Contacts of the helix formed by residues 19 - 26 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I CYS* 3.2 15.0 + - - -
18I THR* 1.3 78.4 - - - +
20I CYS* 1.3 59.6 + - - +
22I GLU* 3.9 2.2 - - - -
23I SER 3.1 19.4 + - - -
149I PRO* 3.4 14.7 - - - +
267I SF4 3.9 10.1 - - - -
66J GLY* 3.6 24.9 - - - -
218J PRO* 3.7 6.2 - - - +
219J HIS* 4.7 0.2 - - - -
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Residues in contact with CYS 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I TYR* 4.0 2.0 - - - -
19I GLY* 1.3 75.7 - - - +
21I SER* 1.3 61.8 + - - +
23I SER* 3.0 21.3 + - - -
24I VAL* 3.5 9.9 + - - +
73I GLU* 3.1 25.9 + - + +
109I ILE* 3.7 15.7 - - + +
110I GLY* 3.2 32.1 - - - -
149I PRO* 3.9 4.7 - - - -
150I PRO* 3.8 14.4 - - - -
267I SF4 2.3 33.7 - - - -
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Residues in contact with SER 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I TYR* 3.6 6.4 + - - -
13I HIS* 2.9 22.0 + - - -
16I GLU* 4.1 0.5 + - - -
18I THR* 3.5 11.6 + - - +
19I GLY 3.4 0.2 - - - -
20I CYS* 1.3 74.0 - - - +
22I GLU* 1.3 65.2 + - - +
24I VAL* 3.0 22.1 + - - +
25I LEU* 3.5 14.2 + - - +
45I HIS* 4.0 21.3 - - - -
47I THR* 4.7 3.6 - - - -
73I GLU* 2.4 33.3 + - - -
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Residues in contact with GLU 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I THR* 3.2 18.9 + - + +
19I GLY 4.2 0.4 - - - +
20I CYS 3.5 0.2 - - - -
21I SER* 1.3 75.0 - - - +
23I SER* 1.3 62.1 + - - +
24I VAL 3.1 0.3 + - - -
25I LEU* 3.3 27.1 + - + +
26I ARG* 2.8 56.2 + - - +
66J GLY 3.7 13.9 - - - +
67J VAL* 3.7 33.6 - - + +
106J HIS* 4.0 7.0 - - - -
110J VAL* 4.6 13.7 - - - +
115J LEU* 6.1 0.9 - - - +
218J PRO* 3.8 12.3 - - + -
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Residues in contact with SER 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I GLY 3.1 18.3 + - - -
20I CYS* 3.0 11.6 + - - -
21I SER 3.2 0.8 - - - -
22I GLU* 1.3 76.5 - - - +
24I VAL* 1.3 66.4 + - - +
26I ARG* 3.2 8.6 + - - +
109I ILE* 4.6 2.8 - - - +
149I PRO* 3.9 14.2 - - - +
150I PRO* 3.8 25.5 + - - +
152I PRO* 3.1 33.6 - - - +
155I PHE* 6.0 0.5 - - - +
218J PRO* 3.8 13.6 - - - +
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Residues in contact with VAL 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I TYR* 4.5 12.1 - - + +
20I CYS 3.6 14.6 - - - +
21I SER* 3.0 10.7 + - - +
23I SER* 1.3 79.6 + - - +
25I LEU* 1.3 58.5 + - + +
26I ARG 3.0 6.7 + - - -
27I THR* 3.0 33.2 + - - +
32I VAL* 4.4 7.1 - - + +
35I LEU* 4.5 19.1 - - + -
36I ILE* 6.1 0.4 - - + -
42I MET* 6.0 5.2 - - + -
45I HIS* 6.3 0.4 - - - +
109I ILE* 4.0 10.8 - - + -
152I PRO* 5.1 3.6 - - + -
155I PHE* 3.7 39.3 - - + -
156I VAL* 4.8 3.4 - - + -
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Residues in contact with LEU 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I SER* 3.5 11.2 + - - +
22I GLU* 3.3 38.1 + - - +
24I VAL* 1.3 74.3 - - + +
26I ARG* 1.3 65.3 + - - +
27I THR* 3.4 4.0 - - - +
32I VAL* 4.1 34.2 + - + +
45I HIS* 6.1 1.1 - - - +
47I THR* 6.3 2.2 - - + -
48I LEU* 4.7 29.8 - - + -
110J VAL* 5.4 10.1 - - + -
114J HIS* 6.3 1.1 - - + +
200J LEU* 5.3 6.7 - - + -
203J GLN* 2.8 34.7 + - - +
204J VAL* 3.7 4.2 - - - +
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Residues in contact with ARG 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I GLU* 2.8 57.7 + - - +
23I SER* 3.5 11.4 - - - +
24I VAL 3.0 1.6 - - - -
25I LEU* 1.3 80.8 - - - +
27I THR* 1.3 67.3 + - - +
28I VAL* 3.4 12.0 + - - +
152I PRO* 4.0 13.5 - - + +
234I ASN* 4.3 9.9 - - - +
235I GLN* 4.7 6.8 + - - +
66J GLY 5.0 2.0 + - - -
67J VAL 5.8 1.6 + - - -
69J THR* 5.7 1.2 - - - +
106J HIS* 3.4 18.9 - - - -
203J GLN* 3.1 25.7 + - - +
204J VAL* 4.4 10.9 - - + +
207J ALA* 3.3 21.3 - - - +
217J ASN* 2.8 44.6 + - - +
218J PRO* 4.0 2.8 - - - +
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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