Contacts of the helix formed by residues 15 - 35 (chain n) in PDB entry 5XTD
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 15 (chain n).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11n HIS 4.9 2.5 - - - +
12n TRP* 3.3 22.4 - - + +
14n HIS* 1.3 78.9 - - + +
16n LEU* 1.3 68.4 + - - +
18n PRO* 3.2 11.5 - - - +
19n MET* 3.4 28.9 + - + +
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Residues in contact with LEU 16 (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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12n TRP* 4.0 25.3 + - + +
13n VAL* 2.9 20.3 + - + +
14n HIS 3.2 0.2 - - - -
15n VAL* 1.3 79.9 - - - +
17n VAL* 1.3 62.9 + - + +
19n MET* 3.0 11.1 + - - +
20n GLY* 2.9 21.5 + - - -
10r MET* 3.5 54.2 - - + +
13r PRO* 3.9 22.4 - - + -
14r LEU* 4.4 8.7 - - + -
17r LEU* 5.0 4.3 - - + -
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Residues in contact with VAL 17 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13n VAL 4.5 1.0 + - - -
16n LEU* 1.3 78.7 - - + +
18n PRO* 1.3 68.9 - - + +
20n GLY* 2.6 23.6 + - - +
21n PHE* 2.9 10.1 + - + +
7r PRO* 4.2 22.1 - - + +
10r MET* 4.0 18.6 - - + +
11r LEU* 4.3 7.0 - - + +
14r LEU* 3.5 37.7 - - + +
30r HIS* 4.0 12.3 - - - +
33r ILE* 6.3 3.4 - - + -
34r ILE* 4.2 17.0 - - + -
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Residues in contact with PRO 18 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14n HIS 3.5 17.5 - - - +
15n VAL* 3.2 13.5 - - - +
17n VAL* 1.3 94.7 - - + +
19n MET* 1.3 56.2 + - - +
21n PHE* 2.9 29.0 + - + +
22n VAL* 3.4 9.9 + - - +
30r HIS* 4.4 8.5 - - + +
33r ILE* 6.1 8.3 - - + -
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Residues in contact with MET 19 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15n VAL* 3.4 25.1 + - + +
16n LEU* 3.0 14.6 + - - +
18n PRO* 1.3 79.3 - - - +
20n GLY* 1.3 55.7 + - - +
22n VAL* 2.9 41.9 + - + +
23n ILE* 3.5 12.8 + - + +
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Residues in contact with GLY 20 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16n LEU 2.9 8.8 + - - -
17n VAL 2.6 14.4 + - - -
19n MET* 1.3 70.2 - - - +
21n PHE* 1.3 65.1 + - - +
23n ILE* 3.9 15.4 + - - +
24n GLY 3.9 1.4 + - - -
6r VAL* 3.4 26.4 - - - +
7r PRO* 4.2 5.2 - - - +
10r MET* 4.1 22.7 - - - -
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Residues in contact with PHE 21 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17n VAL* 2.9 8.0 + - + +
18n PRO* 2.9 18.1 + - + +
20n GLY* 1.3 78.1 - - - +
22n VAL* 1.3 71.7 + - + +
24n GLY* 2.9 13.3 + - - -
25n CYS* 3.2 40.9 + - - -
3r LYS* 4.1 20.2 - - + -
7r PRO* 4.1 11.4 - - + +
37r ILE* 3.7 35.2 - - + -
41r PHE* 4.1 22.9 - + - -
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Residues in contact with VAL 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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18n PRO 3.6 13.7 - - - +
19n MET* 2.9 30.8 + - - +
21n PHE* 1.3 85.3 - - + +
23n ILE* 1.3 60.0 + - + +
25n CYS* 3.0 9.1 + - + +
26n TYR* 2.8 28.6 + - + +
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Residues in contact with ILE 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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19n MET* 3.9 15.9 - - + +
20n GLY* 4.0 14.8 - - - +
21n PHE 3.1 0.2 - - - -
22n VAL* 1.3 78.5 - - + +
24n GLY* 1.3 52.6 + - - +
26n TYR* 2.9 10.6 + - + +
27n LEU* 2.7 59.8 + - + +
101n CDL 5.7 4.7 - - + -
6r VAL* 4.8 12.8 - - + -
10r MET* 5.6 8.3 - - + -
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Residues in contact with GLY 24 (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 GLY 3.9 3.2 + - - -
21n PHE 2.9 10.2 + - - -
23n ILE* 1.3 77.7 - - - +
25n CYS* 1.3 63.0 + - - +
26n TYR 2.9 1.2 + - - -
27n LEU* 3.0 11.4 + - - -
28n ASP* 3.1 17.5 + - - +
2r LEU* 3.7 15.5 - - - -
3r LYS* 3.5 26.2 - - - -
6r VAL* 4.8 3.5 - - - +
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Residues in contact with CYS 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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21n PHE* 3.2 45.4 + - + +
22n VAL* 3.0 12.1 + - + +
24n GLY* 1.3 73.3 - - - +
26n TYR* 1.3 61.3 + - - +
28n ASP* 4.7 2.0 - - - +
29n ARG* 3.1 26.0 + - - +
3r LYS* 4.0 16.8 - - - +
41r PHE* 5.4 4.5 - - - -
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Residues in contact with TYR 26 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22n VAL* 2.8 15.7 + - + +
23n ILE* 2.9 11.9 + - + +
25n CYS* 1.3 78.2 - - - +
27n LEU* 1.3 87.4 + - + +
29n ARG* 2.9 33.3 + - - +
30n LYS* 3.0 30.9 + - + +
101n CDL 3.5 60.8 - - + +
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Residues in contact with LEU 27 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23n ILE* 2.7 40.5 + - + +
26n TYR* 1.3 91.4 - - + +
28n ASP* 1.3 64.7 + - - +
30n LYS* 2.9 8.8 + - + +
31n SER* 2.8 22.6 + - - -
101n CDL 4.2 52.6 - - + +
2r LEU* 3.7 36.1 - - + -
6r VAL* 5.0 3.6 - - + -
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Residues in contact with ASP 28 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24n GLY 3.1 10.4 + - - +
25n CYS* 4.7 3.1 - - - +
27n LEU* 1.3 76.6 - - - +
29n ARG* 1.3 63.5 + - - +
31n SER* 2.6 26.6 + - - -
32n ASP* 3.1 15.3 + - - +
1r MET* 3.5 29.8 - - + +
2r LEU* 3.1 28.6 - - - +
3r LYS* 3.4 37.9 + - + +
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Residues in contact with ARG 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 CYS 3.1 21.6 + - - +
26n TYR* 2.9 23.9 + - - +
28n ASP* 1.3 79.3 - - - +
30n LYS* 1.3 60.8 + - - +
32n ASP* 3.9 13.9 + - - +
33n GLU* 3.8 28.1 + - - +
58n LYS 5.1 6.4 - - - +
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Residues in contact with LYS 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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24g LYS* 4.4 9.4 - - - +
26n TYR* 3.0 32.8 + - + +
27n LEU* 2.9 12.2 + - + +
29n ARG* 1.3 78.1 - - - +
31n SER* 1.3 66.4 - - - +
32n ASP 3.1 1.8 - - - -
33n GLU* 2.9 35.3 + - + +
34n ARG* 3.7 8.0 + - - +
101n CDL 2.9 70.7 + - - +
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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 LEU 2.8 11.7 + - - -
28n ASP* 2.6 26.4 + - - -
30n LYS* 1.3 77.0 - - - +
32n ASP* 1.3 69.6 + - - +
34n ARG* 2.9 44.7 + - - +
35n LEU* 3.5 10.9 + - - +
101n CDL 5.5 7.4 - - - -
1r MET* 4.2 10.5 - - - +
53r SER* 5.4 5.4 - - - -
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Residues in contact with ASP 32 (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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131a LYS* 2.8 35.9 + - - +
135a ARG* 3.5 25.7 + - - +
28n ASP* 3.1 18.1 + - - +
29n ARG* 4.1 10.6 - - - +
30n LYS 3.1 0.4 - - - -
31n SER* 1.3 80.2 + - - +
33n GLU* 1.3 57.9 + - - +
35n LEU* 2.9 26.9 + - - +
36n THR* 3.3 14.5 + - - +
57n TRP* 4.3 10.6 - - + -
58n LYS 4.9 7.1 - - - +
1r MET* 5.1 5.4 - - - +
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Residues in contact with GLU 33 (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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29n ARG* 3.8 29.6 + - - +
30n LYS* 2.9 26.8 + - - +
32n ASP* 1.3 78.7 - - - +
34n ARG* 1.3 56.1 + - - +
35n LEU 3.2 0.4 - - - -
36n THR* 3.2 28.8 + - + +
58n LYS 5.0 10.6 - - - +
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Residues in contact with ARG 34 (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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142a ILE* 5.9 0.9 - - - +
30n LYS* 3.7 10.4 + - - +
31n SER* 2.9 35.5 + - - +
33n GLU* 1.3 79.4 - - - +
35n LEU* 1.3 68.8 + - + +
36n THR* 3.4 2.8 + - - -
37n ALA* 4.7 6.9 + - - +
101n CDL 2.6 87.1 + - - -
54r LEU* 5.0 13.5 - - + -
171u THR* 6.1 0.6 - - - +
172u LYS* 5.6 3.6 - - - +
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Residues in contact with LEU 35 (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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134a GLU 5.1 0.3 - - - +
135a ARG* 4.0 36.0 - - + -
138a ALA* 3.4 24.3 - - + +
139a VAL* 4.3 15.7 - - + -
142a ILE* 4.2 12.3 - - + -
31n SER* 3.8 17.0 - - - +
32n ASP* 2.9 14.3 + - - +
34n ARG* 1.3 87.8 - - + +
36n THR* 1.3 56.3 + - - +
37n ALA* 3.0 10.7 + - - -
38n PHE 4.2 0.2 + - - -
39n ARG 5.2 0.2 + - - -
57n TRP* 4.2 7.5 - - + -
52r CYS 4.6 5.4 - - - +
53r SER* 4.8 6.7 - - - -
54r LEU* 4.0 37.5 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
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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