Contacts of the helix formed by residues 289 - 295 (chain 8) 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 ILE 289 (chain 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1668 TYR* 3.7 40.6 - - + -
1718 LEU* 3.6 32.8 - - + -
2858 CYS* 4.0 7.6 - - + -
2868 ASP* 3.1 42.2 + - + +
2878 ILE 3.2 0.8 - - - -
2888 ASP* 1.4 76.5 - - + +
2908 ARG* 1.3 65.4 + - - +
2918 LYS* 3.3 6.1 - - - +
2928 ASP* 3.0 16.7 + - - +
2938 LEU* 3.3 30.2 + - + +
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Residues in contact with ARG 290 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2828 ILE* 3.4 35.9 + - + +
2838 MET* 3.9 46.9 + - - +
2858 CYS* 2.4 33.0 + - + -
2868 ASP 3.3 8.6 + - - +
2878 ILE* 3.8 11.1 - - - +
2888 ASP 3.4 1.4 - - - -
2898 ILE* 1.3 78.6 - - - +
2918 LYS* 1.4 61.9 + - - +
2928 ASP 3.3 0.3 + - - -
2938 LEU* 4.1 8.0 - - - +
2948 TYR* 3.1 33.1 + - + -
3258 MET* 4.7 4.9 - - + -
201W VAL* 4.5 12.5 - - - +
202W THR* 2.2 40.1 + - - +
205W GLU* 5.3 2.0 + - - -
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Residues in contact with LYS 291 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2878 ILE 4.7 2.7 + - - +
2888 ASP* 3.0 29.4 + - - +
2898 ILE* 3.2 1.6 + - - +
2908 ARG* 1.4 75.6 - - - +
2928 ASP* 1.4 97.3 + - - +
2948 TYR* 3.4 2.9 + - - +
2958 ALA* 3.2 23.4 + - - +
3258 MET* 3.7 24.9 - - + +
3268 LYS* 4.5 2.4 - - - +
204W ALA* 5.6 3.4 - - + -
243W PRO* 6.0 7.6 - - + -
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Residues in contact with ASP 292 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1498 THR* 3.9 21.3 - - + -
1508 GLY* 5.2 0.2 - - - -
1668 TYR* 4.0 20.1 + - - -
2898 ILE* 3.0 9.4 + - - +
2918 LYS* 1.4 104.9 + - - +
2938 LEU* 1.3 68.5 + - - +
2958 ALA* 3.1 5.8 + - - -
2968 ASN* 2.9 31.4 + - - +
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Residues in contact with LEU 293 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1498 THR* 3.8 22.9 - - + -
1508 GLY* 3.8 19.7 - - - +
1518 ILE* 3.4 30.9 - - + +
1648 PRO* 4.4 6.3 - - + -
1658 ILE 4.3 5.2 - - - +
2828 ILE* 4.5 18.4 - - + -
2858 CYS* 4.0 21.5 - - + -
2898 ILE* 3.3 42.3 + - + +
2908 ARG* 4.1 7.2 - - - +
2928 ASP* 1.3 77.3 - - - +
2948 TYR* 1.3 63.1 + - - +
2968 ASN 3.0 21.7 + - - -
2978 ASN* 3.7 1.2 + - - +
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Residues in contact with TYR 294 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2798 TYR* 3.4 19.9 - + - -
2828 ILE* 3.6 37.7 - - + +
2838 MET* 3.4 32.8 - - + +
2908 ARG* 3.1 28.5 + - + +
2918 LYS 3.7 3.4 - - - +
2928 ASP 3.2 1.4 - - - -
2938 LEU* 1.3 78.0 - - - +
2958 ALA* 1.3 59.1 + - - +
2968 ASN 3.1 1.1 + - - -
2978 ASN* 4.6 1.7 + - - +
3178 ILE* 4.0 20.0 - - + +
3218 ALA* 3.6 21.4 - - + +
3228 PRO* 4.7 0.4 - - + -
3258 MET* 3.4 32.3 - - + -
3268 LYS 3.2 16.4 - - - +
3278 ILE* 3.4 16.0 - - + -
3288 LYS 2.8 22.0 + - - +
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Residues in contact with ALA 295 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2918 LYS 3.2 11.2 + - - +
2928 ASP* 3.1 3.6 + - - -
2948 TYR* 1.3 78.3 - - - +
2968 ASN* 1.4 74.3 + - - +
3268 LYS* 3.8 32.8 - - + +
3288 LYS* 3.2 33.4 - - - +
3308 ILE* 3.8 0.7 - - - +
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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