Contacts of the helix formed by residues 37 - 48 (chain E) in PDB entry 1F9N
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 THR 37 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26E VAL* 4.8 4.7 - - - -
36E VAL* 1.3 82.2 - - - +
38E GLN* 1.3 65.7 + - - +
39E ALA* 4.0 8.6 + - - +
40E THR* 2.5 44.3 + - - +
41E VAL* 3.1 9.6 + - - +
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Residues in contact with GLN 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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22E GLN* 4.5 2.3 - - - +
23E ASP* 3.5 24.4 + - - +
26E VAL* 4.3 22.0 - - + +
37E THR* 1.3 72.9 - - - +
39E ALA* 1.3 62.4 + - - +
41E VAL* 3.3 3.6 + - - +
42E SER* 3.0 24.5 + - - -
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Residues in contact with ALA 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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37E THR* 3.2 8.8 - - - +
38E GLN* 1.3 78.9 - - - +
40E THR* 1.3 62.5 + - + +
42E SER* 2.4 26.1 + - - -
43E ARG* 3.2 21.3 + - - +
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Residues in contact with THR 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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6E ARG* 5.3 10.3 - - - +
36E VAL* 2.9 11.8 - - - +
37E THR* 2.5 44.4 + - - +
39E ALA* 1.3 77.8 - - + +
41E VAL* 1.3 55.7 + - - +
43E ARG* 3.0 35.0 + - - +
44E ASP* 3.1 19.7 + - - +
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Residues in contact with VAL 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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10E ILE* 5.9 0.7 - - + -
22E GLN* 4.4 4.9 - - - +
25E LEU* 4.0 22.4 - - + -
26E VAL* 3.5 26.7 - - + -
29E LEU* 4.3 14.8 - - + -
36E VAL* 3.2 27.6 - - + -
37E THR 3.1 6.9 + - - +
38E GLN 3.7 6.5 - - - +
40E THR* 1.3 71.2 - - - +
42E SER* 1.3 58.5 + - - +
43E ARG 2.9 5.2 - - - -
44E ASP* 3.1 11.3 + - + +
45E ILE* 2.9 45.4 + - + +
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Residues in contact with SER 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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22E GLN* 3.3 26.6 + - - -
38E GLN 3.0 11.7 + - - -
39E ALA* 2.4 29.6 + - - -
41E VAL* 1.3 76.2 - - - +
43E ARG* 1.3 60.8 + - - +
45E ILE* 4.1 6.2 - - - +
46E LYS* 3.5 19.4 + - - +
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Residues in contact with ARG 43 (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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3E LYS* 6.1 1.8 - - - +
39E ALA* 3.3 23.0 + - - +
40E THR* 3.0 21.2 + - - +
41E VAL 2.9 0.6 - - - -
42E SER* 1.3 80.9 - - - +
44E ASP* 1.3 57.1 + - - +
46E LYS* 3.1 5.5 + - - +
47E GLU* 2.7 52.2 + - + +
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Residues in contact with ASP 44 (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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3E LYS* 4.7 2.4 - - - -
6E ARG* 2.7 43.7 + - - -
7E HIS* 3.0 25.6 + - + +
10E ILE* 3.6 23.1 - - + +
29E LEU* 4.9 0.2 - - - +
36E VAL* 5.1 0.2 - - - +
40E THR 3.1 14.7 + - - +
41E VAL* 3.1 15.8 + - + +
43E ARG* 1.3 76.7 - - - +
45E ILE* 1.3 57.2 + - + +
47E GLU* 3.0 4.3 + - - +
48E LEU* 2.7 41.3 + - + +
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Residues in contact with ILE 45 (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 ILE* 6.4 0.2 - - + -
22E GLN* 3.3 46.4 - - + +
25E LEU* 4.1 17.5 - - + -
41E VAL* 2.9 32.1 + - + +
42E SER* 4.1 6.1 - - - +
44E ASP* 1.3 77.0 - - + +
46E LYS* 1.3 58.3 + - - +
49E HIS 3.5 0.5 + - - -
50E LEU* 3.0 59.2 + - + +
62E TYR* 3.9 20.2 - - + -
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Residues in contact with LYS 46 (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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42E SER 3.5 15.3 + - - +
43E ARG* 3.1 6.6 + - - +
44E ASP 3.1 0.6 - - - -
45E ILE* 1.3 78.6 - - - +
47E GLU* 1.3 65.9 + - + +
48E LEU 3.3 0.4 - - - -
49E HIS* 3.3 21.7 + - - +
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Residues in contact with GLU 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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3E LYS* 2.9 42.9 + - - -
7E HIS* 3.0 21.5 + - + -
43E ARG* 2.7 38.6 + - - +
44E ASP* 3.7 5.1 - - - +
46E LYS* 1.3 76.1 - - + +
48E LEU* 1.3 60.3 + - - +
49E HIS* 3.1 18.1 + - - -
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Residues in contact with LEU 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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81B MET 5.1 4.3 - - - +
7E HIS* 3.9 46.9 - - + +
10E ILE* 3.9 33.0 - - + -
11E ARG* 4.2 29.2 - - + +
44E ASP 2.7 21.5 + - - +
47E GLU* 1.3 72.4 - - - +
49E HIS* 1.3 74.8 + - - +
50E LEU* 3.2 24.9 + - + +
64E LEU* 4.9 3.4 - - + +
65E PRO* 3.8 10.2 - - - +
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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