Contacts of the helix formed by residues 32 - 38 (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 VAL 32 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E VAL* 4.4 8.3 - - + +
25E LEU* 4.1 39.4 + - + +
27E THR* 3.6 18.4 + - + +
31E TYR* 1.3 72.2 - - - +
33E ASP* 1.3 60.8 + - - +
35E LEU* 3.4 6.8 - - + +
36E ILE* 3.0 51.5 + - + +
48E LEU* 6.4 0.7 - - + -
200F LEU* 3.8 37.0 - - + +
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Residues in contact with ASP 33 (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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31E TYR* 3.2 8.6 - - - +
32E VAL* 1.3 80.9 + - - +
34E GLU* 1.3 69.3 + - - +
36E ILE* 4.7 4.7 - - - -
37E LEU* 2.9 44.2 + - + +
157F LYS* 5.7 4.6 + - - +
197F LEU* 4.6 17.7 - - + +
200F LEU* 4.3 23.4 - - + +
201F ARG* 2.7 47.9 + - - +
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Residues in contact with GLU 34 (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 ASP* 4.7 2.9 - - - +
30E PRO* 3.2 20.4 - - + +
31E TYR* 3.0 42.3 + - - +
33E ASP* 1.3 88.2 + - - +
35E LEU* 1.3 55.6 + - - +
38E ASP* 2.7 46.5 + - + +
39E VAL* 3.1 10.7 + - + +
201F ARG* 3.9 6.8 + - - +
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Residues in contact with LEU 35 (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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24E VAL* 4.5 16.4 - - + -
27E THR* 4.6 4.0 - - + -
30E PRO* 4.4 7.1 - - + +
31E TYR 3.2 12.8 + - - +
32E VAL* 3.4 12.6 - - + +
34E GLU* 1.3 76.0 - - - +
36E ILE* 1.3 73.7 + - + +
39E VAL* 2.9 33.6 + - + +
40E ILE* 2.9 48.0 + - + +
42E MET* 5.9 1.1 - - + -
155E PHE* 5.6 3.6 - - + -
156E VAL* 4.4 36.3 - - + -
159E VAL* 5.1 7.4 - - + -
160E VAL* 5.1 1.6 - - + -
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Residues in contact with ILE 36 (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* 3.1 18.9 + - - -
24E VAL* 6.1 0.4 - - + -
32E VAL* 3.0 28.8 + - + +
33E ASP* 4.6 3.4 - - - +
35E LEU* 1.3 101.6 - - + +
37E LEU* 1.3 71.5 + - + +
40E ILE* 3.3 20.3 - - + +
42E MET* 4.1 33.9 + - + -
48E LEU* 6.4 2.2 - - + -
161F LEU* 5.1 0.9 - - - +
169F ILE* 5.4 13.2 - - + -
200F LEU* 6.3 2.2 - - + -
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Residues in contact with LEU 37 (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* 4.0 17.6 + - - +
33E ASP* 2.9 26.2 + - + +
36E ILE* 1.3 89.9 - - + +
38E ASP* 1.3 73.4 + - - +
157F LYS* 4.5 27.4 - - + +
161F LEU* 4.1 34.5 - - + +
170F PHE* 5.9 4.3 - - + -
197F LEU* 4.5 22.0 - - + -
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Residues in contact with ASP 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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6E ARG* 3.7 15.5 - - - +
34E GLU* 2.7 36.2 + - + +
37E LEU* 1.3 93.7 - - - +
39E VAL* 1.3 63.5 + - + +
40E ILE 3.8 0.4 - - - -
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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