Contacts of the helix formed by residues 19 - 39 (chain A) in PDB entry 2X1L
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 HIS 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.9 13.2 - - + +
18A PRO* 1.3 74.0 - - - +
20A ILE* 1.3 69.7 + - + +
21A GLY 3.2 11.3 + - - -
22A HIS* 3.0 42.8 + + - +
23A ALA* 3.2 10.0 + - - +
310A VAL* 3.6 23.6 - - + +
312A PRO* 3.7 7.6 - - - +
601A ADN 3.3 37.2 + + - -
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Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 1.3 79.0 - - + +
21A GLY* 1.3 60.0 + - - +
23A ALA* 3.4 10.7 + - + +
24A TYR* 2.8 28.9 + - - +
295A LEU* 3.8 31.6 - - + +
296A LEU* 5.6 0.9 - - - -
297A ASN 5.6 0.4 - - - +
310A VAL* 3.0 24.4 + - + +
312A PRO* 4.5 6.5 - - + -
315A LEU* 3.7 25.1 - - + -
324A VAL* 5.0 3.6 - - + -
328A LEU* 3.9 25.8 - - + -
340A TYR* 3.4 34.3 - - + +
601A ADN 5.5 0.9 - - - +
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A HIS* 3.2 5.9 + - - -
20A ILE* 1.3 80.0 - - - +
22A HIS* 1.3 63.3 + - - +
24A TYR* 3.4 6.5 - - - +
25A GLU* 3.3 18.9 + - - +
295A LEU* 5.0 1.8 - - - -
601A ADN 3.4 52.4 + - - -
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Residues in contact with HIS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 3.7 20.7 - - + +
13A TYR 5.1 2.5 + - - -
17A VAL 4.6 1.3 - - - -
18A PRO* 3.7 6.2 - - + +
19A HIS* 3.0 57.4 + + - +
21A GLY* 1.3 73.5 - - - +
23A ALA* 1.3 65.3 + - - +
25A GLU* 3.2 4.8 + - - +
26A TYR* 3.1 47.9 + - + -
78A PHE* 3.8 21.3 - + + -
81A LEU* 5.0 0.7 - - + -
601A ADN 3.6 39.8 + + - -
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS 3.2 3.8 + - - +
20A ILE* 3.6 13.7 - - + +
22A HIS* 1.3 78.3 - - - +
24A TYR* 1.3 61.7 + - - +
26A TYR* 3.9 3.2 - - - -
27A ILE* 3.1 37.9 + - + +
81A LEU* 4.8 1.9 - - + +
85A LEU* 3.8 23.6 - - + -
312A PRO* 3.7 31.0 - - + -
328A LEU* 4.4 1.1 - - + -
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE 2.8 17.9 + - - +
21A GLY* 3.4 7.9 - - - +
22A HIS 3.2 0.2 - - - -
23A ALA* 1.3 77.5 - - - +
25A GLU* 1.3 61.2 + - - +
27A ILE* 4.2 1.2 - - - +
28A ALA* 3.2 25.5 + - - +
292A HIS* 3.9 23.3 - + + -
293A GLY 3.9 19.7 - - - -
294A TRP 5.7 0.2 - - - -
295A LEU* 4.2 25.6 - - + -
328A LEU* 3.3 47.5 - - + +
329A LEU* 4.7 4.8 - - + +
332A VAL* 4.1 26.2 + - + +
334A PHE* 3.3 38.5 - + - -
335A GLY 4.9 0.9 + - - -
336A GLN 4.8 2.3 + - - -
601A ADN 4.5 5.8 - + - -
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 3.5 9.0 - - - -
10A ALA* 3.0 35.0 + - - +
21A GLY 3.3 6.0 + - - +
22A HIS* 3.2 8.7 + - - +
24A TYR* 1.3 77.6 - - - +
26A TYR* 1.3 66.6 + - + +
28A ALA* 3.5 5.3 + - - +
29A THR* 2.7 40.2 + - - +
261A MET* 3.8 14.8 - - + +
263A GLY 3.5 2.6 + - - -
292A HIS* 2.7 40.6 + - + +
601A ADN 2.8 32.3 + - - +
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Residues in contact with TYR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A THR* 4.2 13.7 - - + -
10A ALA 4.5 7.4 - - - -
12A ALA* 4.0 8.7 + - - +
22A HIS* 3.1 44.2 + + + +
23A ALA* 3.9 7.4 - - - +
25A GLU* 1.3 84.3 - - + +
27A ILE* 1.3 56.7 + - - +
29A THR* 4.6 1.1 - - - -
30A ASP* 2.9 27.4 + - - +
45A TYR* 3.1 12.5 + - - +
47A THR* 3.9 11.7 - - - -
48A GLY 4.7 5.1 + - - -
78A PHE* 3.5 26.9 - + - -
81A LEU* 4.3 9.0 - - + -
82A GLN* 3.5 50.4 + - + +
85A LEU* 4.5 6.5 - - + -
87A ILE* 3.6 12.7 - - + +
601A ADN 5.3 2.1 - - - -
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.1 20.4 + - + +
24A TYR 4.2 2.2 - - - +
26A TYR* 1.3 72.7 - - - +
28A ALA* 1.3 61.3 + - - +
30A ASP* 3.3 3.2 + - - +
31A ALA* 2.9 28.6 + - - +
85A LEU* 4.0 25.1 - - + -
87A ILE* 4.0 17.0 - - + -
324A VAL* 4.8 3.6 - - + -
325A ARG* 3.8 55.9 + - + +
328A LEU* 3.7 22.2 - - + -
329A LEU* 4.0 18.2 - - + -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR 3.2 19.8 + - - +
25A GLU* 3.8 4.7 - - - +
27A ILE* 1.3 79.7 - - - +
29A THR* 1.3 60.8 + - - +
31A ALA* 3.5 4.0 + - - +
32A ILE* 3.4 24.8 + - - +
261A MET* 4.0 3.4 - - + -
329A LEU* 3.7 19.7 - - + +
334A PHE* 3.6 36.6 - - + -
409A MET* 3.8 4.9 - - + +
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.6 28.8 - - + +
8A THR 4.0 1.1 - - - +
9A THR* 3.4 14.2 - - + +
25A GLU* 2.7 22.9 + - - +
28A ALA* 1.3 73.0 - - - +
30A ASP* 1.3 66.2 + - - +
32A ILE* 3.2 5.6 + - - +
33A ALA* 3.0 21.5 + - - +
45A TYR* 3.5 30.3 - - + -
261A MET* 3.4 30.3 - - + +
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR 2.9 19.6 + - - +
27A ILE* 3.3 6.0 + - - +
29A THR* 1.3 75.9 - - - +
31A ALA* 1.3 52.7 + - - +
33A ALA* 3.3 0.9 + - - +
34A ARG* 2.8 61.3 + - - +
45A TYR* 3.4 12.6 + - - +
86A ASN 3.4 0.9 - - - +
87A ILE* 3.7 14.4 - - + -
88A SER* 2.7 44.3 + - - -
325A ARG* 2.8 24.2 + - - +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE 2.9 16.1 + - - +
28A ALA 3.6 7.2 - - - +
30A ASP* 1.3 77.7 + - - +
32A ILE* 1.3 56.1 + - - +
35A PHE* 3.0 25.5 + - - +
325A ARG* 5.0 0.2 - - - +
329A LEU* 3.9 21.5 - - + -
404A PHE* 3.4 15.7 - - + -
409A MET* 4.5 2.5 - - + -
467A PRO* 3.2 34.0 - - + +
468A VAL* 4.8 0.7 - - + +
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Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 4.0 17.3 - - + -
7A ILE* 3.8 17.7 - - + -
28A ALA 3.5 16.2 - - - +
29A THR 3.2 4.8 + - - +
31A ALA* 1.3 74.4 - - - +
33A ALA* 1.3 60.2 + - - +
35A PHE* 3.2 2.6 + - + +
36A LYS* 3.0 36.6 + - + +
259A LEU* 4.1 7.6 - - + -
261A MET* 3.6 29.6 - - + -
404A PHE* 4.1 23.1 - - + +
407A PRO* 3.8 24.0 - - + -
409A MET* 4.0 15.5 - - - -
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 5.0 0.9 - - - -
7A ILE* 4.0 18.3 - - + +
29A THR 3.0 15.9 + - - +
30A ASP 3.7 3.6 - - - +
32A ILE* 1.3 77.1 - - - +
34A ARG* 1.3 60.9 + - - +
36A LYS* 3.5 2.4 + - - -
37A ARG* 3.2 33.8 + - - +
43A VAL* 3.8 16.7 - - + +
45A TYR* 3.6 28.7 - - + -
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 2.8 42.1 + - - +
31A ALA 4.0 0.2 - - - +
33A ALA* 1.3 70.1 - - - +
35A PHE* 1.3 66.4 + - - +
37A ARG* 3.3 12.4 + - - +
38A LEU* 3.0 32.4 + - + +
86A ASN* 2.9 43.6 + - - +
88A SER* 3.7 26.9 - - - +
466A GLN 4.3 2.0 + - - -
467A PRO* 3.7 29.6 - - + -
470A PRO* 3.6 25.8 - - - +
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Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA 3.0 19.7 + - - +
32A ILE* 3.2 5.6 + - + +
34A ARG* 1.3 76.4 - - - +
36A LYS* 1.3 69.5 + - + +
38A LEU 3.2 1.7 + - - -
39A ASP* 2.9 42.9 + - + +
397A LEU* 4.9 6.5 - - + -
400A VAL* 3.6 25.1 - - + -
401A ARG* 3.7 36.8 - - + -
404A PHE* 3.6 36.3 - + + -
464A LEU* 5.0 3.6 - - + -
467A PRO* 3.8 12.1 - - + +
489A PHE* 3.3 40.6 - + - -
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Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 3.7 39.6 - - + -
32A ILE* 3.0 27.2 + - + +
33A ALA 3.9 0.4 - - - +
34A ARG 3.3 0.2 - - - -
35A PHE* 1.3 83.1 - - + +
37A ARG* 1.3 63.0 + - - +
39A ASP* 3.3 2.9 + - + +
40A GLY 3.2 5.0 + - - -
41A TYR* 2.8 72.4 + - + +
43A VAL* 3.6 19.3 - - + -
401A ARG* 6.0 2.0 - - - +
404A PHE* 5.6 3.4 - - - -
405A ASP* 2.8 31.3 + - - +
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 3.2 25.0 + - - +
34A ARG* 3.3 16.4 + - - +
36A LYS* 1.3 76.6 - - - +
38A LEU* 1.3 62.9 + - + +
40A GLY* 3.3 13.5 + - - -
41A TYR 4.0 10.9 + - - +
43A VAL* 3.7 24.9 + - + +
45A TYR* 4.1 9.5 - - - +
88A SER* 2.8 51.6 + - - -
90A ASP* 3.6 23.2 + - - -
488A ASP* 4.5 6.3 - - - +
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG* 3.0 22.6 + - + +
37A ARG* 1.3 77.2 - - + +
39A ASP* 1.3 57.2 + - - +
40A GLY 3.3 1.5 + - - -
466A GLN* 3.8 34.8 - - + +
467A PRO* 3.8 20.0 - - + -
487A ARG* 3.6 24.5 - - + +
488A ASP* 3.6 21.7 - - - +
489A PHE* 2.9 50.5 + - + +
490A SER 4.6 0.5 + - - -
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Residues in contact with ASP 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 2.9 27.0 + - + +
36A LYS* 3.9 7.2 + - - +
37A ARG 3.2 0.6 - - - -
38A LEU* 1.3 77.1 - - - +
40A GLY* 1.3 59.4 + - - +
41A TYR* 3.6 26.5 + - + -
401A ARG* 2.9 47.7 + - - +
489A PHE* 3.7 17.4 - - + +
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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