Contacts of the helix formed by residues 19 - 26 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C CYS* 3.2 14.7 - - - -
18C THR* 1.3 78.0 - - - +
20C CYS* 1.3 58.0 + - - +
21C SER 3.4 0.2 - - - -
22C GLU* 3.9 2.5 - - - -
23C SER 3.1 19.6 + - - -
149C PRO* 3.4 15.4 - - - +
267C SF4 3.9 10.5 - - - -
66D GLY* 3.6 24.7 - - - -
218D PRO* 3.7 6.4 - - - +
219D HIS* 4.7 0.2 - - - -
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Residues in contact with CYS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C TYR* 4.0 1.8 - - - -
19C GLY* 1.3 75.1 - - - +
21C SER* 1.3 62.6 + - - +
23C SER* 3.0 21.6 + - - -
24C VAL* 3.5 9.4 + - - +
73C GLU* 3.1 26.3 + - + +
109C ILE* 3.7 15.5 - - + +
110C GLY* 3.2 31.6 - - - -
149C PRO* 3.9 4.9 - - - -
150C PRO* 3.8 15.0 - - - -
267C SF4 2.3 32.6 - - - -
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TYR* 3.6 6.4 + - - -
13C HIS* 2.9 21.8 + - - -
16C GLU* 4.1 0.5 + - - -
18C THR* 3.5 11.4 + - - +
20C CYS* 1.3 73.1 - - - +
22C GLU* 1.3 65.8 + - - +
24C VAL* 3.0 22.2 + - - +
25C LEU* 3.5 13.8 + - - +
45C HIS* 4.0 21.3 - - - -
47C THR* 4.7 4.0 - - - -
73C GLU* 2.4 32.8 + - - -
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Residues in contact with GLU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C THR* 3.2 18.7 + - + +
19C GLY 3.7 0.2 + - - -
21C SER* 1.3 76.5 - - - +
23C SER* 1.3 62.2 + - - +
24C VAL 3.1 0.5 + - - -
25C LEU* 3.3 27.1 + - + +
26C ARG* 2.8 57.8 + - - +
66D GLY 3.7 13.0 - - - +
67D VAL* 3.7 33.2 - - + +
106D HIS* 4.0 8.0 - - - -
110D VAL* 4.6 13.6 - - - +
115D LEU* 6.1 0.9 - - - +
218D PRO* 3.8 12.3 - - + -
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLY 3.1 18.8 + - - -
20C CYS* 3.0 12.0 + - - -
21C SER 3.2 0.2 - - - -
22C GLU* 1.3 76.1 - - - +
24C VAL* 1.3 67.8 + - - +
26C ARG* 3.2 8.0 + - - +
109C ILE* 4.6 2.4 - - - +
149C PRO* 3.9 13.9 - - - +
150C PRO* 3.8 26.4 + - - +
152C PRO* 3.1 33.8 - - - +
155C PHE* 6.0 0.7 - - - +
218D PRO* 3.8 13.4 - - - +
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Residues in contact with VAL 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C TYR* 4.5 12.3 - - + +
20C CYS 3.6 14.4 - - - +
21C SER* 3.0 10.1 + - - +
23C SER* 1.3 79.9 + - - +
25C LEU* 1.3 57.0 + - + +
26C ARG 3.0 7.1 + - - -
27C THR* 3.0 33.2 + - - +
32C VAL* 4.4 6.6 - - + +
35C LEU* 4.5 19.1 - - + -
36C ILE* 6.1 0.2 - - + -
42C MET* 6.0 5.2 - - + -
45C HIS* 6.3 0.2 - - - +
109C ILE* 4.0 10.5 - - + -
152C PRO* 5.1 3.6 - - + -
155C PHE* 3.7 39.5 - - + -
156C VAL* 4.8 4.0 - - + -
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C SER* 4.0 10.3 - - - +
22C GLU* 3.5 39.5 - - - +
24C VAL* 1.3 75.6 - - + +
26C ARG* 1.3 62.8 + - - +
27C THR* 3.4 4.3 - - - +
32C VAL* 4.1 33.5 + - + +
45C HIS* 6.1 0.9 - - - +
47C THR* 6.3 3.1 - - + -
48C LEU* 4.7 29.6 - - + -
110D VAL* 5.4 10.1 - - + -
114D HIS* 6.3 0.9 - - + +
200D LEU* 5.3 6.3 - - + -
203D GLN* 2.8 35.7 + - - +
204D VAL* 3.7 4.3 - - - +
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Residues in contact with ARG 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLU* 2.8 57.7 + - - +
23C SER* 3.5 12.3 - - - +
24C VAL 3.0 2.0 - - - -
25C LEU* 1.3 79.8 - - - +
27C THR* 1.3 66.0 + - - +
28C VAL* 3.4 12.0 + - - +
152C PRO* 4.0 13.1 - - + +
234C ASN* 4.3 10.9 - - - +
235C GLN* 4.7 6.8 + - - +
66D GLY 5.1 1.8 + - - -
67D VAL 5.8 1.6 + - - -
69D THR* 5.7 1.2 - - - +
106D HIS* 3.4 19.4 - - - -
203D GLN* 3.1 25.5 + - - +
204D VAL* 4.4 10.8 - - + +
207D ALA* 3.3 20.0 - - - +
217D ASN* 2.8 45.8 + - - +
218D PRO* 4.0 2.4 - - - +
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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