Contacts of the helix formed by residues 21 - 41 (chain A) in PDB entry 2CT8
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 VAL 4.1 6.2 + - - +
20A PRO* 1.3 78.3 - - - +
22A LEU* 1.3 69.2 + - - +
23A GLY* 3.0 30.9 - - - -
24A HIS* 2.7 48.3 + + - +
25A ALA 3.1 7.3 + - - -
296A MET* 4.8 10.5 - - + -
298A LYS* 6.3 0.6 - - - +
303A VAL* 3.8 24.5 - - + +
304A VAL 3.6 14.6 - - - +
306A PRO* 3.4 10.7 - - - +
501A MSP 3.5 27.6 + + - -
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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
----------------------------------------------------------
21A HIS* 1.3 72.3 - - - +
23A GLY* 1.3 58.1 + - - +
25A ALA* 3.0 8.2 + - + +
26A TYR* 2.7 29.3 + - + +
289A TRP* 4.6 14.8 - - + -
296A MET* 4.0 23.8 - - + -
304A VAL* 3.1 36.4 + - + -
306A PRO* 3.4 12.7 - - + +
309A VAL* 4.7 15.3 - - + -
318A VAL* 5.3 2.2 - - + -
322A LEU* 4.3 26.5 - - + -
334A PHE* 4.1 33.0 - - + -
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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 18.8 + - - -
22A LEU* 1.3 77.8 - - - +
24A HIS* 1.3 59.1 + - - -
26A TYR* 3.2 18.8 + - - +
27A THR* 3.4 12.5 + - - -
289A TRP* 5.5 1.1 - - - -
296A MET* 4.7 2.8 - - - -
501A MSP 3.6 38.6 + - - -
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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
----------------------------------------------------------
14A TYR* 3.0 46.1 + + + -
15A TYR* 5.1 3.1 - - + -
18A ASP* 5.7 4.7 - - + -
19A VAL 4.1 9.2 - - - -
20A PRO* 3.5 6.6 - - + +
21A HIS* 2.7 58.2 + + - +
23A GLY* 1.3 73.5 - - - +
25A ALA* 1.3 61.2 + - - +
27A THR 3.7 0.2 + - - -
28A THR* 3.0 10.7 + - - -
80A PHE* 3.9 28.1 - + + -
84A TRP* 3.9 5.6 - - + -
501A MSP 3.3 38.0 + - - -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS 3.1 7.9 + - - +
22A LEU* 3.0 13.4 + - + +
24A HIS* 1.3 76.3 - - - +
26A TYR* 1.3 60.1 + - - +
28A THR* 3.8 0.6 - - - -
29A ILE* 2.8 41.5 + - + +
83A LEU* 4.7 0.6 - - + +
84A TRP* 3.9 14.3 - - + -
87A LEU* 3.8 24.7 - - + -
306A PRO* 4.3 15.5 - - + -
322A LEU* 5.3 0.2 - - - -
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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
----------------------------------------------------------
22A LEU* 2.7 13.0 + - + +
23A GLY* 3.3 12.6 - - - +
24A HIS 3.2 0.4 - - - -
25A ALA* 1.3 75.1 - - - +
27A THR* 1.3 64.9 + - - +
29A ILE* 3.3 1.7 + - + +
30A ALA* 2.9 22.7 + - + +
286A HIS* 3.7 41.2 - + + +
287A GLY 4.4 4.3 + - - -
289A TRP* 3.2 39.9 + + + +
322A LEU* 3.9 50.6 + - + +
323A LEU* 4.5 11.2 - - + +
326A VAL* 5.3 8.1 + - - +
328A PHE* 3.5 28.0 - + - -
329A GLY 5.3 0.7 + - - -
330A GLN 5.4 1.7 + - - -
501A MSP 3.9 3.1 - + - -
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 3.9 3.5 - - - +
12A PRO* 3.3 32.3 - - + -
14A TYR* 3.4 11.9 - - - +
23A GLY 3.4 9.2 + - - -
24A HIS 4.1 1.1 - - - -
26A TYR* 1.3 78.2 - - - +
28A THR* 1.3 62.6 + - - +
30A ALA* 3.5 5.8 + - + +
31A ALA* 3.1 22.3 + - - +
255A LEU* 3.9 19.0 - - + +
256A VAL 4.6 0.2 - - - +
286A HIS* 2.8 34.8 + - + +
501A MSP 3.9 10.9 + - - -
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Residues in contact with THR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 3.9 10.0 - - + +
14A TYR* 2.6 23.5 + - - -
24A HIS 3.0 7.5 + - - -
25A ALA 3.9 1.3 - - - -
26A TYR 3.1 0.6 - - - -
27A THR* 1.3 76.1 - - - +
29A ILE* 1.3 60.3 + - - +
31A ALA* 3.2 2.8 + - - +
32A ASP* 2.9 26.2 + - - +
47A PHE* 3.8 7.1 - - + -
49A THR* 4.5 3.9 + - + +
84A TRP* 3.1 50.8 - - + +
89A ILE* 3.9 22.9 - - + -
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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 ALA* 2.8 41.3 + - + +
26A TYR* 3.9 3.4 - - + +
28A THR* 1.3 72.5 - - - +
30A ALA* 1.3 56.2 + - - +
32A ASP* 3.0 6.9 + - - +
33A THR* 2.7 40.7 + - + +
87A LEU* 4.4 15.5 - - + -
89A ILE* 4.5 13.7 - - + -
315A LEU* 6.0 0.7 - - + -
318A VAL* 4.8 8.7 - - + -
319A ARG* 4.1 48.5 - - + +
322A LEU* 3.9 22.4 - - + -
323A LEU* 4.6 9.6 - - + -
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 2.9 18.6 + - + +
27A THR* 3.6 9.0 - - - +
29A ILE* 1.3 77.3 - - - +
31A ALA* 1.3 58.5 + - - +
33A THR* 2.9 22.1 - - - +
34A ILE* 3.3 9.5 + - - +
255A LEU* 4.0 7.0 - - + +
286A HIS* 5.4 0.7 - - - +
323A LEU* 4.3 10.7 - - + +
328A PHE* 4.1 31.9 - - + -
398A PHE* 3.4 14.1 - - + -
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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* 4.4 7.5 - - + +
11A THR* 3.4 33.0 - - + -
27A THR 3.1 8.2 + - - +
28A THR 3.6 0.9 - - - +
29A ILE 3.1 0.4 - - - -
30A ALA* 1.3 77.5 - - - +
32A ASP* 1.3 65.6 + - - +
34A ILE* 2.9 21.8 - - - +
35A ALA* 2.9 9.4 + - - +
47A PHE* 3.4 15.8 - - + -
255A LEU* 3.6 17.9 - - + +
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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 THR 2.9 14.0 + - - +
29A ILE 3.0 7.6 + - - +
31A ALA* 1.3 74.6 - - - +
33A THR* 1.3 65.8 + - - +
35A ALA* 3.0 4.3 + - - +
36A ARG* 2.5 55.0 + - - +
47A PHE* 3.3 15.5 - - + -
89A ILE* 3.5 15.9 - - + +
90A GLU* 2.9 33.1 + - - +
319A ARG* 2.9 23.7 + - - +
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Residues in contact with THR 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* 2.7 22.2 + - + +
30A ALA* 2.9 23.3 - - - +
32A ASP* 1.3 73.1 - - - +
34A ILE* 1.3 61.2 + - - +
36A ARG* 2.9 14.7 + - - +
37A TYR* 3.0 9.9 + - - -
319A ARG* 3.7 8.1 - - - +
323A LEU* 3.7 22.5 - - + +
393A MET* 5.3 2.1 - - - +
398A PHE* 3.6 16.6 - - + -
453A PRO* 3.3 38.0 + - - +
454A ILE* 4.0 4.7 + - - +
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Residues in contact with ILE 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 PHE* 4.0 17.5 - - + -
9A VAL* 4.0 21.1 - - + -
30A ALA 3.3 10.8 + - - +
31A ALA* 2.9 23.6 - - - +
33A THR* 1.3 79.1 + - - +
35A ALA* 1.3 67.4 + - - +
37A TYR* 3.2 25.7 + - + +
38A TYR* 3.5 21.1 + - + -
253A LEU* 4.1 17.0 - - + -
255A LEU* 4.7 0.7 - - + -
393A MET* 3.8 26.0 - - + +
396A VAL* 4.8 7.6 - - + -
398A PHE* 4.4 19.0 - - + -
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 4.9 3.4 - - - -
9A VAL* 4.3 4.9 - - + -
31A ALA 2.9 9.9 + - - +
32A ASP* 3.5 8.1 - - - +
34A ILE* 1.3 80.3 - - - +
36A ARG* 1.3 60.9 + - + +
37A TYR 3.4 0.2 + - - -
38A TYR* 3.4 2.0 + - - +
39A ARG* 2.9 37.9 + - - +
45A VAL* 4.0 26.4 - - + +
47A PHE* 4.0 23.3 - - + -
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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* 2.5 37.9 + - - +
33A THR 2.9 7.2 + - - +
35A ALA* 1.3 74.5 - - + +
37A TYR* 1.3 66.7 + - - +
39A ARG* 4.0 11.8 - - - +
40A LEU* 3.0 26.2 + - - +
88A LYS* 3.0 27.7 + - - +
90A GLU* 2.6 42.6 + - + +
319A ARG* 4.2 0.2 - - - +
452A TYR* 2.9 41.7 + - + +
453A PRO* 3.7 22.2 - - + -
456A PRO* 3.6 30.7 - - - +
457A ASN* 5.7 1.4 + - - -
460A LYS* 4.9 3.2 - - - +
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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 THR 3.0 10.1 + - - +
34A ILE* 3.3 16.6 - - + +
36A ARG* 1.3 78.7 - - - +
38A TYR* 1.3 94.4 + + - +
41A ARG* 2.8 71.7 + - + +
389A TYR* 3.8 13.7 - + - -
390A GLU* 3.2 32.0 + - - +
393A MET* 3.3 41.1 - - + -
394A GLU* 3.3 18.2 + - + -
453A PRO* 3.9 14.1 - - + +
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Residues in contact with TYR 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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7A PHE* 3.4 50.8 - + + -
34A ILE* 3.5 19.1 - - + -
35A ALA 3.4 2.7 + - - +
36A ARG 3.3 0.2 - - - -
37A TYR* 1.3 96.0 - + - +
39A ARG* 1.3 68.7 + - - +
40A LEU 3.1 1.8 - - - -
41A ARG* 2.8 15.8 + - - +
42A ASP 3.1 0.2 + - - -
43A TYR* 3.1 70.1 + + + +
45A VAL* 3.9 9.9 - - + -
394A GLU* 3.7 32.2 + - + +
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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 ALA* 2.9 23.4 + - - +
36A ARG* 4.0 10.7 - - - +
38A TYR* 1.3 75.6 - - - +
40A LEU* 1.3 64.0 + - - +
42A ASP* 2.9 16.3 + - - -
43A TYR 4.3 7.5 - - - +
45A VAL* 3.8 45.9 + - + +
47A PHE* 4.2 10.7 - - - +
90A GLU* 3.1 37.5 + - - +
91A TYR 4.9 0.8 - - - -
92A THR* 4.3 7.3 + - - -
452A TYR* 5.9 4.0 - - + +
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Residues in contact with LEU 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 17.9 + - - +
37A TYR 3.7 4.3 - - - +
39A ARG* 1.3 76.9 - - - +
41A ARG* 1.3 86.9 + - - +
42A ASP 3.2 3.5 + - - -
449A HIS* 4.3 26.0 - - + +
452A TYR* 3.6 33.1 - - + -
453A PRO* 4.9 1.6 - - + -
471A PHE* 4.5 11.7 - - + -
472A LEU 3.0 23.1 - - - +
473A LYS* 3.3 19.1 + - - +
475A LEU* 4.1 10.5 - - + -
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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
----------------------------------------------------------
5A LYS* 3.8 13.1 + - - +
37A TYR* 2.8 77.9 + - + +
38A TYR* 2.8 11.2 + - - +
40A LEU* 1.3 102.9 - - - +
42A ASP* 1.3 69.0 + - - +
43A TYR* 3.4 22.6 + - + -
389A TYR* 3.5 16.6 - - - -
390A GLU* 2.9 27.7 + - - -
449A HIS 5.3 1.4 + - - -
453A PRO* 4.6 4.0 - - - +
473A LYS* 3.5 22.5 - - - +
474A GLU* 5.5 0.2 - - - +
475A LEU* 3.9 14.6 - - - +
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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