Contacts of the helix formed by residues 202 - 217 (chain 0) 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 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2010 VAL* 1.3 84.6 - - + +
2030 THR* 1.3 61.1 + - - +
2040 ALA* 3.8 12.3 + - - +
2050 GLU* 2.9 39.3 + - - +
2060 ARG* 3.1 11.1 + - - +
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Residues in contact with THR 203 (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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620 ARG* 3.7 30.3 + - + +
2020 THR* 1.3 74.6 - - - +
2040 ALA* 1.3 62.6 + - + +
2060 ARG* 3.7 11.7 - - - +
2070 GLU* 3.3 27.9 + - - +
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Residues in contact with ALA 204 (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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2020 THR* 3.2 10.6 + - - +
2030 THR* 1.3 80.2 - - + +
2050 GLU* 1.3 64.8 + - - +
2070 GLU* 4.6 5.6 - - - +
2080 ILE* 3.6 11.5 - - - +
2430 PRO* 3.5 32.3 - - + +
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Residues in contact with GLU 205 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1990 SER 4.3 4.5 - - - +
2000 PHE* 3.4 34.0 - - + -
2010 VAL* 3.5 17.6 - - - +
2020 THR* 2.9 37.2 + - - +
2040 ALA* 1.3 86.5 - - - +
2060 ARG* 1.3 68.0 + - - +
2070 GLU 3.4 0.2 - - - -
2080 ILE* 3.1 22.1 - - - +
2090 VAL 3.7 2.8 + - - -
2420 LEU* 3.7 23.9 - - + +
2430 PRO* 4.4 5.5 - - - +
2440 ASP* 5.1 2.8 - - - +
2460 GLN* 5.6 1.4 - - - +
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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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620 ARG* 4.4 13.9 - - - +
1830 ARG* 6.1 2.6 - - - +
1860 THR* 4.6 11.2 - - - +
1870 ASP* 3.4 32.2 + - - -
1900 MET* 3.7 26.3 - - + +
2000 PHE* 4.2 4.1 - - + +
2010 VAL 5.9 0.4 - - - +
2020 THR 3.1 7.7 + - - +
2030 THR* 3.7 15.3 - - - +
2050 GLU* 1.3 75.7 - - - +
2070 GLU* 1.3 67.4 + - - +
2090 VAL* 3.0 29.6 + - - +
2100 ARG* 5.1 0.9 - - - +
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Residues in contact with GLU 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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590 GLN* 3.8 13.0 - - - +
620 ARG* 2.9 39.5 + - - +
2030 THR 3.3 14.5 + - - +
2040 ALA* 5.1 4.2 - - - -
2050 GLU 3.4 0.4 - - - -
2060 ARG* 1.3 82.9 - - - +
2080 ILE* 1.3 57.8 + - - +
2100 ARG* 3.1 39.2 + - - +
2110 ASP* 3.8 2.1 + - - +
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Residues in contact with ILE 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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2000 PHE* 5.4 3.1 - - + -
2040 ALA 3.6 14.6 + - - +
2050 GLU* 3.1 20.4 - - - +
2070 GLU* 1.3 76.4 - - + +
2090 VAL* 1.4 58.2 + - - +
2100 ARG 3.1 2.2 - - - -
2110 ASP* 3.0 11.4 + - + +
2120 ILE* 2.9 32.5 + - + +
2400 TYR* 3.2 41.5 - - + +
2420 LEU* 4.4 13.7 - - + -
2430 PRO* 3.9 28.5 - - + -
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Residues in contact with VAL 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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1860 THR* 3.6 22.7 - - + +
1890 LEU* 3.5 22.2 - - + +
1900 MET* 3.2 48.0 - - + +
1930 LEU* 4.1 13.2 - - + -
2000 PHE* 5.1 5.4 - - + -
2050 GLU 3.7 2.7 + - - +
2060 ARG* 3.0 23.9 + - - +
2080 ILE* 1.4 79.3 - - - +
2100 ARG* 1.3 58.4 + - - +
2120 ILE* 3.2 12.1 + - - +
2130 LYS* 3.0 24.3 + - - +
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Residues in contact with ARG 210 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160 LEU* 6.1 2.8 - - - +
1860 THR* 3.7 31.2 - - + +
2060 ARG* 5.1 0.9 - - - +
2070 GLU* 3.1 25.2 + - - +
2090 VAL* 1.3 82.0 - - + +
2110 ASP* 1.3 61.9 + - - +
2130 LYS* 3.4 13.5 - - - +
2140 GLU* 2.8 67.0 + - - +
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Residues in contact with ASP 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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2070 GLU 3.8 1.0 + - - +
2080 ILE* 3.0 20.3 + - + +
2100 ARG* 1.3 83.0 + - - +
2120 ILE* 1.3 60.7 + - - +
2140 GLU* 4.0 13.1 - - - +
2150 LYS* 2.7 62.9 + - - +
2400 TYR* 2.9 22.4 + - - +
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Residues in contact with ILE 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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1890 LEU* 3.7 17.0 - - + -
1930 LEU* 4.2 24.2 - - + -
2000 PHE* 5.1 7.6 - - + -
2080 ILE* 2.9 19.9 + - + +
2090 VAL* 3.2 12.5 + - - +
2110 ASP* 1.3 75.5 - - - +
2130 LYS* 1.4 60.0 + - - +
2150 LYS 3.2 1.0 + - - -
2160 LEU* 2.9 42.2 + - + +
2170 CYS* 3.7 2.4 + - - -
2400 TYR* 3.9 40.4 - - + -
2420 LEU* 5.2 1.6 - - + -
2480 ILE* 4.3 15.5 - - + -
2500 ILE* 4.5 15.3 - - + -
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Residues in contact with LYS 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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1570 ASP* 5.8 0.6 + - - -
1820 GLY* 2.8 24.6 + - - +
1850 LEU 4.1 3.1 - - - -
1860 THR* 2.7 41.3 + - - +
1890 LEU* 3.6 18.6 - - + -
2090 VAL 3.0 8.1 + - - +
2100 ARG* 3.4 20.2 - - - +
2120 ILE* 1.4 73.8 - - - +
2140 GLU* 1.3 76.9 + - - +
2170 CYS* 3.0 31.1 + - - +
2570 CYS* 4.2 13.5 - - - -
3030 THR* 5.1 1.4 + - - -
3060 TYR* 3.7 32.6 - - + +
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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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2100 ARG* 2.8 56.0 + - - +
2110 ASP* 4.2 10.4 - - - +
2120 ILE 3.3 0.2 - - - -
2130 LYS* 1.3 95.5 + - - +
2150 LYS* 1.3 63.2 + - + +
2170 CYS 4.3 6.1 + - - +
3060 TYR* 5.6 4.0 - - - -
3070 PRO* 5.7 1.9 - - - +
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Residues in contact with LYS 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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2110 ASP* 2.7 52.8 + - - +
2120 ILE* 4.1 1.1 - - - +
2140 GLU* 1.3 78.1 - - + +
2160 LEU* 1.3 73.6 + - + +
2170 CYS 3.8 0.7 - - - +
2180 TYR* 4.8 7.1 - - - -
2400 TYR* 4.1 15.1 + - + -
2540 ARG* 5.4 0.3 + - - -
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Residues in contact with LEU 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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2120 ILE* 2.9 26.4 + - + +
2150 LYS* 1.3 86.0 - - + +
2170 CYS* 1.3 61.8 + - - +
2180 TYR* 3.3 6.0 - - - -
2380 LYS* 3.8 46.7 - - + +
2390 SER 5.8 0.9 - - - +
2400 TYR* 3.9 31.9 - - + +
2500 ILE* 4.6 11.7 - - + -
2540 ARG* 2.9 43.0 + - + +
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Residues in contact with CYS 217 (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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1890 LEU* 4.6 7.6 - - - -
2120 ILE* 3.7 3.1 + - - -
2130 LYS* 3.0 36.3 + - - +
2140 GLU 4.6 4.5 - - - +
2150 LYS 3.8 0.7 - - - +
2160 LEU* 1.3 72.0 - - - +
2180 TYR* 1.3 72.3 - - - +
2500 ILE* 6.2 0.4 - - - -
2530 GLU 4.7 0.2 - - - -
2540 ARG* 2.9 26.9 - - - +
2570 CYS* 4.2 19.3 - - - -
2580 PRO* 4.1 3.4 - - + -
3060 TYR* 4.0 21.9 - - + -
3070 PRO* 3.4 18.0 - - - +
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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