Contacts of the strand formed by residues 40 - 45 (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 ILE 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 ARG* 3.0 25.1 + - - -
7E PRO* 3.3 10.3 - - + +
9E VAL* 3.8 29.8 - - + -
35E LEU* 2.9 30.9 + - + +
36E ILE* 3.3 30.1 - - + +
39E VAL* 1.3 82.9 - - + +
41E SER* 1.3 65.3 - - - +
42E MET* 4.1 19.5 - - + +
159E VAL* 4.0 15.0 - - + -
163E LEU* 3.9 21.5 - - + -
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Residues in contact with SER 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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6E ARG* 3.8 14.4 + - - +
7E PRO 2.5 16.7 + - - -
8E SER* 4.3 0.2 - - - -
9E VAL* 2.9 28.3 + - - -
40E ILE* 1.3 76.4 - - - +
42E MET* 1.3 58.2 + - - +
43E ASP* 2.7 28.1 + - - +
166F GLN* 3.4 43.4 + - - +
168F GLY* 4.5 2.9 - - - -
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Residues in contact with MET 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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6E ARG* 5.1 0.2 - - - +
9E VAL* 4.2 15.5 - - + +
11E TYR* 4.1 17.9 - - + -
24E VAL* 6.0 4.7 - - + -
35E LEU* 5.9 1.3 - - + -
36E ILE* 4.1 33.7 + - + +
40E ILE* 3.9 23.1 + - + +
41E SER* 1.3 69.7 + - - +
43E ASP* 1.3 61.4 + - - +
44E TYR 4.0 14.8 - - - +
45E HIS* 3.8 39.5 - - + -
48E LEU* 5.8 2.5 - - + -
155E PHE* 6.4 1.6 - - + -
168F GLY* 3.1 26.6 - - - -
169F ILE* 3.4 15.2 + - + +
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Residues in contact with ASP 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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8E SER* 2.6 31.4 + - - +
9E VAL 2.9 12.0 + - - +
10E VAL* 4.4 0.7 - - + -
41E SER* 2.7 31.0 + - - -
42E MET* 1.3 75.9 - - - +
44E TYR* 1.3 59.0 + - - +
49E MET* 3.0 19.9 - - - +
59E ALA* 4.5 9.9 - - - +
63E ALA* 4.0 22.6 - - + +
166F GLN* 5.0 4.8 + - - +
168F GLY* 3.8 13.2 + - - +
171F THR* 4.8 3.2 + - - -
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Residues in contact with TYR 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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9E VAL 3.7 2.8 + - - -
10E VAL* 4.3 10.3 - - + -
11E TYR* 2.9 48.3 + - - +
12E LEU* 4.2 9.9 - - + -
42E MET* 4.0 3.5 - - - +
43E ASP* 1.3 79.6 - - - +
45E HIS* 1.3 63.6 + - - +
46E GLU* 3.4 37.8 + - + +
49E MET* 4.0 12.1 - - + -
56E VAL* 3.5 32.5 - - + -
57E GLU* 2.8 26.1 + - - -
59E ALA 5.5 0.2 - - - +
60E LEU* 3.6 52.9 - - + +
87E VAL* 4.7 2.8 - - - +
13F PRO* 4.1 2.6 - - - +
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Residues in contact with HIS 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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11E TYR* 3.6 40.3 - + + -
13E HIS* 3.1 32.8 + + - -
21E SER* 3.8 12.0 + - - -
24E VAL* 6.4 0.4 - - - +
25E LEU* 6.1 1.2 - - - +
42E MET* 3.8 29.4 - - + -
44E TYR* 1.3 77.4 - - - +
46E GLU* 1.3 62.8 + - - +
47E THR* 3.1 21.7 + - - -
48E LEU* 3.1 30.4 + - + +
49E MET* 3.2 22.2 + - - +
169F ILE* 4.4 6.7 - - + +
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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