Contacts of the helix formed by residues 202 - 217 (chain 2) in PDB entry 1O1F
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 THR 202 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2850 CYS 3.6 2.7 - - - +
2870 ILE* 0.6 287.1 - - + +
2900 ARG* 2.2 61.4 + - - +
2012 VAL* 1.3 72.2 - - - +
2032 THR* 1.3 52.8 + - - -
2052 GLU* 2.9 17.8 + - - +
2062 ARG* 3.1 11.4 + - - +
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Residues in contact with THR 203 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2860 ASP* 2.3 33.2 - - - +
2870 ILE* 1.4 36.3 - - - +
2880 ASP* 1.3 76.9 + - + +
622 ARG* 3.7 25.7 + - + +
2022 THR 1.3 66.1 - - - -
2042 ALA* 1.3 54.4 + - - -
2052 GLU 3.2 0.7 - - - -
2062 ARG* 3.7 10.5 - - - +
2072 GLU* 3.3 23.7 + - - +
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Residues in contact with ALA 204 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2870 ILE* 2.8 34.4 - - + +
2880 ASP* 2.7 18.9 + - - +
2910 LYS* 5.6 4.5 - - + -
2032 THR* 1.3 74.3 - - - +
2052 GLU* 1.3 63.6 + - - +
2072 GLU* 4.6 4.0 - - - +
2082 ILE* 3.6 10.8 - - - +
2432 PRO* 3.5 31.7 - - + +
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Residues in contact with GLU 205 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2870 ILE* 3.0 29.7 - - + +
2900 ARG* 5.3 3.2 + - - -
1992 SER 4.2 4.2 - - - +
2002 PHE* 3.4 34.0 - - + -
2012 VAL* 3.5 17.5 - - + +
2022 THR* 2.9 16.0 + - - +
2042 ALA* 1.3 84.7 - - - +
2062 ARG* 1.3 67.3 + - - +
2082 ILE* 3.1 21.8 - - - +
2092 VAL 3.7 2.6 + - - -
2422 LEU* 3.7 22.6 - - - +
2432 PRO* 4.4 5.5 - - - +
2442 ASP* 5.1 3.2 - - - +
2462 GLN* 5.6 1.6 - - - +
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Residues in contact with ARG 206 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622 ARG* 4.4 12.9 - - - +
1832 ARG* 6.1 2.8 - - - +
1862 THR* 4.6 11.6 - - - +
1872 ASP* 3.4 33.2 + - - -
1902 MET* 3.7 27.2 - - + +
2002 PHE* 4.2 3.8 - - + +
2012 VAL 5.9 0.4 - - - +
2022 THR 3.1 8.4 + - - +
2032 THR* 3.7 15.5 - - - +
2052 GLU* 1.3 77.3 - - - +
2072 GLU* 1.3 66.6 + - - +
2092 VAL* 3.0 30.4 + - - +
2102 ARG* 5.1 0.4 - - - +
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Residues in contact with GLU 207 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2880 ASP* 4.1 10.3 - - - +
592 GLN* 3.8 12.6 - - - +
622 ARG* 2.9 38.1 + - - +
2032 THR 3.3 13.4 + - - +
2042 ALA* 5.1 2.2 - - - -
2052 GLU 3.4 0.2 - - - -
2062 ARG* 1.3 84.1 - - - +
2082 ILE* 1.3 57.6 + - - +
2102 ARG* 3.1 39.9 + - - +
2112 ASP* 3.8 2.3 + - - +
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Residues in contact with ILE 208 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2002 PHE* 5.4 3.1 - - + -
2042 ALA 3.6 14.5 + - - +
2052 GLU* 3.1 20.0 - - - +
2072 GLU* 1.3 75.6 - - - +
2092 VAL* 1.4 57.7 + - - +
2102 ARG 3.1 2.2 - - - -
2112 ASP* 3.0 11.8 + - + +
2122 ILE* 2.9 32.9 + - + +
2402 TYR* 3.2 41.1 - - + +
2422 LEU* 4.4 14.8 - - + -
2432 PRO* 3.9 30.1 - - + -
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Residues in contact with VAL 209 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1862 THR* 3.6 21.8 - - + +
1892 LEU* 3.5 22.3 - - + +
1902 MET* 3.2 48.0 - - + +
1932 LEU* 4.1 13.2 - - + -
2002 PHE* 5.1 5.8 - - + -
2052 GLU 3.7 3.1 + - - +
2062 ARG* 3.0 23.9 + - - +
2082 ILE* 1.4 78.3 - - - +
2102 ARG* 1.3 59.1 + - - +
2122 ILE* 3.2 12.7 + - - +
2132 LYS* 3.0 24.8 + - - +
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Residues in contact with ARG 210 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162 LEU* 6.1 2.6 - - - +
1862 THR* 3.7 31.6 - - + +
2062 ARG* 6.2 0.2 - - - +
2072 GLU* 3.1 24.0 + - - +
2092 VAL* 1.3 83.3 - - + +
2112 ASP* 1.3 60.7 + - - +
2132 LYS* 3.4 13.1 - - - +
2142 GLU* 2.8 68.5 + - - +
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Residues in contact with ASP 211 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2072 GLU 3.8 1.3 + - - +
2082 ILE* 3.0 18.5 + - + +
2102 ARG* 1.3 83.5 + - - +
2122 ILE* 1.3 60.0 + - - +
2142 GLU* 4.0 14.1 - - - +
2152 LYS* 2.7 62.9 + - - +
2402 TYR* 2.9 21.6 + - - +
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Residues in contact with ILE 212 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1892 LEU* 3.7 17.7 - - + -
1932 LEU* 4.2 24.0 - - + -
2002 PHE* 5.1 7.6 - - + -
2082 ILE* 2.9 21.2 + - + +
2092 VAL* 3.3 12.6 - - - +
2112 ASP* 1.3 74.4 - - - +
2132 LYS* 1.4 60.6 + - - +
2152 LYS 3.2 0.5 + - - -
2162 LEU* 2.9 41.9 + - + +
2172 CYS* 3.7 2.5 + - - -
2402 TYR* 3.9 39.0 - - + -
2422 LEU* 5.2 1.3 - - + -
2482 ILE* 4.3 15.5 - - + -
2502 ILE* 4.5 15.3 - - + -
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Residues in contact with LYS 213 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1572 ASP* 5.8 0.2 + - - -
1822 GLY* 2.8 25.2 + - - +
1852 LEU 4.1 3.4 - - - -
1862 THR* 2.7 40.6 + - - +
1892 LEU* 3.5 18.1 - - + +
2092 VAL 3.0 8.5 + - - +
2102 ARG* 3.4 19.9 - - - +
2122 ILE* 1.4 73.5 - - - +
2142 GLU* 1.3 77.9 + - - +
2172 CYS* 3.0 32.0 + - - +
2572 CYS* 4.2 13.0 - - - -
3032 THR* 5.1 1.0 + - - -
3062 TYR* 3.7 31.7 - - + +
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Residues in contact with GLU 214 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2102 ARG* 2.8 56.8 + - - +
2112 ASP* 4.2 11.0 - - - +
2122 ILE 3.3 0.2 - - - -
2132 LYS* 1.3 95.4 + - - +
2152 LYS* 1.3 63.7 + - + +
2172 CYS 4.3 5.7 + - - +
3062 TYR* 5.6 4.1 - - - -
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Residues in contact with LYS 215 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2112 ASP* 2.7 53.0 + - - +
2122 ILE* 4.1 0.4 - - - +
2142 GLU* 1.3 78.1 - - + +
2162 LEU* 1.3 72.7 + - + +
2172 CYS 4.9 0.7 - - - +
2182 TYR* 4.8 6.9 - - - -
2402 TYR* 4.1 14.7 + - + -
2542 ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 216 (chain 2).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2122 ILE* 2.9 27.5 + - + +
2152 LYS* 1.3 86.0 - - + +
2172 CYS* 1.3 62.1 + - - +
2182 TYR* 3.3 4.7 - - - -
2382 LYS* 3.8 46.9 - - + +
2392 SER 5.8 0.7 - - - +
2402 TYR* 3.9 32.1 - - + +
2502 ILE* 4.6 11.9 - - + -
2542 ARG* 2.9 43.5 + - + +
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Residues in contact with CYS 217 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1892 LEU* 4.6 7.6 - - - -
2122 ILE* 3.7 2.7 + - - -
2132 LYS* 3.0 36.0 + - - +
2142 GLU 4.6 3.6 - - - +
2152 LYS 3.8 1.3 - - - +
2162 LEU* 1.3 73.0 - - - +
2182 TYR* 1.3 72.8 + - - +
2502 ILE* 6.2 0.4 - - - -
2532 GLU 4.7 0.4 - - - -
2542 ARG* 2.9 27.6 - - - +
2572 CYS* 4.2 19.3 - - - -
2582 PRO* 4.1 2.9 - - + -
3062 TYR* 4.0 22.3 - - + -
3072 PRO* 3.4 17.5 - - - +
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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