Contacts of the helix formed by residues 2065 - 2088 (chain B) in PDB entry 1F5T
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 THR2065 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2052B GLY* 2.8 27.0 + - - +
2053B LEU 2.9 22.8 + - - +
2054B VAL* 3.9 6.5 - - - +
2055B VAL* 4.1 17.0 - - + -
2064B MET* 1.3 76.0 - - - +
2066B PRO* 1.3 76.8 - - - +
2067B THR* 2.9 12.1 + - - -
2068B GLY 2.8 16.8 + - - -
2069B ARG* 2.9 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO2066 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2065B THR* 1.3 89.4 - - - +
2067B THR* 1.3 65.1 + - + +
2069B ARG* 3.5 6.4 + - + +
2070B THR* 2.6 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR2067 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2052B GLY 3.5 10.1 + - - -
2053B LEU* 4.5 10.8 - - + +
2065B THR* 2.9 15.2 + - - -
2066B PRO* 1.3 79.4 - - + +
2068B GLY* 1.3 67.6 + - - +
2070B THR* 3.2 10.1 - - + +
2071B LEU* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2068 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2012B LEU* 3.9 8.8 - - - +
2053B LEU* 3.5 31.6 - - - +
2064B MET* 4.3 6.3 - - - -
2065B THR* 2.8 16.1 + - - -
2067B THR* 1.3 78.2 - - - +
2069B ARG* 1.3 62.3 + - - -
2071B LEU* 3.2 3.6 + - - +
2072B ALA* 2.9 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2069 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2016B TYR* 4.7 15.9 - - - -
2019B GLU* 2.4 39.5 + - - -
2064B MET* 4.0 40.3 + - + +
2065B THR 2.9 12.1 + - - +
2066B PRO* 3.9 8.3 - - + +
2068B GLY* 1.3 70.1 - - - -
2070B THR* 1.3 64.9 + - - +
2072B ALA* 2.8 9.0 + - - +
2073B THR* 2.7 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2070 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2066B PRO 2.6 20.6 + - - -
2067B THR* 3.2 13.7 - - + +
2069B ARG* 1.3 81.0 - - - +
2071B LEU* 1.3 64.7 + - - +
2073B THR* 3.1 17.1 + - - -
2074B ALA* 3.2 11.2 + - + +
2077B ARG* 4.5 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2071 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2008B THR* 4.3 13.2 - - + -
2009B GLU* 3.5 30.7 - - + +
2012B LEU* 3.2 23.8 - - + -
2053B LEU* 4.6 9.9 - - + -
2067B THR 3.1 8.9 + - - +
2068B GLY* 3.5 7.6 - - - +
2070B THR* 1.3 80.6 - - - +
2072B ALA* 1.3 62.6 + - - +
2074B ALA* 3.1 17.5 + - + +
2075B VAL* 3.2 18.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2072 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2012B LEU* 4.0 25.3 - - + +
2013B ARG* 5.0 1.9 - - - -
2016B TYR* 4.3 11.0 - - + -
2064B MET* 3.7 24.9 - - - -
2068B GLY 2.9 13.3 + - - +
2069B ARG* 2.8 9.7 + - - +
2071B LEU* 1.3 76.6 - - - +
2073B THR* 1.3 61.7 + - - +
2074B ALA 3.2 0.3 + - - -
2075B VAL* 3.3 6.6 + - - +
2076B MET* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2073 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2016B TYR* 3.5 31.0 - - + +
2069B ARG* 2.7 28.3 + - + +
2070B THR* 3.1 15.1 + - - -
2072B ALA* 1.3 72.1 - - - +
2074B ALA* 1.3 56.6 + - - +
2075B VAL 3.4 0.2 - - - -
2076B MET* 3.6 9.7 - - - +
2077B ARG* 2.9 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2074 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2070B THR* 3.2 12.6 + - + +
2071B LEU* 3.1 16.1 + - + +
2072B ALA 3.1 0.4 - - - -
2073B THR* 1.3 77.0 + - - +
2075B VAL* 1.3 62.1 + - + +
2077B ARG* 3.5 23.5 - - - +
2078B LYS* 3.0 46.0 + - - +
2110B ASP* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2075 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2009B GLU* 3.8 26.5 - - + +
2012B LEU* 5.6 0.2 - - + -
2013B ARG* 4.3 16.4 - - + -
2071B LEU* 3.2 33.2 + - + +
2072B ALA* 3.3 6.9 + - - +
2074B ALA* 1.3 74.1 - - - +
2076B MET* 1.3 56.5 + - - +
2078B LYS* 3.3 7.2 + - - +
2079B HIS* 2.8 36.1 + - - +
2105B GLU* 3.8 35.2 - - + +
2106B HIS* 4.0 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET2076 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2013B ARG* 3.7 26.4 - - + +
2016B TYR* 3.7 28.3 - - + -
2017B GLU* 4.0 21.3 - - + +
2020B GLU* 4.4 10.3 - - - +
2072B ALA 3.1 14.4 + - - +
2073B THR* 3.6 10.8 - - - +
2075B VAL* 1.3 78.3 - - - +
2077B ARG* 1.3 65.3 + - - +
2079B HIS* 3.1 21.0 + - + +
2080B ARG* 3.0 61.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2077 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2070B THR* 4.5 2.4 + - - +
2073B THR* 2.9 39.1 + - - +
2074B ALA* 3.5 27.1 - - - +
2076B MET* 1.3 78.0 - - - +
2078B LYS* 1.3 63.4 + - - +
2080B ARG* 3.1 11.5 + - - +
2081B LEU* 3.0 27.9 + - + +
2110B ASP* 6.3 0.2 - - - -
2113B GLU* 2.9 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2078 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2074B ALA* 3.0 28.6 + - - +
2075B VAL* 3.8 4.7 - - - +
2077B ARG* 1.3 79.1 - - - +
2079B HIS* 1.3 57.2 + - - +
2081B LEU* 3.7 8.3 - - - +
2082B ALA* 2.8 32.8 + - - +
2105B GLU* 3.8 25.8 - - - +
2108B MET* 3.0 40.0 + - - +
2110B ASP* 3.1 24.1 + - - +
2113B GLU* 2.9 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS2079 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B NI 2.4 39.8 - - + +
2013B ARG* 3.7 17.7 + - - +
2017B GLU* 5.3 2.2 - - - -
2075B VAL 2.8 18.5 + - - +
2076B MET* 3.2 19.5 - - + +
2078B LYS* 1.3 73.7 - - - +
2080B ARG* 1.3 61.3 + - + +
2082B ALA* 3.6 3.3 - - - +
2083B GLU* 2.5 48.1 + - - +
2098B HIS* 2.5 23.7 - + - -
2101B ALA* 3.6 18.9 + - + -
2102B ASP 4.1 0.2 - - - -
2105B GLU* 3.2 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2080 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2016B TYR* 5.3 1.8 + - - -
2020B GLU* 4.0 17.0 + - - -
2076B MET* 3.0 47.9 + - + +
2077B ARG* 3.1 10.9 + - - +
2079B HIS* 1.3 79.2 - - + +
2081B LEU* 1.3 60.2 + - + +
2083B GLU* 2.9 17.0 + - - +
2084B ARG* 2.8 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2081 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2077B ARG* 3.0 15.5 + - + +
2078B LYS* 3.7 6.5 - - - +
2080B ARG* 1.3 80.6 - - + +
2082B ALA* 1.3 63.3 + - - +
2084B ARG* 3.7 21.0 + - - +
2085B LEU* 3.3 19.8 + - - +
2108B MET* 4.6 3.1 - - - -
2113B GLU* 3.4 52.0 - - + +
2116B LEU* 3.7 25.7 - - + +
2117B VAL* 4.5 24.5 - - + +
2120B LEU* 4.8 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2082 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2078B LYS 2.8 17.9 + - - +
2079B HIS* 3.6 5.2 - - - +
2081B LEU* 1.3 74.1 - - - +
2083B GLU* 1.3 68.0 + - - +
2085B LEU* 2.9 9.4 + - - +
2086B LEU* 2.9 29.6 + - + +
2101B ALA* 4.0 14.8 - - + +
2104B TRP* 4.2 19.3 - - + -
2105B GLU 4.8 1.6 - - - +
2108B MET* 3.8 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2083 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B NI 2.0 22.4 - - - +
2079B HIS* 2.5 22.9 + - - +
2080B ARG* 2.9 14.9 + - - +
2082B ALA* 1.3 75.4 - - - +
2084B ARG* 1.3 60.8 + - + +
2086B LEU* 3.9 0.9 - - - -
2087B THR* 3.2 28.2 + - - -
2097B VAL* 3.6 21.8 - - + +
2098B HIS* 2.0 42.9 + - - -
2101B ALA* 3.3 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG2084 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2080B ARG* 2.8 28.4 + - + +
2081B LEU* 3.9 21.2 - - - +
2083B GLU* 1.3 72.3 - - + +
2085B LEU* 1.3 67.2 + - - +
2087B THR* 3.1 4.5 + - - -
2088B ASP* 2.9 45.1 + - - -
2120B LEU* 3.5 41.4 - - + +
2121B LYS* 4.6 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2085 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085A LEU* 4.5 5.8 - - + -
1089A ILE* 4.6 6.1 - - + -
1090A ILE* 4.3 12.3 - - + -
1104A TRP* 4.5 4.7 - - + -
2081B LEU 3.3 10.6 + - - +
2082B ALA* 2.9 8.0 + - - +
2084B ARG* 1.3 78.0 - - - +
2086B LEU* 1.3 58.4 + - - +
2089B ILE* 3.5 37.3 + - + -
2090B ILE* 3.0 43.0 + - + +
2104B TRP* 4.2 25.8 - - + -
2108B MET* 5.2 2.2 - - + -
2116B LEU* 4.0 33.4 - - + -
2120B LEU* 4.2 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2086 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112A VAL* 4.2 18.6 - - + -
2082B ALA* 2.9 21.5 + - + +
2083B GLU 3.9 4.0 - - - +
2085B LEU* 1.3 77.8 - - - +
2087B THR* 1.3 53.2 + - - +
2090B ILE* 3.5 13.1 - - + +
2091B GLY 2.7 30.1 + - - -
2092B LEU* 2.9 21.6 + - + -
2097B VAL* 3.8 15.9 - - + +
2100B GLU* 3.5 27.4 - - + +
2101B ALA* 3.8 20.2 - - + +
2104B TRP* 4.1 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR2087 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2083B GLU 3.2 15.4 + - - -
2084B ARG* 3.1 3.6 + - - -
2086B LEU* 1.3 77.3 - - - +
2088B ASP* 1.3 69.8 + - - +
2091B GLY* 3.5 13.5 - - - -
2092B LEU 4.4 7.7 - - - +
2094B ILE* 3.5 26.6 - - + +
2097B VAL* 3.4 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2088 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2084B ARG* 2.9 42.2 + - - +
2087B THR* 1.3 93.8 - - - +
2089B ILE* 1.3 74.2 + - + +
2091B GLY* 3.3 10.9 + - - -
2120B LEU* 4.1 7.1 - - + +
----------------------------------------------------------
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