Contacts of the helix formed by residues 24 - 38 (chain A) in PDB entry 2CUY
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 SER 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU* 2.7 20.1 + - - +
21A TYR 3.6 4.3 - - - +
22A GLU 3.6 2.0 + - - -
23A ALA* 1.3 76.8 - - - +
25A PRO* 1.3 59.9 - - - +
26A ALA 3.3 0.5 + - - -
27A ALA* 3.0 17.5 + - - -
28A LYS* 2.9 29.2 + - - +
73A ALA* 3.2 27.8 - - - +
76A GLU* 2.8 16.7 + - - -
296A LEU* 5.5 4.0 - - - -
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Residues in contact with PRO 25 (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 4.1 4.9 - - - +
24A SER* 1.3 83.4 - - - +
26A ALA* 1.3 54.5 + - - +
28A LYS* 3.4 11.9 + - + +
29A GLU* 3.1 27.2 + - - +
76A GLU* 3.1 24.2 - - - +
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Residues in contact with ALA 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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24A SER* 3.1 1.8 - - - +
25A PRO* 1.3 74.9 - - - +
27A ALA* 1.3 65.2 + - - +
29A GLU* 3.2 8.1 + - - +
30A VAL* 3.1 26.4 + - - +
72A ARG* 3.6 37.7 + - + +
76A GLU* 2.8 28.7 + - + +
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Residues in contact with ALA 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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20A LEU* 3.7 26.2 - - + +
21A TYR 4.2 0.9 - - - +
24A SER* 3.0 20.6 + - - +
26A ALA* 1.3 75.8 - - - +
28A LYS* 1.3 63.7 + - - +
30A VAL* 3.2 2.1 + - - +
31A LEU* 3.0 31.2 + - + +
69A ALA* 3.7 33.8 + - + +
73A ALA* 4.1 3.8 - - + -
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Residues in contact with LYS 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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21A TYR* 3.5 50.0 + - + +
24A SER 2.9 17.0 + - - +
25A PRO* 3.5 11.2 - - + +
27A ALA* 1.3 76.9 - - - +
29A GLU* 1.3 56.9 + - - +
31A LEU 3.5 0.2 + - - -
32A ASP* 2.9 54.0 + - - +
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Residues in contact with GLU 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 PRO 3.1 13.8 + - - +
26A ALA* 3.6 10.3 - - - +
27A ALA 3.2 0.4 - - - -
28A LYS* 1.3 73.6 - - - +
30A VAL* 1.3 68.6 + - + +
32A ASP* 3.3 8.7 + - - +
33A ARG* 2.9 54.1 + - - +
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Residues in contact with VAL 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 ALA 3.1 12.9 + - - +
27A ALA 3.6 6.3 - - - +
29A GLU* 1.3 78.3 - - + +
31A LEU* 1.3 59.2 + - - +
33A ARG* 3.2 14.9 + - - +
34A ALA* 2.9 24.9 + - - +
65A ALA* 3.6 26.0 - - + +
68A TYR* 3.8 24.7 - - + -
69A ALA* 3.7 13.9 - - + +
72A ARG* 3.7 35.7 - - + +
104A LEU* 3.7 10.7 - - + +
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Residues in contact with LEU 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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16A MET 6.0 0.4 - - - +
17A GLY* 3.7 26.2 - - - +
21A TYR* 3.5 35.0 - - + +
27A ALA* 3.0 17.6 + - + +
30A VAL* 1.3 74.2 - - - +
32A ASP* 1.3 61.5 + - - +
34A ALA* 3.1 6.3 + - - +
35A GLU* 2.9 25.6 + - - +
42A LEU* 4.1 23.4 - - + +
45A MET* 4.6 8.1 - - + -
46A TRP* 4.2 7.0 - - + +
65A ALA* 4.0 34.8 - - + +
66A ALA* 4.5 3.1 - - - +
69A ALA* 3.9 14.1 - - + -
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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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21A TYR* 2.9 22.5 + - - -
28A LYS* 2.9 50.4 + - - +
29A GLU* 3.3 12.0 + - - +
31A LEU* 1.3 71.7 - - - +
33A ARG* 1.3 67.9 + - - +
35A GLU* 2.9 10.2 + - - +
36A ALA* 2.9 23.4 + - - +
42A LEU* 4.5 5.5 - - - +
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Residues in contact with ARG 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 GLU* 2.9 45.5 + - - +
30A VAL* 3.3 11.3 - - - +
32A ASP* 1.3 76.1 - - - +
34A ALA* 1.3 57.9 + - - +
36A ALA* 3.4 8.4 + - - +
37A ALA* 3.0 29.0 + - - +
68A TYR* 4.4 14.6 + - - -
72A ARG* 4.7 9.3 - - - +
103A GLU* 5.6 3.0 - - - +
104A LEU* 3.9 27.3 - - + +
105A GLU* 3.0 47.9 + - - +
108A LEU* 5.1 0.2 - - - -
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Residues in contact with ALA 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 VAL 2.9 11.7 + - - +
31A LEU* 3.2 12.8 - - + +
32A ASP 3.1 0.4 - - - -
33A ARG* 1.3 75.1 - - - +
35A GLU* 1.3 59.9 + - - +
37A ALA* 3.3 2.1 + - - +
38A LEU* 2.8 32.2 + - - +
41A LEU* 3.8 19.1 - - + +
45A MET* 5.4 0.9 - - + -
65A ALA* 3.9 15.9 - - + -
104A LEU* 5.1 0.7 - - + -
108A LEU* 3.6 26.9 - - + +
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Residues in contact with GLU 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 LEU 2.9 9.1 + - - +
32A ASP* 2.9 11.9 + - - +
34A ALA* 1.3 75.9 - - - +
36A ALA* 1.3 64.0 + - - +
38A LEU 3.0 1.2 - - - -
39A PRO* 2.9 32.7 - - - +
40A GLY* 3.1 19.1 + - - -
41A LEU* 2.8 14.9 + - - -
42A LEU* 2.7 60.4 + - + +
43A LYS 5.3 0.4 - - - -
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Residues in contact with ALA 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 2.9 11.3 + - - +
33A ARG* 3.6 11.7 - - - +
35A GLU* 1.3 78.5 - - - +
37A ALA* 1.3 62.0 + - - +
39A PRO* 3.7 12.1 - - - +
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Residues in contact with ALA 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 ARG 3.0 17.3 + - - +
34A ALA 3.6 4.3 - - - +
35A GLU 3.2 0.2 - - - -
36A ALA* 1.3 79.9 - - - +
38A LEU* 1.3 70.1 + - + +
39A PRO* 3.5 5.2 - - - +
105A GLU* 4.0 24.7 - - + +
108A LEU* 4.3 14.4 - - + -
109A ARG* 4.4 18.6 + - - +
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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
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34A ALA 2.8 13.4 + - - +
35A GLU* 3.0 4.7 - - - +
37A ALA* 1.3 83.2 - - - +
39A PRO* 1.3 69.6 - - - +
40A GLY 3.3 0.2 + - - -
41A LEU* 3.0 30.9 + - + +
61A PRO* 3.6 32.8 - - + -
108A LEU* 4.0 23.6 - - + +
109A ARG* 4.5 22.0 - - + -
112A ARG* 3.8 42.1 + - - +
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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