Contacts of the helix formed by residues 19 - 26 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A CYS* 3.2 16.2 + - - -
18A THR* 1.3 78.4 - - - +
20A CYS* 1.3 58.6 + - - +
22A GLU* 3.9 3.1 - - - -
23A SER 3.1 19.6 + - - -
149A PRO* 3.4 14.9 - - - +
267A SF4 3.9 9.9 - - - -
66B GLY* 3.6 24.0 - - - -
218B PRO* 3.7 7.0 - - - +
219B HIS* 4.7 0.2 - - - -
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Residues in contact with CYS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 4.0 2.2 - - - -
19A GLY* 1.3 76.4 - - - +
21A SER* 1.3 62.1 + - - +
23A SER* 3.0 20.7 + - - -
24A VAL* 3.5 9.9 + - - +
73A GLU* 3.1 26.3 + - + +
109A ILE* 3.7 15.9 - - + +
110A GLY* 3.2 31.0 - - - -
149A PRO* 3.9 4.9 - - - -
150A PRO* 3.8 14.6 - - - -
267A SF4 2.3 33.7 - - - -
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.6 5.9 + - - -
13A HIS* 2.9 21.6 - - - -
16A GLU* 4.1 0.5 + - - -
18A THR* 3.5 11.3 + - - +
19A GLY 3.4 0.4 - - - -
20A CYS* 1.3 74.8 - - - +
22A GLU* 1.3 66.2 + - - +
24A VAL* 3.0 21.8 + - - +
25A LEU* 3.5 13.9 + - - +
45A HIS* 4.0 21.5 - - - -
47A THR* 4.7 3.8 - - - -
73A GLU* 2.4 32.7 + - - -
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A THR* 3.2 18.9 + - + +
19A GLY 3.7 0.6 + - - +
20A CYS 3.5 0.2 - - - -
21A SER* 1.3 75.1 - - - +
23A SER* 1.3 61.5 + - - +
24A VAL 3.1 0.7 + - - -
25A LEU* 3.3 26.9 + - + +
26A ARG* 2.8 55.2 + - - +
66B GLY 3.7 13.9 - - - +
67B VAL* 3.7 34.3 - - + +
106B HIS* 4.0 7.1 - - - -
110B VAL* 4.6 13.6 - - - +
115B LEU* 6.1 0.9 - - - +
218B PRO* 3.8 12.3 - - + -
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Residues in contact with SER 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLY 3.1 18.4 + - - -
20A CYS* 3.0 12.0 + - - -
21A SER 3.2 0.4 - - - -
22A GLU* 1.3 76.7 - - - +
24A VAL* 1.3 67.5 + - - +
26A ARG* 3.2 8.4 + - - +
109A ILE* 4.6 2.3 - - - +
149A PRO* 3.9 13.5 - - - +
150A PRO* 3.8 25.7 + - - +
152A PRO* 3.1 33.6 - - - +
155A PHE* 6.0 0.9 - - - +
218B PRO* 3.8 13.8 - - - +
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 4.5 12.6 - - + +
20A CYS 3.6 14.1 - - - +
21A SER* 3.0 10.5 + - - +
23A SER* 1.3 80.5 + - - +
25A LEU* 1.3 57.0 + - + +
26A ARG 3.0 7.4 + - - -
27A THR* 3.0 32.8 + - - +
32A VAL* 4.4 6.5 - - + +
35A LEU* 4.5 19.1 - - + -
36A ILE* 6.1 0.4 - - + -
42A MET* 6.0 5.2 - - + -
45A HIS* 6.4 0.4 - - - +
109A ILE* 4.0 10.1 - - + -
152A PRO* 5.1 4.0 - - + -
155A PHE* 3.7 39.5 - - + -
156A VAL* 4.8 4.0 - - + -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A SER* 3.5 10.7 + - - +
22A GLU* 3.3 39.2 + - - +
24A VAL* 1.3 75.2 - - + +
26A ARG* 1.3 64.0 - - - +
27A THR* 3.4 4.0 - - - +
32A VAL* 4.1 33.6 + - + +
45A HIS* 6.1 1.3 - - - +
47A THR* 6.3 2.7 - - + -
48A LEU* 4.7 29.8 - - + -
110B VAL* 5.4 10.3 - - + -
114B HIS* 6.3 0.9 - - + +
200B LEU* 5.3 6.7 - - + -
203B GLN* 2.8 34.7 + - - +
204B VAL* 3.7 4.0 - - - +
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLU* 2.8 57.8 + - - +
23A SER* 3.5 12.3 - - - +
24A VAL 3.0 1.6 - - - -
25A LEU* 1.3 80.4 - - - +
27A THR* 1.3 68.2 + - - +
28A VAL* 3.4 12.1 + - - +
152A PRO* 4.0 13.4 - - + +
234A ASN* 4.3 10.5 - - - +
235A GLN* 4.7 7.3 + - - +
66B GLY 5.1 2.0 + - - -
67B VAL 5.8 1.2 + - - -
69B THR* 5.7 1.4 - - - +
106B HIS* 3.4 18.1 - - - -
203B GLN* 3.1 25.9 + - - +
204B VAL* 4.4 10.4 - - + +
207B ALA* 3.3 19.6 - - - +
217B ASN* 2.8 45.8 + - - +
218B 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