Contacts of the helix formed by residues 40 - 45 (chain E) in PDB entry 4O9U
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 ALA 40 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E VAL 4.5 0.9 - - - +
7E PRO 3.4 32.3 - - - +
8E LYS* 3.8 15.0 - - + +
16E ARG 3.7 9.7 - - - +
17E VAL* 3.3 22.2 - - + +
36E VAL* 4.4 13.4 - - + +
37E GLU* 3.8 12.4 + - + +
38E ARG 3.7 0.6 - - - -
39E GLY* 1.3 77.7 - - - +
41E GLY* 1.3 60.3 + - - +
42E GLU 3.2 2.5 + - - -
43E GLY 4.2 4.5 + - - -
48E ASP* 4.5 0.6 + - - -
51E TYR* 5.9 0.2 - - - -
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Residues in contact with GLY 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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17E VAL* 3.7 12.4 - - - +
39E GLY* 4.6 0.2 - - - -
40E ALA* 1.3 74.3 - - - +
42E GLU* 1.3 58.3 + - - +
43E GLY 3.1 3.6 - - - -
44E ALA* 2.9 20.1 + - - +
45E TYR 3.0 0.2 + - - -
46E HIS* 3.0 33.6 + - - -
51E TYR* 3.6 25.5 + - - -
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Residues in contact with GLU 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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8E LYS* 4.6 8.2 + - - +
15E ARG* 5.8 0.5 + - - -
39E GLY* 3.6 31.2 - - - +
40E ALA 3.2 1.2 - - - -
41E GLY* 1.3 76.9 - - - +
43E GLY* 1.3 60.0 + - - +
45E TYR* 3.5 18.5 + - - +
46E HIS 3.6 9.4 + - - +
47E PRO* 5.0 8.9 - - + +
48E ASP* 4.8 10.7 + - - +
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Residues in contact with GLY 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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15E ARG* 3.1 40.8 + - - +
16E ARG 5.5 0.2 - - - -
39E GLY 5.0 0.2 + - - -
40E ALA 4.2 5.7 + - - -
41E GLY 3.1 1.2 - - - -
42E GLU* 1.3 77.8 - - - +
44E ALA* 1.3 51.3 + - - +
45E TYR* 3.3 10.5 + - - -
319E SER* 2.7 22.2 + - - -
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Residues in contact with ALA 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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15E ARG 3.5 3.0 + - - +
16E ARG* 5.3 0.4 - - - +
17E VAL* 4.2 9.2 - - + -
40E ALA 5.2 0.4 + - - -
41E GLY 2.9 8.1 + - - +
43E GLY* 1.3 76.2 - - - +
45E TYR* 1.3 70.3 - - - +
46E HIS* 3.2 22.9 + - + -
319E SER* 3.4 30.1 - - - +
320E VAL* 3.7 13.2 - - - +
323E SER* 3.5 18.4 - - - +
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Residues in contact with TYR 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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15E ARG* 3.0 34.8 + - - -
41E GLY 3.0 3.0 + - - -
42E GLU* 3.5 13.1 + - - +
43E GLY 3.3 9.6 - - - -
44E ALA* 1.3 81.1 - - - +
46E HIS* 1.3 62.3 + - - +
47E PRO* 3.3 11.3 - - - +
319E SER* 4.3 2.2 - - - -
320E VAL* 3.9 17.7 - - + -
152F PRO* 4.3 16.6 - - + +
277F PRO* 3.8 39.7 - - + +
278F GLY* 4.3 9.4 - - - -
302F GLU* 3.1 23.5 + - - -
304F ARG 5.8 0.2 - - - -
305F GLY* 4.4 18.3 + - - -
307F ARG* 3.6 12.1 + - + +
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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