Contacts of the helix formed by residues 2149 - 2169 (chain D) in PDB entry 6X34
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 SER2149 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2146D SER* 3.7 14.8 + - - -
2147D PRO 3.4 0.4 - - - -
2148D SER* 1.3 80.0 - - - +
2150D VAL* 1.3 62.4 + - - +
2151D GLU* 3.3 3.4 - - - +
2152D ASP* 3.4 10.1 + - - +
2153D THR* 3.2 25.4 + - - +
2190D LYS* 6.4 0.4 - - - -
2191D VAL* 3.7 25.2 - - - +
2194D GLN* 4.6 8.4 + - - -
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Residues in contact with VAL2150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1737D PRO* 4.2 20.4 - - + -
1739D THR* 5.6 0.9 - - - +
1772D LEU* 5.1 4.3 - - + -
2145D ILE* 5.6 1.8 - - + -
2146D SER 4.4 2.5 - - - +
2147D PRO* 3.8 35.0 - - + +
2148D SER 4.1 1.1 + - - -
2149D SER* 1.3 73.4 - - - +
2151D GLU* 1.3 64.5 + - + +
2153D THR* 2.6 25.3 + - - +
2154D MET* 2.9 32.0 + - + +
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Residues in contact with GLU2151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2149D SER* 3.3 1.0 - - - +
2150D VAL* 1.3 85.0 - - + +
2152D ASP* 1.3 55.8 + - - +
2154D MET* 3.3 7.6 + - - +
2155D SER* 2.9 29.5 + - - -
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Residues in contact with ASP2152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2149D SER* 3.4 15.9 + - - +
2150D VAL 3.3 0.4 - - - -
2151D GLU* 1.3 77.6 - - - +
2153D THR* 1.3 57.8 + - - +
2155D SER* 2.7 23.2 + - - -
2156D LEU* 2.9 16.8 + - - +
2189D ASN* 3.4 14.9 + - - +
2190D LYS* 5.5 4.3 - - + +
2191D VAL* 3.9 19.5 - - + -
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Residues in contact with THR2153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1735D ILE* 5.9 1.1 - - - -
1772D LEU* 3.3 25.9 - - - +
2145D ILE* 3.7 24.0 - - + +
2149D SER* 3.2 16.4 + - - +
2150D VAL* 2.6 24.1 + - - -
2152D ASP* 1.3 76.6 - - - +
2154D MET* 1.3 55.6 + - - +
2156D LEU* 3.3 8.0 + - + +
2157D LEU* 2.9 38.0 + - - +
2191D VAL* 4.3 22.7 - - + -
2198D LEU* 5.3 6.5 - - + -
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Residues in contact with MET2154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1772D LEU* 3.8 31.0 - - + -
1773D ARG 4.2 20.9 - - - +
1774D PRO* 5.0 4.7 - - + +
1775D PRO* 5.4 11.3 - - + +
2150D VAL* 2.9 29.0 + - + +
2151D GLU* 3.7 7.2 - - - +
2153D THR* 1.3 80.7 + - - +
2155D SER* 1.3 57.7 + - - +
2157D LEU* 3.3 8.9 + - - +
2158D GLU* 2.9 29.7 + - - +
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Residues in contact with SER2155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2151D GLU 2.9 13.8 + - - -
2152D ASP* 2.7 26.7 + - - -
2154D MET* 1.3 75.0 - - - +
2156D LEU* 1.3 56.7 + - - +
2158D GLU* 3.4 6.3 + - - +
2159D CYS* 2.9 32.1 + - - +
2185D ASN* 5.3 4.6 + - - +
2189D ASN* 4.3 5.0 + - - -
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Residues in contact with LEU2156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2152D ASP 2.9 18.1 + - - +
2153D THR* 3.6 8.5 - - - +
2154D MET 3.3 0.2 - - - -
2155D SER* 1.3 77.5 + - - +
2157D LEU* 1.3 59.1 + - + +
2159D CYS* 3.1 19.4 - - - -
2160D LEU* 2.9 39.5 + - + +
2185D ASN* 5.9 0.4 - - - +
2186D ILE* 4.3 18.8 - - + +
2189D ASN* 3.7 32.5 - - + +
2191D VAL* 5.6 5.6 - - + -
2192D PHE* 5.4 12.8 - - + +
2198D LEU* 5.8 7.2 - - + -
2202D LEU* 5.2 8.3 - - + -
2204D MET* 4.8 19.3 - - + -
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Residues in contact with LEU2157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1730D MET* 3.4 30.9 - - + +
1733D GLU* 6.0 4.0 - - + -
1735D ILE* 4.0 27.8 - - + -
1772D LEU* 4.1 37.0 - - + +
1773D ARG 5.0 0.4 - - - +
1774D PRO* 5.0 7.6 - - + -
2153D THR* 2.9 25.4 + - - +
2154D MET* 3.3 6.7 + - - +
2156D LEU* 1.3 80.2 - - + +
2158D GLU* 1.3 61.7 + - - +
2160D LEU* 3.2 21.2 - - + +
2161D GLY 2.9 19.4 + - - -
2198D LEU* 6.2 0.7 - - + -
2202D LEU* 4.3 8.1 - - + -
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Residues in contact with GLU2158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1730D MET* 4.7 3.1 - - - +
1774D PRO* 4.3 19.2 - - + +
1775D PRO* 5.3 5.2 - - + -
1777D HIS* 6.3 3.1 - - + -
2154D MET 2.9 16.9 + - - +
2155D SER* 3.8 7.0 - - - +
2157D LEU* 1.3 77.6 - - - +
2159D CYS* 1.3 57.2 + - - +
2161D GLY* 3.3 2.3 + - - -
2162D GLN* 2.9 27.6 + - - +
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Residues in contact with CYS2159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2155D SER 2.9 18.6 + - - +
2156D LEU* 3.1 33.4 - - - -
2158D GLU* 1.3 76.5 - - - +
2160D LEU* 1.3 58.8 + - - +
2162D GLN* 3.2 13.6 + - - +
2163D ILE* 2.9 34.6 + - + +
2182D SER* 4.9 6.4 - - - -
2185D ASN* 4.3 16.4 - - + +
2186D ILE* 3.5 30.7 - - + -
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Residues in contact with LEU2160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1730D MET* 4.9 9.0 - - + -
2156D LEU* 2.9 28.1 + - + +
2157D LEU* 3.2 25.6 - - + +
2159D CYS* 1.3 75.1 - - - +
2161D GLY* 1.3 64.6 + - - +
2163D ILE* 3.3 15.2 + - + +
2164D ARG* 2.9 69.9 + - - +
2186D ILE* 6.1 0.9 - - + -
2202D LEU* 3.7 31.6 - - + -
2204D MET* 5.3 9.9 - - + -
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Residues in contact with GLY2161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1726D SER* 4.8 10.0 + - - -
1729D SER* 5.6 2.9 - - - -
1730D MET* 3.7 24.5 - - - -
2157D LEU 2.9 11.9 + - - -
2158D GLU 3.7 1.8 - - - -
2160D LEU* 1.3 80.7 - - - +
2162D GLN* 1.3 55.1 + - - +
2164D ARG* 3.3 9.7 + - - +
2165D SER* 2.9 29.1 + - - -
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Residues in contact with GLN2162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1796D PRO* 6.2 2.4 - - - +
2158D GLU 2.9 13.6 + - - +
2159D CYS* 3.2 16.9 + - - +
2161D GLY* 1.3 74.1 - - - +
2163D ILE* 1.3 61.3 + - + +
2165D SER* 3.0 8.7 + - - +
2166D LEU* 2.9 45.1 + - + +
2178D LEU* 3.4 38.5 - - + +
2182D SER* 5.7 5.9 - - - -
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Residues in contact with ILE2163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2159D CYS 2.9 25.9 + - - +
2160D LEU* 3.3 15.9 + - + +
2162D GLN* 1.3 75.7 - - - +
2164D ARG* 1.3 58.6 + - - +
2166D LEU* 3.4 5.3 + - - +
2167D LEU* 2.9 27.6 + - + +
2179D MET* 3.7 33.2 - - + +
2182D SER* 3.6 29.8 - - - -
2183D ILE* 5.0 2.5 - - + -
2186D ILE* 4.0 28.7 - - + -
2207D THR* 5.1 13.2 - - - +
2208D VAL* 6.3 1.6 - - + -
2211D VAL* 5.0 5.2 - - + -
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Residues in contact with ARG2164 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1729D SER* 2.7 49.1 + - - +
1730D MET* 4.7 3.0 - - - +
1732D SER* 5.9 0.2 + - - -
2160D LEU* 2.9 46.2 + - - +
2161D GLY* 3.7 5.6 - - - +
2162D GLN 3.3 0.2 - - - -
2163D ILE* 1.3 77.8 - - + +
2165D SER* 1.3 56.6 + - - +
2167D LEU* 3.2 6.3 + - - +
2168D ILE* 2.9 37.8 + - + +
2202D LEU* 3.3 28.1 + - - +
2204D MET* 6.0 0.2 - - - +
2207D THR* 4.1 29.7 - - + +
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Residues in contact with SER2165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1677D GLY* 6.0 4.6 - - - -
1725D ARG* 5.5 9.4 - - - +
1726D SER* 4.9 10.5 - - - -
2161D GLY 2.9 15.5 + - - -
2162D GLN* 3.0 14.1 + - - +
2164D ARG* 1.3 77.3 - - - +
2166D LEU* 1.3 73.5 + - - +
2168D ILE* 3.5 11.1 + - - +
2169D VAL* 3.3 27.4 + - - +
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Residues in contact with LEU2166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2162D GLN* 2.9 33.8 + - + +
2163D ILE* 3.9 5.2 - - - +
2165D SER* 1.3 86.8 + - - +
2167D LEU* 1.3 59.3 + - - +
2168D ILE 3.4 0.2 - - - -
2169D VAL* 2.8 33.2 + - + +
2170D GLN 4.9 0.5 - - - +
2171D MET* 5.3 1.9 + - - -
2174D GLN* 5.2 3.1 - - - +
2175D GLU* 4.0 36.0 - - + +
2178D LEU* 3.7 38.1 - - + -
2179D MET* 5.6 9.6 - - + +
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Residues in contact with LEU2167 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2163D ILE* 2.9 18.8 + - + +
2164D ARG* 3.2 7.8 + - - +
2166D LEU* 1.3 75.0 - - - +
2168D ILE* 1.3 64.2 + - + +
2169D VAL 3.4 5.8 - - - +
2179D MET* 6.0 1.3 - - + -
2210D GLU* 6.5 0.4 - - + -
2211D VAL* 3.7 29.2 - - + -
2214D ASN* 4.4 15.4 + - - -
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Residues in contact with ILE2168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611D GLY 4.2 19.5 - - - +
612D VAL* 4.7 7.4 - - - +
613D ALA* 4.8 1.6 + - + +
1676D LEU* 4.9 16.2 - - + +
1725D ARG* 3.7 35.7 - - + +
2164D ARG* 2.9 25.9 + - + +
2165D SER* 3.8 6.7 - - - +
2166D LEU 3.4 0.2 - - - -
2167D LEU* 1.3 79.1 - - + +
2169D VAL* 1.3 64.3 + - + +
2170D GLN 3.8 1.0 + - - -
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Residues in contact with VAL2169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613D ALA* 3.8 21.3 - - + +
615D CYS* 4.5 17.0 - - - -
1676D LEU 3.3 26.7 - - - +
1677D GLY* 4.1 13.0 - - - +
2165D SER 3.3 16.6 + - - +
2166D LEU* 2.8 30.4 - - + +
2167D LEU* 3.3 6.3 - - - +
2168D ILE* 1.3 79.1 - - + +
2170D GLN* 1.3 76.8 + - - +
2171D MET* 3.5 1.2 + - - -
2175D GLU* 5.9 1.8 - - + -
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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