Contacts of the helix formed by residues 205 - 216 (chain 0) in PDB entry 5IY6
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 VAL 205 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1710 PHE* 3.7 17.0 - - + -
1730 SER 4.7 2.7 - - - +
1740 LEU* 3.5 43.5 - - + +
2030 ALA* 3.7 5.8 - - + -
2040 GLU* 1.3 79.6 - - - +
2060 ARG* 1.4 67.4 + - - +
2070 VAL* 3.3 3.6 + - + -
2080 CYS* 3.4 32.4 + - + +
2090 THR* 3.4 6.9 + - - -
2190 TYR* 4.6 0.7 - - - +
533W ASP* 5.6 2.7 - - - +
586W GLU 4.0 0.2 - - - -
587W ALA* 4.7 7.9 - - - +
588W CYS 5.2 4.0 - - - +
612W HIS* 5.4 0.9 - - - -
616W ARG* 5.1 14.0 - - - +
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Residues in contact with ARG 206 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1830 TYR* 5.6 4.7 + - - -
2040 GLU 3.2 6.8 + - - -
2050 VAL* 1.4 72.1 - - - +
2070 VAL* 1.3 62.5 + - - +
2090 THR* 3.1 6.3 + - - -
2100 VAL* 3.0 43.7 + - + +
585W GLN* 2.8 57.6 + - - +
586W GLU* 3.4 7.3 + - - +
610W PHE* 3.3 24.4 - - - -
612W HIS* 3.8 36.3 - - + +
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Residues in contact with VAL 207 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1450 LEU* 6.3 0.7 - - + -
1750 THR* 5.4 4.5 - - - +
1760 THR* 6.1 4.5 - - + -
1820 ILE* 3.9 34.3 - - + -
1830 TYR* 3.9 24.9 - - + -
1860 ILE* 4.7 3.2 - - + +
2050 VAL* 5.1 1.1 - - + +
2060 ARG* 1.3 71.9 - - - +
2080 CYS* 1.3 72.7 + - - +
2100 VAL* 3.6 2.4 + - - +
2110 LEU* 2.9 30.6 + - + +
586W GLU* 2.9 36.6 + - + +
587W ALA* 4.1 14.6 - - + -
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Residues in contact with CYS 208 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1450 LEU* 4.4 14.4 - - - -
1710 PHE* 3.5 37.2 - - + -
1750 THR* 5.4 4.0 - - - -
1980 VAL* 4.3 9.3 - - + +
2050 VAL* 3.6 18.8 - - + +
2060 ARG 3.3 0.4 - - - -
2070 VAL* 1.3 83.7 - - - +
2090 THR* 1.4 61.8 + - - +
2110 LEU* 3.2 10.1 + - - +
2120 ALA* 2.9 30.3 + - - +
2190 TYR* 3.8 17.7 - - + +
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Residues in contact with THR 209 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2040 GLU* 3.2 34.1 + - + +
2050 VAL 3.4 1.6 + - - -
2060 ARG* 3.1 10.5 + - - -
2080 CYS* 1.4 78.1 - - - +
2100 VAL* 1.3 62.4 + - - +
2120 ALA* 3.3 3.8 + - - +
2130 ARG* 3.0 56.8 + - - +
2190 TYR* 3.4 38.3 - - + +
612W HIS* 6.3 1.1 - - + -
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Residues in contact with VAL 210 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1830 TYR* 4.2 30.3 - - + +
1860 ILE* 5.0 3.1 - - + -
2060 ARG* 3.0 48.8 + - + +
2070 VAL 3.9 3.1 - - - +
2090 THR* 1.3 71.5 - - - +
2110 LEU* 1.3 68.1 + - - +
2130 ARG* 4.4 11.0 - - - +
2140 GLU* 2.8 35.3 + - + +
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Residues in contact with LEU 211 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1450 LEU* 5.9 7.2 - - + -
1490 LEU* 3.9 25.8 - - + -
1690 ILE* 4.7 5.6 - - + -
1820 ILE* 4.1 15.7 - - + -
1860 ILE* 3.7 36.1 - - + -
1890 LEU* 5.3 1.1 - - + -
1960 VAL* 3.6 34.1 - - + -
1980 VAL* 4.9 4.3 - - + -
2070 VAL* 2.9 21.4 + - + +
2080 CYS* 3.2 10.3 + - - +
2100 VAL* 1.3 80.3 - - - +
2120 ALA* 1.3 61.1 + - - +
2140 GLU* 4.3 0.3 - - - +
2150 THR* 2.9 31.1 + - + +
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Residues in contact with ALA 212 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1960 VAL 3.4 16.4 - - - +
1980 VAL* 3.9 17.0 - - + -
2080 CYS 2.9 16.7 + - - +
2090 THR 3.3 4.0 + - - +
2110 LEU* 1.3 79.5 - - - +
2130 ARG* 1.3 54.5 + - - +
2150 THR* 3.3 2.7 + - - -
2160 GLY 3.1 10.2 + - - -
2170 GLY 3.0 19.2 + - - -
2180 THR 3.7 29.5 + - - +
2190 TYR* 4.2 6.5 - - + +
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Residues in contact with ARG 213 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2040 GLU* 5.3 6.1 + - - -
2090 THR* 3.0 44.0 + - + +
2100 VAL* 3.8 10.4 - - - +
2120 ALA* 1.3 71.6 - - - +
2140 GLU* 1.3 66.0 + - - +
2160 GLY* 3.2 11.4 + - - -
2170 GLY* 3.5 21.9 + - - +
2190 TYR* 5.5 5.2 - - + +
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Residues in contact with GLU 214 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1860 ILE* 3.7 26.7 - - + +
1870 LYS* 5.6 5.5 - - + +
1900 LYS* 2.9 65.3 + - + +
2100 VAL* 2.8 29.6 + - + +
2130 ARG* 1.3 74.9 - - - +
2150 THR* 1.4 60.7 + - - +
2160 GLY* 4.8 0.3 - - - -
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Residues in contact with THR 215 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1860 ILE* 4.2 12.6 - - + +
1890 LEU* 3.6 42.0 - - + -
1900 LYS* 4.8 8.8 - - - +
1940 ILE 3.7 7.9 - - - +
1950 ARG* 3.5 22.4 - - - +
1960 VAL* 3.2 36.6 + - + +
2110 LEU* 2.9 23.6 + - + +
2120 ALA 3.3 1.4 + - - -
2140 GLU* 1.4 78.4 - - - +
2160 GLY* 1.4 54.2 + - - +
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Residues in contact with GLY 216 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1950 ARG* 3.5 32.4 + - - -
1960 VAL 4.7 1.5 + - - -
2120 ALA 3.1 5.1 + - - -
2130 ARG 3.2 8.0 + - - -
2140 GLU 3.5 0.6 - - - -
2150 THR* 1.4 78.8 - - - +
2170 GLY* 1.3 59.4 + - - +
2180 THR* 5.5 0.2 - - - -
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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