Contacts of the helix formed by residues 53 - 65 (chain E) in PDB entry 2FRV
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 GLY 53 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E ALA* 1.3 72.1 - - - +
54E HIS* 1.3 61.7 + - - -
56E VAL* 3.0 21.7 + - - +
57E GLU* 3.5 3.9 + - - +
10F VAL 5.2 1.3 - - - -
11F VAL* 3.7 9.1 - - - +
12F ASP 3.7 28.3 - - - -
13F PRO* 2.8 22.7 + - - +
174F TYR* 4.8 0.7 - - - -
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Residues in contact with HIS 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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52E ALA 3.5 0.4 + - - -
53E GLY* 1.3 69.9 - - - -
55E ALA* 1.3 63.0 + - - +
57E GLU* 3.8 12.1 - - + +
58E GLU* 3.1 41.8 + - - +
10F VAL* 4.4 29.7 + - + +
12F ASP 5.2 7.6 + - - -
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Residues in contact with ALA 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 GLY* 4.6 1.3 - - - -
52E ALA 3.3 15.5 + - - +
53E GLY 3.2 1.8 + - - -
54E HIS* 1.3 76.1 - - - +
56E VAL* 1.3 60.0 + - - +
58E GLU* 3.7 5.5 + - - -
59E ALA* 3.4 6.9 + - - +
172F ASN* 2.5 62.7 + - + +
174F TYR* 4.4 12.3 - - + -
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Residues in contact with VAL 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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44E TYR* 3.5 18.3 - - + -
49E MET* 3.8 24.7 - - + -
51E GLY* 3.2 33.9 - - - +
53E GLY 3.0 26.5 - - - +
55E ALA* 1.3 76.7 - - + +
57E GLU* 1.3 72.2 + - - +
58E GLU 3.3 0.2 - - - -
59E ALA* 3.1 8.0 - - - +
60E LEU 2.9 23.6 + - - -
13F PRO* 3.7 17.9 - - + -
15F THR* 3.9 9.4 - - + -
171F THR 5.1 3.4 - - - +
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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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44E TYR* 2.8 31.3 + - - -
53E GLY 3.5 5.3 + - - +
54E HIS* 3.3 16.3 + - + +
56E VAL* 1.3 74.8 - - - +
58E GLU* 1.3 58.8 + - - +
60E LEU* 4.0 15.7 - - - +
61E HIS* 3.0 27.7 + - - +
87E VAL* 4.3 12.1 - - - +
88E GLY* 5.8 4.2 - - - -
90E ARG* 6.0 2.6 + - - -
95E ILE* 5.7 4.3 - - - +
12F ASP 4.4 4.5 - - - +
13F PRO* 3.4 28.8 - - + +
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Residues in contact with GLU 58 (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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54E HIS* 3.1 33.9 + - - +
55E ALA* 3.8 8.6 - - - +
57E GLU* 1.3 76.3 - - + +
59E ALA* 1.3 58.7 + - - +
61E HIS* 3.4 7.3 + - - +
62E GLU* 3.1 35.9 + - + +
172F ASN* 4.0 9.4 + - - +
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Residues in contact with ALA 59 (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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43E ASP 4.5 14.7 - - - +
44E TYR* 4.8 0.9 - - + -
49E MET* 4.6 6.1 - - + -
55E ALA 3.4 11.8 + - - +
56E VAL* 3.1 14.4 - - - +
58E GLU* 1.3 77.0 - - - +
60E LEU* 1.3 67.9 + - - +
62E GLU* 4.2 3.8 - - - +
63E ALA* 2.9 26.5 + - - +
171F THR* 4.2 20.2 - - + +
172F ASN* 3.8 8.2 - - - +
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Residues in contact with LEU 60 (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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10E VAL* 3.2 35.4 - - + -
12E LEU* 4.2 12.6 - - + -
44E TYR* 3.6 43.5 - - + -
56E VAL 2.9 11.6 + - - +
57E GLU* 3.6 19.7 + - - +
59E ALA* 1.3 80.0 - - - +
61E HIS* 1.3 64.6 + - - +
63E ALA* 3.0 9.8 + - - +
64E ILE* 3.1 30.6 + - + +
90E ARG* 6.1 1.6 - - - +
95E ILE* 4.3 15.7 - - + -
98E GLU* 6.5 0.4 - - - -
99E VAL* 4.4 7.2 - - + -
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Residues in contact with HIS 61 (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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57E GLU 3.0 20.3 + - - +
58E GLU* 3.5 7.6 - - - +
59E ALA 3.2 0.2 - - - -
60E LEU* 1.3 77.1 - - - +
62E GLU* 1.3 83.8 + - - +
64E ILE* 3.6 18.8 - - + +
65E LYS* 3.5 33.8 + - - +
98E GLU* 4.8 11.1 + - - -
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Residues in contact with GLU 62 (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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58E GLU* 3.1 19.6 + - + +
59E ALA* 4.2 4.3 - - - +
61E HIS* 1.3 87.7 - - - +
63E ALA* 1.3 67.0 + - - +
64E ILE 3.2 0.2 - - - -
65E LYS* 2.9 51.7 + - - +
66E GLY 4.2 1.6 + - - -
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Residues in contact with ALA 63 (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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8E SER* 4.7 3.6 + - - +
10E VAL* 3.7 23.6 - - + -
43E ASP* 4.0 22.9 - - + +
59E ALA 2.9 20.3 + - - +
60E LEU* 3.0 4.2 + - - +
62E GLU* 1.3 79.8 - - - +
64E ILE* 1.3 58.1 + - - +
65E LYS 3.1 4.2 + - - -
66E GLY* 3.2 13.0 + - - -
68E PHE* 3.8 13.7 - - - +
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Residues in contact with ILE 64 (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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10E VAL* 4.2 6.5 - - + -
60E LEU* 3.1 35.5 + - + +
61E HIS* 3.6 21.1 - - - +
62E GLU 3.2 0.2 - - - -
63E ALA* 1.3 75.1 - - - +
65E LYS* 1.3 63.4 + - + +
66E GLY 3.2 2.6 + - - +
68E PHE* 3.5 35.6 - - + -
98E GLU* 3.7 28.5 - - + +
99E VAL* 3.9 25.6 - - + -
102E LYS* 3.9 29.5 - - + +
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Residues in contact with LYS 65 (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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61E HIS* 3.5 40.8 + - - +
62E GLU* 2.9 42.7 + - - +
63E ALA 3.1 1.2 - - - -
64E ILE* 1.3 81.4 - - + +
66E GLY* 1.3 55.8 + - - +
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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