Contacts of the helix formed by residues 2146 - 2155 (chain H) in PDB entry 1F2I
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 ARG2146 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010A C 3.9 0.6 - - - +
2003B G 3.4 29.7 + - - +
2004B G 2.9 49.3 + - - -
2124H ARG* 3.5 48.5 - - + +
2127H ARG* 4.3 1.1 - - - +
2135H PHE* 3.3 10.7 - - - -
2144H PHE* 3.7 9.1 - - - +
2145H SER* 1.3 88.1 + - - +
2147H SER* 1.3 59.4 + - - +
2148H ASP* 2.7 44.5 + - - +
2149H HIS* 3.1 34.4 + - + +
2150H LEU* 3.3 19.6 + - - +
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Residues in contact with SER2147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008A C 4.8 19.9 + - - +
1009A G 5.2 4.2 + - - -
2127H ARG* 5.3 0.6 - - - +
2135H PHE* 3.4 36.6 - - - -
2146H ARG* 1.3 70.9 - - - +
2148H ASP* 1.3 63.1 + - - +
2149H HIS 3.2 0.4 - - - -
2150H LEU* 3.8 5.9 - - - +
2151H THR* 2.9 35.9 + - - -
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Residues in contact with ASP2148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009A G 3.5 37.4 + - + +
1010A C 3.1 21.1 + - + +
1011A C 4.2 1.7 + - - -
2124H ARG* 5.5 1.5 - - - -
2146H ARG* 2.7 51.4 + - - +
2147H SER* 1.3 80.8 + - - +
2149H HIS* 1.3 77.7 + - - +
2151H THR* 3.5 6.4 - - - +
2152H THR* 3.2 28.3 + - - +
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Residues in contact with HIS2149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012A C 5.0 1.6 - - - -
2002B T 3.4 54.5 - + + +
2003B G 2.7 47.1 + - - -
2144H PHE* 4.5 14.1 - - + -
2146H ARG* 3.1 33.0 + - + +
2147H SER 3.2 0.4 - - - -
2148H ASP* 1.3 94.3 + - - +
2150H LEU* 1.3 63.1 + - - +
2152H THR* 2.8 21.5 + - - +
2153H HIS* 3.0 12.5 + - - +
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Residues in contact with LEU2150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2135H PHE* 3.7 23.8 - - + -
2136H GLN 4.0 12.3 - - - +
2137H CYS* 3.9 10.5 - - + +
2144H PHE* 3.7 36.3 - - + -
2146H ARG 3.3 15.4 + - - +
2147H SER* 3.8 5.8 - - - +
2148H ASP 3.4 0.2 - - - -
2149H HIS* 1.3 77.2 - - - +
2151H THR* 1.3 67.7 + - - +
2153H HIS* 2.7 15.8 + - + +
2154H ILE* 2.8 43.4 + - + -
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Residues in contact with THR2151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009A G 3.4 36.9 + - + +
2147H SER* 2.9 20.5 + - - -
2148H ASP* 3.5 8.0 - - - +
2150H LEU* 1.3 83.4 - - - +
2152H THR* 1.3 63.3 + - + +
2154H ILE* 3.5 18.2 + - - +
2155H ARG* 3.5 35.1 + - - +
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Residues in contact with THR2152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010A C 3.8 22.0 - - - +
2002B T 5.1 5.9 - - - +
2148H ASP* 3.2 13.4 + - + +
2149H HIS* 2.8 27.6 + - - +
2151H THR* 1.3 76.0 - - + +
2153H HIS* 1.3 62.0 + - - +
2155H ARG* 3.0 35.2 + - - +
2156H THR* 3.9 7.0 + - - +
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Residues in contact with HIS2153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2137H CYS* 3.6 8.9 - - + -
2140H CYS* 3.2 11.1 - - - -
2142H ARG* 4.7 11.0 + - - -
2144H PHE* 3.1 40.2 - + + -
2149H HIS 3.0 9.4 + - - +
2150H LEU* 2.7 14.2 + - + +
2152H THR* 1.3 77.5 + - - +
2154H ILE* 1.3 64.0 + - - +
2155H ARG 2.9 1.2 + - - -
2156H THR* 2.7 40.3 + - - +
2157H HIS* 3.6 8.9 - + - -
2202H ZN 2.1 36.1 - - - -
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Residues in contact with ILE2154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2137H CYS* 3.3 34.8 - - + -
2138H ARG* 4.7 7.2 - - + +
2139H ILE* 4.9 11.1 - - + +
2150H LEU* 2.8 43.4 + - + +
2151H THR* 3.5 12.3 - - - +
2152H THR 3.3 0.2 - - - -
2153H HIS* 1.3 71.2 - - - +
2155H ARG* 1.3 61.9 + - + +
2157H HIS* 3.5 24.0 + - + +
2158H THR* 4.4 7.4 - - + +
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Residues in contact with ARG2155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009A G 4.5 5.3 + - - -
1010A C 3.3 32.7 + - - -
2151H THR* 3.5 38.4 + - - +
2152H THR* 3.0 20.3 + - - +
2153H HIS 2.9 1.4 + - - -
2154H ILE* 1.3 78.7 - - + +
2156H THR* 1.3 58.8 + - + +
2157H HIS 3.1 5.8 - - - -
2158H THR* 3.0 30.1 + - + +
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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