 1.3 62.4 + - + +
28E LYS* 4.7 0.7 - - - -
29E LYS* 2.4 57.9 + - - +
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Residues in contact with ARG 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLU* 3.6 6.7 + - - -
18C TYR* 2.8 33.4 + - + -
22C ASN* 3.4 25.2 + - - +
26C ARG* 2.5 36.1 - - - +
22E ASN* 3.0 26.9 + - - +
23E ALA* 3.4 13.2 - - - +
25E ALA* 1.3 78.4 - - + +
27E LEU* 1.3 59.1 + - + +
29E LYS* 3.8 4.8 + - - +
30E LEU* 3.2 25.3 + - - +
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Residues in contact with LEU 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ALA* 2.9 29.4 + - + +
24E VAL* 4.0 8.1 - - + +
26E ARG* 1.3 77.2 - - + +
28E LYS* 1.3 59.1 - - + +
29E LYS 3.2 1.6 - - - -
30E LEU* 3.2 21.9 + - + +
31E VAL* 2.9 34.8 + - + +
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Residues in contact with LYS 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E VAL* 2.9 41.8 + - + +
25E ALA* 5.2 0.2 - - - -
27E LEU* 1.3 76.5 - - + +
29E LYS* 1.3 80.7 + - + +
31E VAL* 2.9 36.0 + - + +
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Residues in contact with LYS 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ALA* 2.4 54.6 + - - +
26E ARG* 4.0 5.8 - - - +
28E LYS* 1.3 92.8 - - + +
30E LEU* 1.3 61.7 + - - +
31E VAL 3.5 4.7 + - - -
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Residues in contact with LEU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ARG 3.2 15.0 + - - +
27E LEU* 3.2 28.2 + - + +
29E LYS* 1.3 78.1 - - - +
31E VAL* 1.3 59.6 + - + +
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LEU* 2.9 22.1 + - + +
28E LYS* 2.9 33.1 + - + +
29E LYS 3.9 4.9 - - - -
30E LEU* 1.3 80.0 - - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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