Contacts of the helix formed by residues 46 - 57 (chain E) in PDB entry 4YC6
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 46 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E LEU* 5.6 1.4 - - - +
40E GLU* 3.1 26.7 + - - -
44E VAL* 5.6 1.1 - - - -
45E PRO* 1.3 69.5 - - - +
47E THR* 1.3 61.5 + - - +
48E ALA* 3.3 16.6 + - - +
49E ILE* 3.3 28.3 + - - +
50E ARG* 2.9 34.6 + - - +
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Residues in contact with THR 47 (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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45E PRO* 3.3 8.0 + - + +
46E SER* 1.3 70.3 + - - +
48E ALA* 1.3 66.4 + - - +
50E ARG* 3.2 12.7 + - + +
51E GLU* 3.0 34.0 + - - +
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Residues in contact with ALA 48 (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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37E LEU* 4.9 8.3 - - + -
38E GLU* 5.8 1.1 - - - +
46E SER* 3.3 9.6 + - - +
47E THR* 1.3 81.2 + - - +
49E ILE* 1.3 66.4 + - + +
51E GLU* 3.5 4.0 - - - +
52E ILE* 3.2 26.7 + - - +
152E ALA* 3.2 29.7 - - - +
153E PHE* 4.2 15.5 - - + -
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Residues in contact with ILE 49 (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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37E LEU* 3.6 30.3 - - + -
40E GLU* 5.4 0.9 - - - +
46E SER* 3.3 28.6 + - - +
47E THR 3.4 0.2 - - - -
48E ALA* 1.3 74.9 - - + +
50E ARG* 1.3 69.0 + - - +
52E ILE* 2.9 9.6 + - + +
53E SER* 2.6 41.6 + - - +
69E VAL* 6.3 2.5 - - + -
71E MET* 5.0 11.2 - - - -
76E LEU* 4.8 15.7 - - + -
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Residues in contact with ARG 50 (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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45E PRO* 3.5 26.6 - - - +
46E SER* 2.9 36.9 + - - +
47E THR* 3.2 19.4 + - + +
49E ILE* 1.3 84.8 - - - +
51E GLU* 1.3 66.0 + - + +
53E SER* 3.2 21.6 + - - -
54E LEU* 3.3 20.9 + - + +
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Residues in contact with GLU 51 (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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47E THR* 3.0 21.7 + - - +
48E ALA 3.5 7.9 - - - +
50E ARG* 1.3 78.0 - - - +
52E ILE* 1.3 61.9 + - - +
54E LEU* 3.0 19.7 + - - +
55E LEU* 3.0 31.0 + - + +
148E GLY 5.2 1.2 - - - +
151E ARG* 3.1 46.4 + - + +
152E ALA* 3.5 27.4 - - + -
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Residues in contact with ILE 52 (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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48E ALA 3.2 15.9 - - - +
49E ILE* 2.9 15.3 + - + +
51E GLU* 1.3 69.2 - - - +
53E SER* 1.3 67.6 - - - +
55E LEU* 3.1 8.0 + - + +
56E LYS* 3.0 21.8 + - - +
66E LEU* 4.4 8.7 - - + -
69E VAL* 3.7 34.8 - - + -
76E LEU* 4.9 9.6 - - + -
78E LEU* 4.5 12.6 - - + -
149E LEU* 3.7 30.7 - - + -
152E ALA* 4.0 15.5 - - + -
153E PHE* 4.1 15.7 - - + -
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Residues in contact with SER 53 (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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49E ILE* 2.6 36.2 + - - +
50E ARG* 3.2 14.0 + - - -
52E ILE* 1.3 73.8 - - - +
54E LEU* 1.3 70.4 + - - +
56E LYS* 3.1 30.9 - - - +
57E GLU* 3.1 17.5 - - - +
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Residues in contact with LEU 54 (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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50E ARG* 3.3 22.6 + - + +
51E GLU* 3.0 19.7 + - - +
53E SER* 1.3 88.1 - - - +
55E LEU* 1.3 62.6 + - + +
57E GLU* 3.3 25.4 + - + +
58E LEU* 3.3 15.6 - - + +
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Residues in contact with LEU 55 (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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51E GLU* 3.0 27.7 + - + +
52E ILE* 3.1 11.4 + - + +
54E LEU* 1.3 71.6 - - + +
56E LYS* 1.3 65.8 + - - +
57E GLU 3.1 1.8 - - - -
58E LEU* 3.2 29.9 + - + +
66E LEU* 4.0 21.1 - - + +
124E VAL* 3.9 33.7 - - + -
147E PHE* 4.0 27.4 - - + +
148E GLY* 3.6 28.3 - - - +
149E LEU* 4.1 14.4 - - + -
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Residues in contact with LYS 56 (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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52E ILE 3.0 7.2 + - - +
53E SER* 3.1 30.0 - - - +
55E LEU* 1.3 77.5 - - - +
57E GLU* 1.3 61.9 + - - +
58E LEU 3.3 0.7 + - - +
59E ARG* 2.6 33.8 + - - +
66E LEU* 3.7 23.0 - - + +
67E GLN 4.6 6.5 - - - +
68E ASP* 4.8 6.7 + - - +
69E VAL* 3.8 42.6 + - + +
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Residues in contact with GLU 57 (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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53E SER 3.1 21.5 - - - +
54E LEU* 3.3 22.4 - - + +
55E LEU 3.1 0.8 - - - -
56E LYS* 1.3 84.5 - - - +
58E LEU* 1.3 69.0 + - + +
59E ARG* 3.2 13.9 + - - +
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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