Contacts of the helix formed by residues 14 - 38 (chain R) in PDB entry 6LTJ
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 GLU 14 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1808L LYS* 4.9 8.4 + - - +
1809L PHE* 4.0 26.0 - - + -
13R GLY* 1.3 79.7 + - - -
15R GLN* 1.3 91.5 + - + +
17R TYR* 3.6 6.6 - - - +
18R LYS* 2.9 30.8 + - - +
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Residues in contact with GLN 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R GLY* 4.5 4.0 - - - -
14R GLU* 1.3 110.4 + - + +
16R TYR* 1.3 57.3 + - - +
18R LYS* 3.4 5.5 + - - +
19R ASP* 2.9 29.0 + - - +
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Residues in contact with TYR 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338M ILE* 5.4 6.6 - - + +
340M ILE* 3.4 37.3 + - + +
341M ARG 5.2 0.2 - - - -
342M ASN* 3.5 20.9 - - + +
343M THR* 4.0 27.6 - - + -
13R GLY* 3.6 18.0 + - - +
14R GLU 3.3 0.2 - - - -
15R GLN* 1.3 76.9 + - - +
17R TYR* 1.3 65.7 + + - +
19R ASP* 4.1 7.2 - - + -
20R ALA* 2.9 31.2 + - + +
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Residues in contact with TYR 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809L PHE* 3.6 28.3 - + + -
340M ILE* 4.1 23.7 - - + +
435O TYR* 5.4 1.6 - - - -
464O ALA* 4.2 2.6 + - - -
467O ASN* 3.7 8.8 - - - +
468O PHE* 3.2 46.9 + + - +
471O ASP* 3.6 12.7 + - - -
13R GLY 2.8 19.0 + - - +
14R GLU* 3.6 9.0 - - - +
15R GLN 3.3 0.2 - - - -
16R TYR* 1.3 80.1 - + - +
18R LYS* 1.3 63.7 + - - +
20R ALA* 3.2 5.7 + - - +
21R MET* 3.0 55.3 + - + +
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Residues in contact with LYS 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809L PHE* 4.5 24.3 - - + +
1811L LYS* 3.9 32.3 - - - +
475O LEU* 5.9 4.0 - - + -
14R GLU 2.9 18.7 + - - +
15R GLN* 3.7 6.7 - - - +
17R TYR* 1.3 76.7 - - - +
19R ASP* 1.3 56.8 + - - +
21R MET* 3.2 16.5 - - + +
22R GLU* 2.9 56.1 + - + +
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Residues in contact with ASP 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343M THR* 4.0 10.2 - - - +
15R GLN 2.9 18.1 + - - +
16R TYR* 3.6 11.0 - - + +
17R TYR 3.1 0.2 - - - -
18R LYS* 1.3 73.2 - - - +
20R ALA* 1.3 67.0 + - - +
22R GLU* 3.3 7.8 + - - +
23R GLN* 2.9 38.6 + - - +
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Residues in contact with ALA 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340M ILE* 4.1 18.4 - - + -
341M ARG 5.3 2.2 - - - +
343M THR* 4.6 4.5 - - + +
468O PHE* 4.0 17.5 - - + -
489O ASN* 4.1 4.6 - - + +
16R TYR* 2.9 26.5 + - + +
17R TYR* 3.6 5.6 - - - +
19R ASP* 1.3 78.3 + - - +
21R MET* 1.3 58.8 + - - +
23R GLN* 3.4 13.4 - - - +
24R CYS* 2.9 27.9 + - - +
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Residues in contact with MET 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1809L PHE* 4.8 10.8 - - + -
468O PHE* 3.9 14.8 - - + +
471O ASP* 3.4 27.8 - - + -
472O THR* 3.3 27.7 - - - +
475O LEU* 3.6 24.8 - - + +
17R TYR* 3.0 54.6 + - + +
18R LYS* 3.2 25.1 - - + +
20R ALA* 1.3 74.7 - - - +
22R GLU* 1.3 61.1 + - - +
25R HIS* 2.9 24.8 + - - +
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Residues in contact with GLU 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1811L LYS* 5.1 6.1 + - - -
475O LEU* 3.8 21.3 - - + +
18R LYS* 2.9 45.6 + - + +
19R ASP* 4.0 6.0 - - - +
21R MET* 1.3 75.5 - - - +
23R GLN* 1.3 59.5 + - - +
25R HIS* 3.4 6.0 + - + +
26R ASN* 2.9 37.6 + - - +
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Residues in contact with GLN 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341M ARG 5.6 0.2 + - - -
343M THR* 3.3 50.7 + - - +
346M ALA* 4.1 0.4 - - - +
347M ASP* 3.5 7.4 + - - +
488O ARG* 3.5 15.2 + - - +
489O ASN* 3.3 14.5 + - - +
19R ASP* 2.9 27.7 + - - +
20R ALA* 3.4 10.4 + - - +
22R GLU* 1.3 74.5 - - - +
24R CYS* 1.3 63.8 + - - +
26R ASN* 3.8 9.6 - - - +
27R TYR* 2.9 30.5 + - - +
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Residues in contact with CYS 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468O PHE* 3.9 15.5 - - + -
472O THR* 3.7 18.8 - - + -
481O LEU* 4.7 4.7 - - - -
485O ALA* 3.5 26.9 - - - +
486O CYS* 4.2 3.1 - - - -
488O ARG* 4.6 0.2 - - - +
489O ASN* 3.2 31.4 - - - +
20R ALA 2.9 17.2 + - - +
21R MET 3.6 4.7 - - - +
23R GLN* 1.3 77.2 - - - +
25R HIS* 1.3 56.8 + - - +
27R TYR* 3.4 1.9 + - - +
28R ASN* 2.9 29.5 + - - +
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Residues in contact with HIS 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472O THR* 3.9 13.6 + - + +
475O LEU* 4.2 21.9 + - + +
476O ASN* 3.3 35.1 + - + +
479O GLU* 2.7 32.9 + - - +
481O LEU* 5.5 0.4 - - - +
21R MET 2.9 17.7 + - - +
22R GLU* 3.6 6.7 - - + +
24R CYS* 1.3 77.8 - - - +
26R ASN* 1.3 70.7 + - - +
28R ASN* 3.3 7.4 + - - +
29R ALA* 2.9 31.4 + - + +
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Residues in contact with ASN 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22R GLU* 2.9 27.5 + - - +
23R GLN* 3.8 7.7 - - - +
24R CYS 3.3 0.2 - - - -
25R HIS* 1.3 89.3 + - - +
27R TYR* 1.3 57.6 + - - +
29R ALA* 3.3 6.5 + - - +
30R ARG* 2.9 42.7 + - - +
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Residues in contact with TYR 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350M CYS* 3.1 24.6 - - + +
351M PRO* 3.1 38.9 + - - +
484O THR* 4.4 3.4 - - + -
485O ALA* 3.9 23.3 - - + -
488O ARG* 3.5 39.3 - - - +
23R GLN 2.9 17.6 + - - +
24R CYS 3.9 2.2 - - - +
26R ASN* 1.3 75.8 - - - +
28R ASN* 1.3 59.7 + - - +
30R ARG* 3.3 28.8 + - + +
31R LEU* 2.9 53.0 + - + +
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Residues in contact with ASN 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479O GLU* 3.1 18.6 + - - -
480O TYR 2.7 24.2 + - - +
481O LEU* 3.2 25.5 - - + +
482O THR* 3.3 16.8 + - - -
485O ALA* 3.8 15.3 - - + -
24R CYS 2.9 18.7 + - - +
25R HIS 3.5 4.0 - - - +
26R ASN 3.2 0.2 - - - -
27R TYR* 1.3 78.1 - - - +
29R ALA* 1.3 58.3 + - - +
31R LEU* 3.2 4.5 + - - +
32R CYS* 2.9 40.1 + - - -
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Residues in contact with ALA 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479O GLU* 3.4 22.4 - - - +
25R HIS* 2.9 21.1 + - + +
26R ASN* 3.3 6.9 + - - +
28R ASN* 1.3 76.3 - - - +
30R ARG* 1.3 58.0 + - - +
32R CYS* 3.4 4.3 + - - +
33R ALA* 2.9 30.1 + - - +
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Residues in contact with ARG 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488O ARG* 5.8 2.0 - - - +
26R ASN* 2.9 29.9 + - - +
27R TYR* 3.5 45.2 - - + +
29R ALA* 1.3 76.7 - - - +
31R LEU* 1.3 57.3 + - - +
33R ALA* 3.2 7.0 + - - +
34R GLU* 3.0 55.8 + - + +
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Residues in contact with LEU 31 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300M GLU* 3.3 28.5 - - + +
301M LEU* 4.0 22.2 - - + -
482O THR* 3.9 26.2 - - + +
484O THR* 3.9 20.4 - - + -
27R TYR* 2.9 49.4 + - + +
28R ASN* 3.6 4.7 - - - +
30R ARG* 1.3 76.0 - - - +
32R CYS* 1.3 61.9 + - - +
34R GLU* 3.4 14.4 + - - +
35R ARG* 2.9 28.4 + - - +
38R ARG* 5.4 0.7 + - - -
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Residues in contact with CYS 32 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479O GLU* 5.0 4.0 - - + +
480O TYR* 3.8 20.9 - - - -
482O THR* 4.2 15.0 - - - -
520O PRO* 5.5 4.9 - - - -
28R ASN* 2.9 36.9 + - - +
29R ALA* 3.9 7.0 - - - +
31R LEU* 1.3 77.6 - - - +
33R ALA* 1.3 57.8 + - - +
35R ARG* 3.3 10.5 + - - +
36R SER* 2.9 29.5 + - - -
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Residues in contact with ALA 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29R ALA 2.9 17.2 + - - +
30R ARG* 3.5 7.6 - - - +
32R CYS* 1.3 76.1 - - - +
34R GLU* 1.3 64.3 + - + +
36R SER* 2.8 24.4 + - - -
37R VAL* 3.0 12.8 + - - +
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Residues in contact with GLU 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301M LEU* 6.0 1.7 - - - +
353M LEU* 5.3 5.5 + - - +
30R ARG* 3.0 41.9 + - + +
31R LEU* 3.9 10.9 - - - +
33R ALA* 1.3 76.6 - - + +
35R ARG* 1.3 64.4 + - - +
37R VAL* 3.1 25.1 - - + +
38R ARG* 3.3 35.8 + - - +
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Residues in contact with ARG 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299M SER 2.8 22.3 + - - -
300M GLU 3.6 14.4 - - - +
301M LEU 3.8 13.2 - - - +
302M GLY* 3.6 8.0 - - - +
519O ARG 5.2 1.2 + - - +
520O PRO* 3.8 23.3 - - - +
521O THR 3.0 19.6 + - - +
523O MET* 3.6 12.5 - - - -
31R LEU 2.9 17.4 + - - +
32R CYS* 3.5 11.0 - - - +
34R GLU* 1.3 80.1 - - - +
36R SER* 1.3 63.6 + - - +
37R VAL 3.2 0.5 + - - -
38R ARG* 3.3 19.8 + - - +
39R LEU* 3.4 32.8 + - + +
52R ASN* 2.5 37.2 + - - +
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Residues in contact with SER 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R CYS 2.9 14.4 + - - -
33R ALA* 2.8 22.2 + - - -
35R ARG* 1.3 78.2 - - - +
37R VAL* 1.3 62.5 + - - +
39R LEU* 3.7 20.0 - - - +
40R PRO* 5.4 0.2 - - - +
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Residues in contact with VAL 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33R ALA 3.0 14.1 + - - +
34R GLU* 3.1 24.2 - - + +
36R SER* 1.3 78.8 + - - +
38R ARG* 1.3 61.1 + - + +
39R LEU 3.3 3.1 + - - -
40R PRO* 5.0 2.6 - - - +
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Residues in contact with ARG 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273M ILE* 5.6 5.6 - - - -
301M LEU* 2.2 35.4 + - - +
302M GLY 4.1 15.0 - - - +
303M LEU* 4.2 11.4 - - - +
353M LEU* 3.3 44.6 + - - +
31R LEU 5.4 0.2 + - - -
34R GLU* 3.4 42.0 + - - +
35R ARG* 3.3 11.6 + - - +
37R VAL* 1.3 81.2 - - + +
39R LEU* 1.3 66.3 - - - +
40R PRO* 3.4 11.7 - - - +
41R PHE* 4.3 7.8 + - - +
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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