Contacts of the helix formed by residues 25 - 40 (chain E) in PDB entry 3CFV
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 25 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E ASP* 1.3 77.1 - - - +
26E ILE* 1.3 65.8 + - + +
27E GLN* 3.4 27.6 + - - +
28E GLY* 3.3 21.7 + - - +
29E ILE* 3.1 21.0 + - - +
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Residues in contact with ILE 26 (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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25E ASN* 1.3 73.2 - - + +
27E GLN* 1.3 65.2 + - - +
29E ILE* 3.1 22.7 + - + +
30E THR* 3.1 19.0 + - + +
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Residues in contact with GLN 27 (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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406B ASN* 3.1 38.7 + - - +
25E ASN* 3.3 14.5 + - - +
26E ILE* 1.3 79.6 - - - +
28E GLY* 1.3 57.9 + - - +
29E ILE 3.2 0.2 + - - -
30E THR* 3.2 8.6 + - - +
31E LYS* 2.9 49.8 + - - +
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Residues in contact with GLY 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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24E ASP* 6.4 0.4 - - - -
25E ASN* 3.3 21.3 + - - +
26E ILE 3.3 0.6 - - - -
27E GLN* 1.3 77.7 - - - +
29E ILE* 1.3 64.1 + - - +
31E LYS* 4.1 13.2 - - - +
32E PRO* 3.4 17.7 - - - +
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Residues in contact with ILE 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ASP* 4.4 21.3 - - + +
25E ASN 3.1 23.1 - - - +
26E ILE* 3.1 18.7 + - + +
27E GLN 3.1 0.8 - - - -
28E GLY* 1.3 83.1 - - - +
30E THR* 1.3 69.9 + - + +
32E PRO* 3.3 13.5 - - - +
33E ALA* 4.5 5.7 + - - +
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Residues in contact with THR 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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406B ASN* 4.8 3.5 + - - -
26E ILE* 3.1 15.2 + - + +
27E GLN* 3.2 10.0 + - - +
29E ILE* 1.3 86.9 - - + +
31E LYS* 1.3 60.1 + - - +
32E PRO* 3.5 0.9 - - - -
33E ALA* 3.8 11.2 - - + -
34E ILE* 2.8 47.4 + - + +
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Residues in contact with LYS 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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406B ASN* 3.1 39.7 + - - +
409B ASN 4.5 1.6 - - - -
410B ASP* 2.7 45.5 + - - +
27E GLN* 2.9 37.2 + - - +
28E GLY* 4.3 9.9 - - - +
30E THR* 1.3 78.0 - - - +
32E PRO* 1.3 64.7 - - + +
34E ILE* 4.0 0.5 - - - +
35E ARG* 3.0 52.6 + - - +
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Residues in contact with PRO 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 GLY 3.4 12.8 - - - +
29E ILE 3.3 16.8 - - - +
31E LYS* 1.3 96.8 - - + +
33E ALA* 1.3 55.1 + - - +
35E ARG* 4.2 6.6 - - + +
36E ARG* 3.1 41.1 + - - +
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Residues in contact with ALA 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 ILE 4.5 4.0 + - - +
30E THR* 3.8 19.1 - - + +
31E LYS 3.2 0.2 - - - -
32E PRO* 1.3 79.1 - - - +
34E ILE* 1.3 63.5 + - + +
36E ARG* 3.4 20.6 + - - +
37E LEU* 3.0 26.7 + - - +
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Residues in contact with ILE 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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29B PHE* 3.6 54.1 - - + +
30B LEU* 3.8 5.6 - - + +
406B ASN* 3.8 21.3 - - + +
407B ILE* 4.0 23.1 - - + -
30E THR* 2.8 32.6 + - + +
31E LYS 4.1 1.1 - - - +
33E ALA* 1.3 76.3 - - + +
35E ARG* 1.3 61.0 + - + +
37E LEU* 3.1 10.3 + - + +
38E ALA* 2.8 27.2 + - - +
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Residues in contact with ARG 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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348B LYS* 4.2 19.2 - - - +
366B LEU* 4.8 1.3 - - + +
406B ASN* 3.7 20.0 + - - +
407B ILE* 3.5 37.7 + - + -
408B TYR 4.9 2.2 + - - -
409B ASN 4.2 2.8 + - - +
410B ASP* 4.1 27.3 - - - +
31E LYS* 3.0 37.0 + - - +
32E PRO* 4.2 6.5 - - + +
34E ILE* 1.3 77.2 - - + +
36E ARG* 1.3 58.5 + - - +
38E ALA* 3.6 7.7 + - - +
39E ARG* 3.2 34.9 + - - +
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Residues in contact with ARG 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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356B GLU* 5.0 16.5 + - - -
357B ASP* 3.1 31.9 + - - +
360B ASP* 4.3 7.9 - - - +
32E PRO* 3.1 26.8 + - - +
33E ALA* 3.7 19.0 + - - +
34E ILE 3.2 0.2 - - - -
35E ARG* 1.3 76.1 - - - +
37E LEU* 1.3 63.4 + - - +
38E ALA 3.1 0.2 - - - -
39E ARG* 3.2 17.5 + - - +
40E ARG* 3.2 58.5 + - - +
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Residues in contact with LEU 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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26B ASN* 3.6 33.4 - - - +
29B PHE* 4.0 21.3 - - + -
30B LEU* 4.0 25.9 - - + +
33E ALA 3.0 14.5 + - - +
34E ILE* 3.1 14.1 + - + +
36E ARG* 1.3 76.4 - - - +
38E ALA* 1.3 62.1 + - - +
40E ARG* 3.4 13.5 + - + +
41E GLY 3.2 26.3 + - - -
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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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30B LEU* 3.6 10.5 - - + +
366B LEU 4.0 8.1 - - - +
367B PHE* 3.6 25.1 - - + -
368B ILE* 2.9 28.7 + - - +
407B ILE* 3.8 17.0 - - + -
34E ILE 2.8 15.1 + - - +
35E ARG 3.7 8.5 - - - +
36E ARG 3.1 0.2 - - - -
37E LEU* 1.3 78.7 - - - +
39E ARG* 1.3 60.7 + - - +
41E GLY* 3.5 6.2 + - - -
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Residues in contact with ARG 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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353B GLN* 3.9 7.6 - - - +
357B ASP* 3.3 28.1 + - - +
360B ASP* 3.5 35.1 + - + +
361B GLY* 2.8 21.5 + - - -
362B PRO 2.6 30.9 + - - -
363B PRO* 4.2 4.3 + - - +
365B LEU* 2.8 33.2 + - + +
366B LEU* 3.7 12.8 - - - +
368B ILE* 3.4 26.8 - - - +
35E ARG* 3.2 22.0 - - - +
36E ARG* 3.2 10.2 + - - +
38E ALA* 1.3 76.0 - - - +
40E ARG* 1.3 60.6 + - - +
41E GLY 3.3 1.1 - - - -
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Residues in contact with ARG 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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356B GLU* 5.1 4.4 + - - +
360B ASP* 3.0 35.0 + - - +
368B ILE* 4.9 3.8 - - - -
36E ARG* 3.2 58.7 + - - +
37E LEU* 4.0 13.4 - - + +
38E ALA 3.3 0.2 - - - -
39E ARG* 1.3 78.1 - - - +
41E GLY* 1.3 60.1 + - - +
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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