Contacts of the helix formed by residues 2051 - 2067 (chain C) in PDB entry 1G24
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 ASN2051 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2049C PHE* 3.7 1.5 - - - +
2050C THR* 1.3 83.6 + - - +
2052C ILE* 1.3 69.2 + - - +
2053C ASP* 3.2 23.6 + - - +
2054C GLN* 3.1 30.4 + - + +
2055C ALA* 3.0 19.1 + - - +
2178C MET* 3.1 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2052 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2050C THR 4.3 0.4 + - - -
2051C ASN* 1.3 74.4 - - - +
2053C ASP* 1.3 70.8 + - - +
2055C ALA* 3.3 1.2 + - - +
2056C LYS* 2.9 27.6 + - + +
2178C MET* 3.1 34.8 - - + +
2180C VAL* 4.8 5.4 - - + -
2212C GLN* 4.7 20.6 - - - +
2213C LEU* 3.4 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP2053 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2051C ASN* 3.2 16.2 + - - +
2052C ILE* 1.3 83.9 - - - +
2054C GLN* 1.3 59.6 + - + +
2056C LYS* 3.6 8.8 + - - +
2057C ALA* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2054 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2049C PHE* 4.6 6.7 - - + -
2051C ASN* 3.1 28.0 + - + +
2053C ASP* 1.3 78.9 - - + +
2055C ALA* 1.3 56.5 + - - +
2057C ALA* 3.2 18.2 + - - +
2058C TRP* 2.7 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2055 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2049C PHE* 3.5 28.6 - - + -
2051C ASN 3.0 5.7 + - - -
2052C ILE 3.7 0.9 - - - +
2054C GLN* 1.3 75.7 - - - +
2056C LYS* 1.3 59.9 + - - +
2058C TRP* 3.3 1.2 + - - +
2059C GLY* 2.8 28.2 + - - -
2177C LEU* 3.6 20.0 - - + +
2178C MET* 3.0 33.9 - - + -
2213C LEU* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2056 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2052C ILE* 2.9 21.9 + - + +
2053C ASP* 3.7 9.0 - - - +
2055C ALA* 1.3 77.2 - - - +
2057C ALA* 1.3 57.8 + - - +
2059C GLY* 3.3 0.7 + - - -
2060C ASN* 2.8 52.6 + - - +
2202C TYR* 3.5 17.9 + - - +
2204C ASP* 4.2 18.2 + - - -
2213C LEU* 4.0 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2057 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2053C ASP 3.0 18.7 + - - +
2054C GLN* 3.2 19.5 + - - +
2056C LYS* 1.3 77.5 - - - +
2058C TRP* 1.3 56.8 + - - +
2060C ASN* 3.4 7.8 + - - +
2061C ALA* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP2058 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2049C PHE* 3.3 35.1 - + + -
2054C GLN 2.7 21.2 + - - +
2055C ALA 3.6 2.2 - - - +
2057C ALA* 1.3 71.6 - - - +
2059C GLY* 1.3 80.5 + - - +
2061C ALA* 3.2 5.3 + - - +
2062C GLN* 2.9 54.3 + - + +
2120C THR* 3.7 19.7 - - - -
2121C PRO* 3.7 29.3 - - + +
2122C GLU* 4.2 22.8 + - + +
2124C ILE* 4.1 11.7 - - + -
2177C LEU* 4.1 21.8 - - + -
2215C MET* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2059 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2055C ALA 2.8 18.6 + - - -
2058C TRP* 1.3 83.6 - - - +
2060C ASN* 1.3 55.9 + - - +
2062C GLN* 3.1 5.0 + - - +
2063C TYR* 2.9 25.3 + - - +
2202C TYR* 3.2 41.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2060 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2056C LYS* 2.8 43.8 + - - +
2057C ALA* 3.7 8.1 - - - +
2059C GLY* 1.3 71.2 - - - +
2061C ALA* 1.3 62.3 + - - +
2063C TYR* 3.3 8.3 + - + +
2064C LYS* 3.0 30.3 + - + +
2202C TYR* 3.4 20.8 + - - -
2204C ASP* 5.3 0.8 + - - -
2205C PRO* 3.9 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2061 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2057C ALA 2.9 16.6 + - - +
2058C TRP* 3.4 8.1 - - + +
2059C GLY 3.2 0.2 - - - -
2060C ASN* 1.3 78.7 - - - +
2062C GLN* 1.3 71.5 + - - +
2064C LYS* 3.5 12.4 + - - +
2065C LYS* 3.5 20.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2062 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2058C TRP* 2.9 66.1 + - + +
2059C GLY* 3.1 5.6 + - - +
2061C ALA* 1.3 80.9 - - - +
2063C TYR* 1.3 66.8 + - - +
2065C LYS* 2.9 44.0 + - - +
2066C TYR* 3.2 35.3 + - + +
2119C LYS 5.1 2.4 - - - +
2121C PRO* 3.4 27.7 - - + +
2202C TYR* 5.2 0.7 - - + -
2215C MET* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR2063 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2059C GLY 2.9 16.6 + - - +
2060C ASN* 3.5 10.8 - - + +
2062C GLN* 1.3 77.3 - - - +
2064C LYS* 1.3 78.7 + - + +
2065C LYS 3.2 1.0 + - - -
2066C TYR* 3.2 38.2 + + + +
2067C GLY 4.4 2.1 + - - -
2068C LEU* 4.3 11.2 - - + -
2073C LYS* 3.5 29.1 + - - +
2202C TYR 4.2 4.7 - - - +
2205C PRO* 3.9 29.4 + - + -
2206C ILE* 3.4 37.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2064 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2060C ASN* 3.0 21.7 + - + +
2061C ALA* 3.7 10.3 - - - +
2062C GLN 3.2 0.6 - - - -
2063C TYR* 1.3 91.5 - - + +
2065C LYS* 1.3 61.6 + - + +
2066C TYR 3.5 0.4 + - - -
2067C GLY* 4.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS2065 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2061C ALA* 3.5 21.7 - - - +
2062C GLN* 2.9 35.5 + - - +
2064C LYS* 1.3 80.1 - - + +
2066C TYR* 1.3 66.1 + - + +
2067C GLY* 3.5 1.7 - - - -
2117C LYS 5.0 1.0 - - - +
2121C PRO* 5.1 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR2066 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2062C GLN* 3.2 34.9 - - + +
2063C TYR* 3.2 34.8 + + + +
2065C LYS* 1.3 81.5 - - + +
2067C GLY* 1.3 65.2 + - - +
2068C LEU* 3.8 19.5 - - + +
2117C LYS* 3.4 37.8 - - - +
2118C MET* 3.6 43.1 - - + -
2119C LYS 4.5 8.3 + - - -
2200C ALA 3.9 3.6 + - - -
2201C GLY* 3.6 3.8 - - - -
2202C TYR* 3.0 41.7 + - - +
2215C MET* 5.2 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2067 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2063C TYR 4.4 2.2 + - - -
2064C LYS 4.7 3.0 + - - -
2065C LYS* 3.5 3.2 - - - +
2066C TYR* 1.3 79.5 - - - +
2068C LEU* 1.3 65.1 + - - +
2069C SER* 4.7 0.2 - - - -
2117C LYS* 3.0 19.8 + - - +
----------------------------------------------------------
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