Contacts of the helix formed by residues 21 - 41 (chain A) in PDB entry 1PFY
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 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A SER 4.2 5.4 - - - +
20A ILE* 1.3 74.6 - - - +
22A LEU* 1.3 67.1 + - - +
23A GLY* 2.9 24.1 + - - -
24A HIS* 3.0 51.7 + + - +
25A MET* 3.1 14.4 + - - +
333A MET* 3.6 17.6 - - + +
340A PHE* 3.8 31.9 - + + -
341A ILE 3.3 18.4 - - - +
342A LYS* 4.2 2.7 - - + -
343A ALA 3.8 4.7 - - - +
553A MSP 3.4 29.2 + - - -
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Residues in contact with LEU 22 (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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21A HIS* 1.3 71.8 - - - +
23A GLY* 1.3 60.4 + - - +
24A HIS 3.4 0.2 - - - -
25A MET* 3.4 6.9 + - + +
26A LEU 3.2 13.2 + - - -
87A PHE* 4.9 0.7 - - + -
326A VAL* 3.9 5.0 - - + +
328A VAL* 5.1 4.5 - - + -
333A MET* 4.6 8.5 - - - -
341A ILE* 3.0 53.1 + - + +
342A LYS 4.7 2.2 - - - +
343A ALA* 4.8 5.2 - - - -
346A TRP* 4.0 25.6 - - + -
355A LEU* 3.5 26.7 - - + -
359A TYR* 2.9 25.4 + - - +
372A LEU* 3.7 28.3 - - + -
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS* 2.9 13.6 + - - -
22A LEU* 1.3 78.6 - - - +
24A HIS* 1.3 62.9 + - - +
26A LEU* 3.3 12.6 + - - +
27A GLU 3.8 1.2 + - - -
326A VAL* 3.9 7.9 - - - -
333A MET* 4.1 4.8 - - - +
553A MSP 3.4 48.3 + - - -
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Residues in contact with HIS 24 (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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14A PRO* 5.1 3.8 - - + +
18A GLY 5.7 1.6 - - - -
19A SER 3.7 13.0 - - - -
20A ILE* 3.6 26.4 - - + +
21A HIS* 3.0 56.5 + + - +
23A GLY* 1.3 74.4 - - - +
25A MET* 1.3 64.5 + - - +
27A GLU* 2.9 14.8 + - - +
28A HIS* 3.2 27.5 + - + +
553A MSP 3.4 58.9 + + - -
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Residues in contact with MET 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 3.7 20.9 - - - -
21A HIS 3.1 12.7 + - - +
22A LEU* 3.7 13.0 - - + +
23A GLY 3.2 0.2 - - - -
24A HIS* 1.3 77.9 - - - +
26A LEU* 1.3 60.2 + - - +
28A HIS* 4.4 2.7 - - + +
29A ILE* 2.8 56.8 + - + +
84A PHE* 3.8 16.4 - - + -
87A PHE* 3.4 51.4 - - + -
89A ILE* 4.0 15.0 - - + -
343A ALA* 4.0 15.0 - - + -
355A LEU* 4.6 3.8 - - + -
359A TYR* 4.1 4.0 - - + -
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Residues in contact with LEU 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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22A LEU 3.2 6.1 + - - -
23A GLY 3.5 3.8 - - - +
24A HIS 3.2 0.8 - - - -
25A MET* 1.3 75.4 - - - +
27A GLU* 1.3 59.5 + - - +
29A ILE* 3.9 0.9 - - - +
30A GLN* 2.9 30.0 + - + +
323A HIS* 4.4 9.0 - - + -
324A GLY 3.8 21.8 - - - +
326A VAL* 3.2 34.8 - - + +
359A TYR* 3.4 45.0 - - + -
363A LEU* 4.0 24.9 - - + +
370A ILE* 3.8 22.4 - - + -
553A MSP 4.3 3.6 - - + -
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Residues in contact with GLU 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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11A CYS* 3.9 9.6 - - - +
12A ALA* 2.9 33.8 + - - +
23A GLY 3.8 2.1 + - - +
24A HIS* 2.9 13.7 + - - +
26A LEU* 1.3 81.3 - - - +
28A HIS* 1.3 67.9 + - + +
30A GLN* 3.4 5.2 + - - +
31A ALA* 3.2 23.0 + - - +
292A PHE* 3.9 19.5 - - + +
294A GLY 3.4 2.6 + - - -
323A HIS* 2.7 44.5 + - + +
553A MSP 2.7 32.2 + - - +
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Residues in contact with HIS 28 (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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11A CYS* 3.7 28.8 - - + +
12A ALA 4.2 1.3 + - - -
14A PRO* 4.1 10.0 - - + +
24A HIS* 3.2 22.9 + - + +
25A MET* 4.2 5.4 - - + +
27A GLU* 1.3 89.3 + - + +
29A ILE* 1.3 58.1 + - - +
31A ALA* 3.6 1.4 + - - +
32A ASP* 3.0 29.8 + - - +
49A CYS* 3.9 16.4 - - - -
84A PHE* 3.5 30.8 - + + -
89A ILE* 3.7 23.5 - - + +
91A TYR* 2.6 30.9 + - - -
553A MSP 6.0 1.6 - - - -
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Residues in contact with ILE 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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25A MET* 2.8 44.9 + - + +
26A LEU 3.9 2.9 - - - +
28A HIS* 1.3 75.6 - - - +
30A GLN* 1.3 67.0 + - - +
32A ASP* 3.3 2.2 + - - +
33A VAL* 3.0 32.7 + - + +
87A PHE* 4.3 13.0 - - + -
89A ILE* 4.2 9.0 - - + -
355A LEU* 4.3 3.1 - - + -
356A ARG* 3.9 55.4 - - + +
359A TYR* 3.8 27.8 - - + -
360A THR* 4.5 2.7 - - - +
363A LEU* 5.6 0.9 - - + -
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Residues in contact with GLN 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 LEU* 2.9 19.3 + - - +
27A GLU 3.8 3.2 - - - +
29A ILE* 1.3 77.7 - - - +
31A ALA* 1.3 64.1 + - - +
33A VAL 3.5 0.5 + - - -
34A TRP* 3.3 17.2 + - - +
292A PHE* 3.6 28.1 - - + -
321A PHE* 5.0 1.9 - - - +
322A VAL 5.3 3.3 + - - -
323A HIS* 3.6 30.4 + - - +
363A LEU* 3.7 35.8 - - + +
364A SER 4.0 14.5 + - - -
366A ARG 5.8 0.6 + - - -
435A ARG* 5.2 12.6 + - + +
437A PHE* 3.5 28.4 - - + -
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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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9A VAL* 4.8 0.2 - - + -
11A CYS* 3.4 33.4 - - - -
27A GLU 3.2 6.2 + - - +
28A HIS 3.9 0.7 - - - +
30A GLN* 1.3 80.2 - - - +
32A ASP* 1.3 57.7 + - - +
34A TRP* 3.2 3.6 + - - +
35A VAL* 2.8 33.6 + - - +
47A PHE* 3.8 9.6 - - + -
292A PHE* 3.7 32.0 - - + -
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Residues in contact with ASP 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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28A HIS 3.0 19.8 + - - +
29A ILE 3.3 4.5 + - - +
31A ALA* 1.3 76.9 - - - +
33A VAL* 1.3 58.4 + - - +
35A VAL* 3.7 0.8 - - - +
36A ARG* 2.8 44.1 + - - +
47A PHE* 3.8 12.6 - - + -
88A ASN 3.2 8.1 - - - +
89A ILE* 3.8 9.4 - - + -
90A SER* 2.8 39.6 + - - -
356A ARG* 2.7 32.3 + - - +
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Residues in contact with VAL 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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29A ILE* 3.0 25.4 + - + +
30A GLN* 5.0 0.2 - - - -
32A ASP* 1.3 75.5 - - - +
34A TRP* 1.3 63.9 + - - +
36A ARG 3.4 0.2 + - - -
37A TYR* 3.0 22.6 + - + +
356A ARG* 4.0 8.7 - - - +
360A THR* 3.8 20.4 - - + +
432A TRP* 4.2 20.4 - - + -
437A PHE* 3.7 26.7 - - + -
493A PRO* 3.6 36.3 - - + +
494A VAL* 4.2 9.4 - - + +
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Residues in contact with TRP 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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7A ILE* 4.3 5.4 - - + -
9A VAL* 3.6 28.5 - - + -
30A GLN 3.3 9.8 + - - +
31A ALA 3.2 7.9 + - - +
33A VAL* 1.3 80.0 - - - +
35A VAL* 1.3 58.0 + - - +
37A TYR* 3.3 6.5 + + - +
38A GLN* 3.0 65.2 + - + +
288A GLU* 5.5 0.2 - - - -
290A TYR* 3.7 33.0 - + - -
292A PHE* 3.9 25.6 - + + -
321A PHE* 4.1 20.4 - + - -
432A TRP* 3.3 22.6 + - - -
433A GLU* 2.9 31.6 + - - -
435A ARG* 3.8 14.7 - - + +
437A PHE* 4.0 7.4 - + + -
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Residues in contact with VAL 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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9A VAL* 3.9 30.1 - - + -
31A ALA 2.8 20.5 + - - +
32A ASP* 3.7 6.3 - - - +
34A TRP* 1.3 74.4 - - + +
36A ARG* 1.3 65.5 + - - +
38A GLN* 3.2 9.3 + - - +
39A ARG* 3.0 56.1 + - - +
45A VAL* 3.9 13.5 - - + -
47A PHE* 3.8 30.3 - - + -
90A SER* 4.3 0.9 - - - +
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Residues in contact with ARG 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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32A ASP* 2.8 40.9 + - - +
33A VAL 3.9 0.4 - - - +
35A VAL* 1.3 72.9 - - - +
37A TYR* 1.3 63.1 + - - +
39A ARG* 3.3 14.2 + - - +
40A MET* 3.0 28.2 + - + +
88A ASN* 2.9 33.9 + - - +
90A SER* 3.8 26.8 - - - +
356A ARG* 3.9 1.1 - - - +
492A LYS* 4.5 3.0 + - + -
493A PRO* 3.6 33.2 - - + -
496A PRO* 3.7 22.5 - - - +
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Residues in contact with TYR 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 VAL 3.0 14.5 + - - +
34A TRP* 3.5 9.2 - + - +
36A ARG* 1.3 77.6 - - - +
38A GLN* 1.3 76.6 + - - +
40A MET* 3.0 14.5 + - + +
41A ARG* 2.9 56.6 + - + +
429A GLY* 3.1 34.5 + - - -
432A TRP* 3.6 31.6 - + + -
433A GLU* 3.7 22.9 - - - +
493A PRO* 4.0 15.2 - - + +
512A TRP* 3.8 31.4 - + - -
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Residues in contact with GLN 38 (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 LYS* 5.3 0.9 - - - +
7A ILE* 4.0 12.1 - - + +
34A TRP* 3.0 58.4 + - + +
35A VAL* 3.5 9.0 - - - +
37A TYR* 1.3 86.8 - - - +
39A ARG* 1.3 61.8 + - - +
41A ARG* 3.3 10.0 + - - +
42A GLY 3.6 0.2 + - - -
43A HIS* 3.0 50.4 + - - +
45A VAL* 3.9 18.8 - - + -
433A GLU* 2.8 33.7 + - - +
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Residues in contact with ARG 39 (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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35A VAL* 3.0 41.2 + - - +
36A ARG* 3.6 19.4 - - - +
37A TYR 3.2 0.4 - - - -
38A GLN* 1.3 74.8 - - - +
40A MET* 1.3 58.8 + - + +
42A GLY* 2.9 20.4 + - - -
43A HIS 4.5 6.0 - - - +
45A VAL* 4.0 24.9 + - + +
47A PHE* 3.9 0.8 - - - +
90A SER* 2.8 49.8 + - - -
92A ASP* 3.1 29.6 + - - -
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Residues in contact with MET 40 (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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36A ARG* 3.0 16.0 + - + +
37A TYR* 3.0 9.8 + - - +
39A ARG* 1.3 76.9 - - + +
41A ARG* 1.3 61.5 + - - +
42A GLY 3.2 3.4 + - - -
489A THR* 3.7 23.8 - - + +
492A LYS* 3.8 35.2 - - + -
493A PRO* 3.7 29.4 - - - -
510A LEU 4.0 7.0 - - - +
511A THR* 4.4 1.2 - - - -
512A TRP* 3.8 51.0 + - + +
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Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 2.9 57.0 + - + +
38A GLN* 3.3 7.4 + - - +
39A ARG 3.1 1.0 - - - -
40A MET* 1.3 76.9 - - - +
42A GLY* 1.3 60.2 + - - +
43A HIS* 3.5 27.0 + - + -
425A ALA 5.6 0.4 + - - -
426A GLU* 6.3 0.6 - - - +
429A GLY* 4.9 1.6 - - - -
433A GLU* 5.9 0.2 - - - +
512A TRP* 3.5 47.6 - - - +
513A ASP* 4.8 6.9 + - - -
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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