Contacts of the helix formed by residues 19 - 39 (chain S) in PDB entry 6CP3
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 LEU 19 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R GLY 3.3 28.5 - - - +
61R THR* 3.4 28.9 - - - +
62R GLY* 4.5 0.9 - - - -
64R PHE* 4.2 21.3 - - + -
65R CYS* 4.2 13.7 - - + +
68R VAL* 5.9 0.4 - - + -
16S THR* 3.4 22.4 - - + +
17S ILE 3.1 1.2 - - - -
18S GLY* 1.3 72.9 - - - +
20S LEU* 1.3 53.4 + - - +
21S GLY 3.2 2.0 - - - -
22S ALA* 2.9 16.6 + - + +
23S GLY* 2.8 29.6 + - - -
62S GLY* 4.2 9.9 - - - +
63S LEU* 6.4 0.4 - - + -
65S CYS* 3.2 13.4 - - - -
66S LEU* 4.3 21.8 - - + -
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Residues in contact with LEU 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R ILE* 5.3 4.5 - - + +
18R GLY* 3.9 14.2 + - - +
20R LEU* 3.7 31.2 - - + -
21R GLY* 3.3 28.5 - - - +
24R ILE* 5.6 0.7 - - + -
17S ILE* 2.8 28.6 + - + +
19S LEU* 1.3 78.2 - - - +
21S GLY* 1.3 55.8 + - - +
23S GLY* 2.9 1.8 + - - +
24S ILE* 2.8 48.3 + - + +
20T LEU* 3.7 21.5 - - + -
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Residues in contact with GLY 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S GLY 3.4 3.9 + - - -
19S LEU 3.2 1.2 - - - -
20S LEU* 1.3 75.1 - - - +
22S ALA* 1.3 59.8 + - - +
25S GLY 3.0 15.9 + - - -
20T LEU* 3.3 36.4 - - - +
23T GLY* 2.9 28.9 - - - +
24T ILE* 3.5 8.8 + - - -
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Residues in contact with ALA 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61R THR* 4.9 14.6 - - + -
18S GLY 4.2 1.2 + - - -
19S LEU* 2.9 19.3 + - + +
21S GLY* 1.3 76.8 - - - +
23S GLY* 1.3 56.4 + - - +
25S GLY* 2.9 16.4 + - - -
26S ILE* 3.2 24.5 + - + +
58S SER* 4.6 9.6 - - - +
59S GLU* 4.8 10.3 - - - +
62S GLY* 3.8 26.9 - - - +
63S LEU* 6.1 0.9 - - + -
23T GLY* 4.5 2.8 - - - -
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Residues in contact with GLY 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R GLY* 2.9 36.2 - - - +
25R GLY* 3.3 12.5 - - - -
58R SER* 5.0 4.8 - - - +
61R THR* 4.3 13.9 - - - -
19S LEU* 2.8 16.8 + - - -
20S LEU 2.9 4.1 + - - -
22S ALA* 1.3 72.1 - - - +
24S ILE* 1.3 60.3 + - - +
26S ILE* 4.8 2.6 - - - +
27S ALA* 3.7 3.8 + - - +
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Residues in contact with ILE 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21R GLY* 4.6 2.5 - - - -
24R ILE* 4.5 27.1 - - + -
25R GLY* 4.9 2.5 - - - -
28R ILE* 5.4 4.7 - - + -
20S LEU* 2.8 36.9 + - + +
21S GLY* 5.4 0.2 - - - -
23S GLY* 1.3 76.7 - - - +
25S GLY* 1.3 62.6 + - - +
26S ILE 3.6 0.2 - - - -
27S ALA* 2.6 30.4 - - - +
28S ILE* 3.4 14.4 + - + +
20T LEU* 6.5 0.2 - - + -
24T ILE* 3.8 38.8 - - + -
28T ILE* 6.2 0.2 - - + -
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Residues in contact with GLY 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S GLY 3.0 17.2 + - - -
22S ALA 2.9 7.7 + - - -
24S ILE* 1.3 80.0 - - - +
26S ILE* 1.3 61.5 + - - -
27S ALA 3.1 1.2 + - - -
28S ILE* 3.1 29.1 + - - +
29S VAL 3.6 0.3 + - - -
23T GLY 3.6 12.8 - - - -
24T ILE* 4.3 3.6 - - - -
27T ALA* 3.3 15.8 - - - +
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Residues in contact with ILE 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57R LEU 3.6 18.6 - - - +
58R SER* 3.7 22.0 - - - +
61R THR* 4.0 8.3 - - + -
22S ALA 3.2 19.8 + - - +
23S GLY 4.8 2.7 - - - +
25S GLY* 1.3 69.7 - - - +
27S ALA* 1.3 66.6 + - - +
29S VAL* 3.1 19.4 + - - +
30S PHE* 3.2 19.9 + - - -
55S PHE* 3.6 35.7 - - + +
58S SER* 3.7 24.4 - - - -
59S GLU* 3.4 25.8 - - - +
27T ALA* 4.3 0.2 - - - +
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Residues in contact with ALA 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R GLY* 3.3 39.3 - - - +
28R ILE* 3.8 9.9 - - + -
29R VAL* 3.4 18.3 - - - +
58R SER* 4.9 4.0 - - - -
23S GLY 3.7 2.2 - - - +
24S ILE 2.6 19.0 + - - +
26S ILE* 1.3 79.0 - - - +
28S ILE* 1.3 56.6 + - - +
30S PHE 3.1 4.3 + - - -
31S ALA* 2.9 23.9 + - - +
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Residues in contact with ILE 28 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28R ILE* 3.6 22.4 - - + -
24S ILE* 4.3 9.6 - - + +
25S GLY* 3.1 22.0 - - - +
27S ALA* 1.3 78.7 - - - +
29S VAL* 1.3 59.6 + - - +
31S ALA* 3.2 10.0 - - + +
32S ALA* 2.5 38.0 + - - +
27T ALA* 3.4 33.4 - - + +
28T ILE* 3.6 23.3 - - + -
31T ALA* 3.8 10.9 - - + +
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Residues in contact with VAL 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25S GLY 3.8 12.8 - - - +
26S ILE* 3.3 11.9 - - - +
28S ILE* 1.3 76.9 - - - +
30S PHE* 1.3 57.7 + - + +
32S ALA* 3.0 8.8 + - - +
33S LEU* 2.6 34.3 + - - +
51S ALA* 3.6 29.6 - - + +
52S ILE* 5.6 0.2 - - - -
54S GLY 5.3 5.8 - - - -
55S PHE* 4.9 6.3 - - + +
58S SER* 5.3 1.6 - - - +
27T ALA* 3.6 32.5 - - + +
30T PHE* 4.5 9.6 - - + -
31T ALA* 4.8 1.1 - - - +
34T ILE* 3.4 17.0 - - + +
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Residues in contact with PHE 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29R VAL* 4.1 17.9 - - + -
50R MET* 4.6 5.6 - - + -
51R ALA* 5.9 1.6 - - - -
53R LEU* 3.6 32.5 - - + -
54R GLY* 3.5 24.2 - - - -
57R LEU* 5.2 2.0 - - + -
58R SER* 3.9 12.8 - - - -
26S ILE* 3.2 20.1 + - + -
27S ALA* 3.1 6.9 + - - +
29S VAL* 1.3 80.0 - - + +
31S ALA* 1.3 57.8 - - - +
33S LEU* 3.0 26.5 + - + +
34S ILE* 2.8 36.2 + - + +
51S ALA* 5.9 0.9 - - + -
52S ILE* 4.7 12.1 - - + -
55S PHE* 3.6 38.8 - + + -
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Residues in contact with ALA 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28R ILE* 4.1 15.7 - - + +
29R VAL* 4.5 5.7 - - - +
32R ALA* 3.3 29.7 - - + +
27S ALA 2.9 13.8 + - - +
28S ILE* 3.2 18.8 - - + +
30S PHE* 1.3 75.4 - - - +
32S ALA* 1.3 62.7 + - - +
34S ILE* 3.0 3.6 + - - -
35S ASN* 3.0 22.0 + - - +
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Residues in contact with ALA 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S ILE 2.5 19.3 + - - +
29S VAL 3.4 4.3 - - - +
31S ALA* 1.3 72.1 - - - +
33S LEU* 1.3 51.5 + - - +
35S ASN* 3.0 10.1 + - - +
36S GLY 2.4 32.6 + - - -
31T ALA* 3.6 33.9 - - + +
34T ILE* 3.3 19.9 - - + +
35T ASN* 4.5 9.9 - - - +
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Residues in contact with LEU 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50R MET* 3.7 35.7 - - + -
29S VAL 2.6 16.4 + - - +
30S PHE* 3.0 34.3 + - + +
32S ALA* 1.3 73.5 - - - +
34S ILE* 1.3 61.3 + - - +
36S GLY* 3.0 8.5 + - - -
37S VAL* 3.0 17.0 + - + +
44S LYS* 6.4 0.4 - - + -
47S VAL* 3.6 41.5 - - + +
48S PHE* 4.9 7.4 - - + +
51S ALA* 3.8 20.9 - - + -
52S ILE* 5.6 0.9 - - + +
34T ILE* 3.7 7.4 - - + +
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Residues in contact with ILE 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29R VAL* 3.4 33.0 - - + +
32R ALA* 3.3 25.8 - - + +
33R LEU* 3.5 18.6 - - + +
36R GLY* 4.0 12.1 - - - -
47R VAL* 4.9 14.4 - - + -
50R MET* 4.9 9.2 - - + -
51R ALA* 4.0 22.9 - - + -
30S PHE* 2.8 18.5 + - + +
31S ALA 3.0 5.8 + - - +
33S LEU* 1.3 76.4 - - + +
35S ASN* 1.3 56.7 + - - +
37S VAL* 3.0 7.9 + - - +
38S SER* 2.8 31.4 + - - -
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Residues in contact with ASN 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32R ALA* 4.1 13.5 - - - +
35R ASN* 4.2 21.7 - - - +
39R ARG* 4.9 7.6 + - - -
31S ALA* 3.0 19.9 + - - +
32S ALA* 3.1 8.8 - - - +
34S ILE* 1.3 75.6 - - - +
36S GLY* 1.3 61.1 + - - +
37S VAL 3.3 0.2 - - - -
38S SER* 3.4 13.5 + - - +
39S ARG* 3.3 25.9 + - + +
35T ASN* 4.1 19.9 + - - +
38T SER* 4.1 2.2 + - - -
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Residues in contact with GLY 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32S ALA 2.4 22.7 + - - -
33S LEU 3.0 5.6 + - - -
35S ASN* 1.3 72.8 - - - +
37S VAL* 1.3 58.5 + - - +
38S SER 3.6 0.2 - - - -
39S ARG* 4.7 0.2 - - - -
40S ASN 3.5 16.0 + - - +
43S ILE* 4.2 3.3 - - - +
47S VAL* 5.2 6.3 - - - -
34T ILE* 3.9 9.6 - - - -
38T SER* 3.3 35.2 - - - -
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Residues in contact with VAL 37 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R ASN* 3.9 1.9 + - - -
43R ILE* 4.1 4.1 - - + +
46R THR* 4.3 13.9 - - + -
47R VAL* 3.7 24.0 - - + -
50R MET* 3.8 15.5 - - + -
33S LEU* 3.0 13.9 + - + +
34S ILE* 3.3 12.3 - - - +
36S GLY* 1.3 77.5 - - - +
38S SER* 1.3 66.9 + - - +
39S ARG 3.5 0.4 - - - -
40S ASN 3.8 4.9 - - - -
41S PRO* 3.5 27.3 - - + +
44S LYS* 3.7 39.9 - - + -
47S VAL* 5.8 0.4 - - + -
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Residues in contact with SER 38 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R GLY* 3.7 31.9 - - - -
39R ARG* 3.9 18.7 - - - +
40R ASN* 2.7 34.9 + - - +
43R ILE* 5.0 2.7 - - - -
47R VAL* 6.1 0.2 - - - -
34S ILE* 2.8 17.1 + - - -
35S ASN* 3.4 19.4 + - - -
37S VAL* 1.3 79.5 - - - +
39S ARG* 1.3 69.5 + - - +
40S ASN 3.4 0.3 + - - -
41S PRO* 4.2 1.0 - - - +
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Residues in contact with ARG 39 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G GLY* 2.9 46.8 + - - +
196G LYS 5.2 0.4 + - - -
197G PHE 5.2 0.2 + - - -
198G GLU* 3.5 34.4 - - - +
39R ARG* 3.7 36.4 - - - +
35S ASN* 3.3 20.2 + - + +
38S SER* 1.3 81.4 + - - +
40S ASN* 1.3 61.0 + - - +
41S PRO* 4.1 2.0 - - - -
35T ASN* 4.7 9.3 + - - -
38T SER* 3.4 29.0 + - - -
39T ARG* 3.4 51.9 + - - +
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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