Contacts of the helix formed by residues 19 - 26 (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 GLY 19 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E CYS* 3.2 14.6 + - - -
18E THR* 1.3 78.7 - - - +
20E CYS* 1.3 58.4 + - - +
22E GLU* 3.9 2.5 - - - -
23E SER 3.1 19.9 + - - -
149E PRO* 3.4 15.1 - - - +
267E SF4 3.9 9.9 - - - -
66F GLY* 3.6 26.0 - - - -
218F PRO* 3.7 6.7 - - - +
219F HIS* 4.7 0.2 - - - -
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Residues in contact with CYS 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E TYR* 4.0 2.5 - - - -
19E GLY* 1.3 74.9 - - - +
21E SER* 1.3 63.3 + - - +
23E SER* 3.0 20.9 + - - -
24E VAL* 3.5 10.2 + - - +
73E GLU* 3.1 25.8 + - + +
109E ILE* 3.7 15.6 - - + +
110E GLY* 3.2 31.9 - - - -
149E PRO* 3.9 4.7 - - - -
150E PRO* 3.8 14.4 - - - -
267E SF4 2.3 33.7 - - - -
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Residues in contact with SER 21 (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 6.6 + - - -
13E HIS* 2.9 21.2 + - - -
16E GLU* 4.1 0.3 + - - -
18E THR* 3.5 11.7 + - - +
19E GLY 3.4 0.2 - - - -
20E CYS* 1.3 72.6 - - - +
22E GLU* 1.3 64.2 + - - +
24E VAL* 3.0 21.1 + - - +
25E LEU* 3.5 13.7 + - - +
45E HIS* 4.0 21.3 - - - -
47E THR* 4.7 3.8 - - - -
73E GLU* 2.4 33.0 + - - -
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Residues in contact with GLU 22 (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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18E THR* 3.2 18.5 + - + +
19E GLY 4.2 0.4 - - - +
20E CYS 3.5 0.2 - - - -
21E SER* 1.3 75.0 - - - +
23E SER* 1.3 62.1 + - - +
24E VAL 3.1 0.7 + - - -
25E LEU* 3.3 26.7 + - + +
26E ARG* 2.8 55.8 + - - +
66F GLY 3.7 14.1 - - - +
67F VAL* 3.7 33.9 - - + +
106F HIS* 4.0 7.0 - - - -
110F VAL* 4.6 13.7 - - - +
115F LEU* 6.1 0.9 - - - +
218F PRO* 3.8 12.1 - - + -
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Residues in contact with SER 23 (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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19E GLY 3.1 19.6 + - - -
20E CYS* 3.0 12.0 + - - -
21E SER 3.2 0.6 - - - -
22E GLU* 1.3 75.1 - - - +
24E VAL* 1.3 67.6 + - - +
26E ARG* 3.2 8.7 + - - +
109E ILE* 4.6 2.6 - - - +
149E PRO* 3.9 13.2 - - - +
150E PRO* 3.8 25.7 + - - +
152E PRO* 3.1 33.8 - - - +
155E PHE* 6.0 0.5 - - - +
218F PRO* 3.8 13.8 - - - +
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Residues in contact with VAL 24 (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* 4.5 12.1 - - + +
20E CYS 3.6 14.1 - - - +
21E SER* 3.0 10.5 + - - +
23E SER* 1.3 79.4 + - - +
25E LEU* 1.3 58.0 + - + +
26E ARG 3.0 6.9 + - - -
27E THR* 3.0 32.8 + - - +
32E VAL* 4.4 6.9 - - + +
35E LEU* 4.5 18.4 - - + -
36E ILE* 6.1 0.4 - - + -
42E MET* 6.0 5.6 - - + -
45E HIS* 6.4 0.4 - - - +
109E ILE* 4.0 10.8 - - + -
152E PRO* 5.1 3.4 - - + -
155E PHE* 3.7 39.9 - - + -
156E VAL* 4.8 4.0 - - + -
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Residues in contact with LEU 25 (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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21E SER* 4.0 10.1 - - - +
22E GLU* 3.5 37.9 - - + +
24E VAL* 1.3 75.4 - - + +
26E ARG* 1.3 64.5 + - - +
27E THR* 3.4 4.4 + - - +
32E VAL* 4.1 33.5 + - + +
45E HIS* 6.1 0.9 - - - +
47E THR* 6.3 2.5 - - + -
48E LEU* 4.7 28.5 - - + -
110F VAL* 5.4 10.1 - - + -
114F HIS* 6.3 1.3 - - + +
200F LEU* 5.3 7.0 - - + -
203F GLN* 2.8 33.2 + - - +
204F VAL* 3.7 4.3 - - - +
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Residues in contact with ARG 26 (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 GLU* 2.8 57.6 + - - +
23E SER* 3.5 12.3 - - - +
24E VAL 3.0 1.6 - - - -
25E LEU* 1.3 79.8 - - - +
27E THR* 1.3 66.2 + - - +
28E VAL* 3.4 12.6 + - - +
152E PRO* 4.0 11.9 - - + +
234E ASN* 4.3 10.1 - - - +
235E GLN* 4.7 5.9 + - - +
66F GLY 5.1 2.0 + - - -
67F VAL 5.8 1.2 + - - -
69F THR* 5.7 1.4 - - - +
106F HIS* 3.4 19.8 + - - -
203F GLN* 3.1 25.7 + - - -
204F VAL* 4.4 11.8 - - + +
207F ALA* 3.3 20.2 - - - +
217F ASN* 2.8 44.8 + - - +
218F PRO* 4.0 3.0 - - - +
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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