Contacts of the helix formed by residues 27 - 42 (chain E) in PDB entry 2CNW
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 ASN 27 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26E GLY* 1.3 71.5 - - - -
28E LEU* 1.3 56.0 + - - +
29E GLU* 2.7 33.7 + - - +
30E GLU* 2.7 47.5 + - - +
31E VAL* 3.0 9.4 + - - +
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Residues in contact with LEU 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E GLY 3.6 2.1 + - - -
27E ASN* 1.3 70.8 - - - +
29E GLU* 1.3 69.1 + - + +
31E VAL* 4.3 5.6 - - - +
32E LEU* 3.1 43.2 + - + +
57E ARG* 5.2 9.0 - - + -
60E GLY* 6.3 1.6 - - - -
61E ARG 4.7 16.4 - - - +
64E LEU* 4.4 20.9 - - + +
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Residues in contact with GLU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ASN* 2.7 19.2 + - - +
28E LEU* 1.3 90.5 - - + +
30E GLU* 1.3 64.7 + - - +
31E VAL 3.3 0.2 - - - -
32E LEU* 3.3 8.5 + - - +
33E GLU* 2.9 27.9 + - - +
57E ARG* 4.9 7.3 - - - -
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Residues in contact with GLU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E PRO* 4.1 24.2 - - - +
26E GLY* 3.4 22.3 - - - -
27E ASN* 2.7 32.5 + - - +
29E GLU* 1.3 74.3 - - - +
31E VAL* 1.3 54.9 + - - +
33E GLU* 3.8 6.3 - - - +
34E GLU* 2.9 46.6 + - + +
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Residues in contact with VAL 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E PRO 3.5 16.4 - - - +
24E TRP* 3.6 33.4 - - + -
25E GLY 3.8 7.9 - - - +
26E GLY* 3.3 39.9 - - - +
27E ASN 3.0 6.9 + - - +
28E LEU 4.3 2.2 - - - +
30E GLU* 1.3 75.5 - - - +
32E LEU* 1.3 59.4 + - - +
34E GLU* 3.1 4.3 + - - +
35E LEU* 2.9 28.9 + - + +
64E LEU* 3.7 30.5 - - + -
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Residues in contact with LEU 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LEU* 3.1 30.1 + - + +
29E GLU* 3.3 7.2 + - - +
31E VAL* 1.3 79.3 - - + +
33E GLU* 1.3 58.5 + - - +
35E LEU* 3.8 20.9 - - + -
36E GLU* 3.5 4.9 + - - +
53E LEU* 3.4 33.3 - - + +
56E VAL* 3.7 29.8 - - + -
57E ARG* 3.4 54.3 - - + +
64E LEU* 4.8 8.5 - - + -
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Residues in contact with GLU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E GLU 2.9 17.7 + - - +
30E GLU* 3.9 5.0 - - - +
32E LEU* 1.3 74.8 - - - +
34E GLU* 1.3 72.4 + - - +
35E LEU 3.4 0.2 - - - -
36E GLU* 3.4 17.8 + - - +
37E MET* 3.1 50.4 + - + +
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Residues in contact with GLU 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E PRO* 3.7 34.9 - - + +
30E GLU* 2.9 36.4 + - + +
31E VAL* 3.7 4.7 - - - +
33E GLU* 1.3 78.8 + - - +
35E LEU* 1.3 60.5 + - - +
36E GLU 3.2 0.2 - - - -
37E MET* 3.2 35.6 + - - +
38E ALA* 3.0 28.8 + - - +
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Residues in contact with LEU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E TRP* 4.2 21.1 - - + -
31E VAL* 2.9 17.0 + - + +
32E LEU* 3.8 18.4 - - + +
34E GLU* 1.3 77.3 - - - +
36E GLU* 1.3 52.6 + - - +
38E ALA* 3.3 5.1 + - - +
39E LEU* 2.8 63.3 + - + +
52E ILE* 4.7 4.3 - - + -
53E LEU* 3.3 23.8 - - + -
56E VAL* 5.1 0.7 - - + -
68E VAL* 3.7 45.3 - - + -
302E LEU* 4.4 8.1 - - + -
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Residues in contact with GLU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ARG* 6.0 0.2 + - - -
32E LEU 3.5 12.1 + - - +
33E GLU* 3.4 21.7 + - - +
34E GLU 3.2 0.4 - - - -
35E LEU* 1.3 80.6 - - - +
37E MET* 1.3 60.0 + - - +
39E LEU* 4.1 0.5 - - - +
40E LEU* 3.1 50.2 + - + +
46E LEU* 5.9 2.1 - - - +
49E THR* 3.7 16.8 - - + +
53E LEU* 3.6 27.8 - - + +
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Residues in contact with MET 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 3.7 19.7 - - + +
49B ARG* 5.0 13.5 - - - +
33E GLU* 3.1 45.6 + - - +
34E GLU* 3.2 36.1 + - - +
36E GLU* 1.3 81.8 - - - +
38E ALA* 1.3 56.4 + - - +
40E LEU* 5.4 0.9 - - + -
41E ALA* 2.9 32.1 + - - +
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Residues in contact with ALA 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLU 3.0 15.5 + - - +
35E LEU* 3.7 6.3 - - - +
37E MET* 1.3 73.6 - - - +
39E LEU* 1.3 62.3 + - - +
41E ALA* 3.8 4.9 - - - +
42E ALA* 3.0 29.8 + - - +
262E LYS* 5.8 0.2 - - - +
301E LEU* 4.8 7.3 - - - +
302E LEU* 4.8 17.3 - - + -
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Residues in contact with LEU 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LEU* 2.8 55.5 + - + +
38E ALA* 1.3 73.1 - - - +
40E LEU* 1.3 60.6 + - - +
42E ALA* 3.2 8.2 + - - -
44E VAL* 3.0 42.2 + - + +
49E THR* 3.6 32.1 - - + +
52E ILE* 4.0 34.5 - - + -
53E LEU* 4.5 1.1 - - + -
72E LEU* 4.7 8.3 - - + -
267E ILE* 6.4 0.2 - - + -
301E LEU* 3.9 23.8 - - + -
302E LEU* 4.5 4.3 - - + -
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Residues in contact with LEU 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B MET* 3.8 36.7 - - + +
45B LEU* 3.8 16.6 - - + -
49B ARG* 5.6 2.2 - - - +
224B GLN* 3.4 16.1 + - - +
36E GLU* 3.1 38.6 + - + +
37E MET* 5.4 0.7 - - + -
39E LEU* 1.3 76.5 - - - +
41E ALA* 1.3 60.3 + - - +
43E ASP* 3.3 10.9 + - - -
44E VAL 4.7 1.8 - - - +
45E GLY* 3.4 35.7 + - - +
46E LEU* 3.9 19.1 - - + +
49E THR* 3.6 11.0 - - + +
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Residues in contact with ALA 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 3.9 17.9 - - + +
224B GLN* 3.6 24.6 - - + +
225B GLU* 4.5 9.9 - - - +
37E MET 2.9 19.8 + - - +
38E ALA* 4.0 5.6 - - - +
40E LEU* 1.3 72.0 - - - +
42E ALA* 1.3 58.0 + - - +
43E ASP* 3.1 10.8 + - - +
262E LYS* 5.9 0.3 - - - +
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Residues in contact with ALA 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ALA 3.0 19.5 + - - +
39E LEU 3.2 7.3 + - - +
41E ALA* 1.3 77.1 - - - +
43E ASP* 1.3 63.2 + - - +
44E VAL* 3.3 1.3 - - + -
262E LYS* 4.3 20.4 - - + +
263E GLY 4.2 2.9 + - - -
264E GLY* 2.9 28.8 + - - -
301E LEU* 3.8 33.4 - - + +
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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
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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