Contacts of the helix formed by residues 3146 - 3156 (chain I) 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 ARG3146 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3003C G 3.3 46.4 + - - +
3004C G 2.8 48.7 + - - -
3005C G 3.8 1.0 + - - -
3124I ARG* 3.4 50.3 - - + +
3127I ARG* 4.7 1.3 - - - +
3135I PHE* 3.7 5.6 - - - -
3144I PHE* 3.7 9.6 - - - +
3145I SER* 1.3 90.3 + - - +
3147I SER* 1.3 64.2 + - - +
3148I ASP* 3.1 34.0 + - - +
3149I HIS* 3.5 21.9 + - + +
3150I LEU* 3.2 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3147 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4008D C 4.6 21.8 + - - +
4009D G 5.6 2.1 + - - -
3127I ARG* 5.3 0.6 - - - +
3135I PHE* 3.3 39.6 - - - -
3146I ARG* 1.3 71.5 - - - +
3148I ASP* 1.3 63.2 + - - +
3150I LEU* 3.1 4.7 + - - +
3151I THR* 2.9 36.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP3148 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4009D G 3.8 32.7 + - + +
4010D C 3.1 31.3 + - + -
4011D C 4.5 1.4 + - - -
3124I ARG* 5.3 2.5 - - - -
3146I ARG* 3.1 39.2 + - - +
3147I SER* 1.3 76.3 + - - +
3149I HIS* 1.3 74.0 + - - -
3151I THR* 3.4 7.3 + - - -
3152I THR* 3.0 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS3149 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3002C T 3.5 48.1 - + + +
3003C G 2.8 44.7 + - - -
4011D C 5.5 0.2 - - - -
4012D C 5.1 1.3 - - - -
3144I PHE* 4.2 17.3 - - + -
3145I SER* 5.4 0.2 - - - -
3146I ARG* 3.5 37.2 + - + +
3147I SER 3.2 0.4 - - - -
3148I ASP* 1.3 89.4 + - - +
3150I LEU* 1.3 65.5 + - - +
3152I THR* 3.3 11.6 + - - +
3153I HIS* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU3150 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3135I PHE* 3.6 36.3 - - + -
3136I GLN 4.1 7.6 - - - +
3137I CYS* 3.8 26.2 - - + +
3144I PHE* 3.8 23.7 - - + -
3146I ARG 3.2 13.0 + - - +
3147I SER* 3.1 8.6 + - - +
3149I HIS* 1.3 76.5 - - - +
3151I THR* 1.3 59.9 + - - +
3153I HIS* 3.3 2.0 + - + +
3154I ILE* 2.9 58.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR3151 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4009D G 4.0 25.4 + - + +
3147I SER* 2.9 22.3 + - - -
3148I ASP* 3.7 7.4 - - - -
3150I LEU* 1.3 77.4 - - - +
3152I THR* 1.3 67.0 + - - +
3154I ILE* 3.3 20.4 + - + +
3155I ARG* 3.5 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR3152 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3002C T 5.7 2.8 - - - +
4009D G 6.3 1.3 - - + -
4010D C 4.8 5.2 - - - +
3148I ASP* 3.0 17.4 + - + +
3149I HIS* 3.3 17.0 + - - +
3151I THR* 1.3 76.0 - - - +
3153I HIS* 1.3 65.4 + - - +
3155I ARG* 3.4 43.4 + - - +
3156I THR* 3.5 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS3153 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3137I CYS* 3.4 10.4 - - + +
3140I CYS* 3.5 2.7 - - - -
3142I ARG* 3.8 24.3 + - - -
3144I PHE* 3.4 32.5 - + + -
3149I HIS 3.0 16.4 + - - +
3150I LEU* 3.5 5.6 - - + +
3151I THR 3.1 0.2 - - - -
3152I THR* 1.3 81.7 + - - +
3154I ILE* 1.3 67.0 + - - +
3156I THR* 2.6 41.9 + - - +
3157I HIS* 3.2 9.4 + + - -
3202I ZN 2.1 38.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3154 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3137I CYS* 4.3 13.7 - - - -
3138I ARG 6.0 0.7 - - - +
3139I ILE* 4.4 17.0 - - + -
3150I LEU* 2.9 53.0 + - + +
3151I THR* 3.3 13.0 + - + +
3153I HIS* 1.3 76.4 - - - +
3155I ARG* 1.3 63.5 + - + +
3157I HIS* 3.0 27.3 + - + +
3158I THR* 3.6 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG3155 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4009D G 4.9 4.2 + - - +
4010D C 3.2 30.8 + - - -
3151I THR* 3.7 29.0 + - + +
3152I THR* 3.4 34.2 + - - +
3153I HIS 3.2 0.6 - - - -
3154I ILE* 1.3 73.6 - - + +
3156I THR* 1.3 54.4 + - + +
3157I HIS 2.9 5.6 - - - -
3158I THR* 2.6 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR3156 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3152I THR 3.5 11.9 - - - +
3153I HIS* 2.6 39.0 + - - +
3155I ARG* 1.3 75.7 - - + +
3157I HIS* 1.3 64.1 + - - +
3158I THR 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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