Contacts of the helix formed by residues 46 - 51 (chain E) in PDB entry 2QJK
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 PRO 46 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ARG* 4.2 15.9 - - + +
86D ASN* 4.8 5.8 - - - +
44E PHE 3.3 11.4 - - - +
45E VAL* 1.3 83.2 - - + +
47E ILE* 1.3 54.4 + - - +
48E ARG* 3.2 38.8 - - + +
49E SER* 2.2 57.7 + - - +
52E GLU* 5.8 0.2 - - - +
85E PRO 5.1 0.2 - - - +
86E THR 5.7 1.6 - - - +
87E ASP 3.8 5.6 - - - +
88E HIS* 3.1 24.2 - - + +
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Residues in contact with ILE 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 VAL 3.4 1.4 + - - -
46E PRO* 1.3 69.1 - - - +
48E ARG* 1.3 52.6 + - - +
50E LEU* 2.6 60.7 + - + +
63E VAL* 4.2 9.6 - - + +
66E TYR* 4.3 7.0 - - + -
67E ALA* 4.1 26.2 - - + +
70E PHE* 3.8 31.9 - - + -
72E VAL* 6.4 0.2 - - + -
83E GLY* 5.8 0.4 - - - -
84E LYS 4.3 3.6 - - - +
85E PRO* 3.9 4.7 - - + +
87E ASP* 2.8 30.5 + - + +
88E HIS 4.3 6.7 - - - +
89E PHE* 3.8 26.2 - - + +
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Residues in contact with ARG 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ASN* 3.0 28.5 + - - +
46E PRO* 4.0 25.0 - - + +
47E ILE* 1.3 71.5 - - - +
49E SER* 1.3 62.0 + - - +
50E LEU 3.1 0.7 - - - -
51E SER* 3.3 19.4 + - - +
52E GLU* 3.0 34.4 + - - +
63E VAL* 4.3 5.8 - - - -
85E PRO* 2.7 40.8 + - + +
86E THR* 4.1 20.0 + - - +
88E HIS* 5.8 0.8 - - - -
42F ALA* 3.5 23.9 + - - +
43F ASP* 3.4 26.5 + - - +
46F ALA* 5.0 6.7 - - - +
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Residues in contact with SER 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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85D ARG* 5.9 1.8 - - - -
45E VAL* 3.7 15.4 - - - +
46E PRO* 2.2 45.2 + - - +
47E ILE 2.6 4.0 + - - -
48E ARG* 1.3 70.5 - - - +
50E LEU* 1.3 64.7 + - - +
51E SER 2.8 6.7 + - - -
52E GLU* 3.1 36.3 + - - +
56E PRO* 4.6 0.2 - - - +
217E TRP* 3.5 25.3 - - - -
221E PRO* 5.7 4.7 - - - -
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Residues in contact with LEU 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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29E LEU* 3.6 33.2 - - + -
47E ILE* 2.6 40.7 + - + +
49E SER* 1.3 80.4 + - - +
51E SER* 1.3 54.6 + - - +
56E PRO* 3.9 10.3 - - + +
57E GLU 3.1 13.7 + - - -
58E LEU* 2.9 26.5 + - + -
63E VAL* 3.9 16.2 - - + -
66E TYR* 4.2 16.6 - - + -
89E PHE* 4.0 22.9 - - + -
214E PHE* 4.7 1.8 - - + -
217E TRP* 4.1 24.2 - - + -
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Residues in contact with SER 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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48E ARG* 3.4 12.3 + - - +
49E SER 2.8 0.8 - - - -
50E LEU* 1.3 76.1 - - - +
52E GLU* 1.3 70.9 + - - +
53E PRO* 3.6 1.0 - - - +
57E GLU* 3.5 13.5 - - - +
58E LEU 3.5 15.9 + - - +
60E GLU* 4.0 22.9 - - - +
63E VAL* 3.2 26.9 - - - +
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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