Contacts of the helix formed by residues 3165 - 3186 (chain D) in PDB entry 3CMT
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 GLY3165 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2199D ILE* 4.3 6.6 - - - +
3163D HIS 3.2 2.0 + - - -
3164D MET* 1.3 70.4 - - - +
3166D LEU* 1.3 57.4 + - - +
3167D ALA 3.5 1.6 - - - -
3168D ALA* 3.4 15.2 + - - +
3169D ARG* 2.9 38.4 + - - +
1009E C 4.2 14.6 + - - -
1010E T 4.6 15.0 + - - -
1011E T 5.2 5.6 - - - -
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Residues in contact with LEU3166 (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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3123D GLU* 4.7 8.3 - - - +
3151D PRO* 3.9 26.9 - - + -
3153D ALA* 3.9 24.9 - - + -
3154D GLU 4.8 0.2 - - - +
3163D HIS* 3.1 36.7 + - + +
3164D MET 3.0 3.6 + - - -
3165D GLY* 1.3 73.5 - - - +
3167D ALA* 1.3 61.4 + - - +
3169D ARG* 3.2 24.9 + - + +
3170D MET* 2.9 29.7 + - + +
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Residues in contact with ALA3167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3149D LEU 4.8 3.4 - - - +
3151D PRO* 3.9 26.1 - - + +
3163D HIS 4.9 0.2 + - - -
3166D LEU* 1.3 78.2 - - - +
3168D ALA* 1.3 58.2 + - - +
3170D MET* 3.4 11.0 + - + +
3171D MET* 2.9 35.3 + - + +
3210D THR* 6.4 1.1 - - + -
3211D GLY* 4.7 6.7 - - - -
4176D ARG* 4.8 12.8 - - - +
1011E T 4.0 13.0 + - - +
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Residues in contact with ALA3168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3165D GLY 3.4 9.1 + - - +
3166D LEU 3.2 0.4 - - - -
3167D ALA* 1.3 79.6 - - - +
3169D ARG* 1.3 56.6 + - - +
3171D MET* 3.4 3.6 + - - +
3172D SER* 2.9 29.9 + - - -
3211D GLY 4.0 12.2 - - - +
3212D GLY* 3.8 9.1 - - - -
3214D ALA* 5.1 1.2 + - - +
1009E C 3.4 25.3 - - - +
1010E T 3.7 27.2 + - - +
1011E T 3.7 4.8 + - - +
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Residues in contact with ARG3169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3164D MET 3.5 7.3 + - - -
3165D GLY 2.9 30.1 + - - +
3166D LEU* 3.6 31.3 - - + +
3168D ALA* 1.3 75.1 - - - +
3170D MET* 1.3 58.6 + - - +
3172D SER* 3.5 2.3 + - - -
3173D GLN* 3.0 27.8 + - - +
3176D ARG* 4.5 1.0 + - - +
1008E C 3.4 41.3 + - - +
1009E C 2.7 45.6 + - - +
2007F G 3.4 7.9 - - - +
2008F G 3.6 23.2 + - - +
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Residues in contact with MET3170 (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 ILE* 4.2 12.3 - - + +
2160D GLY* 5.5 1.6 - - - +
3122D GLY* 4.1 2.0 - - - -
3123D GLU* 3.6 43.5 - - + +
3126D LEU* 3.9 13.2 - - + -
3149D LEU* 3.6 26.5 - - + +
3151D PRO* 4.3 9.9 - - - -
3166D LEU* 2.9 21.1 + - + +
3167D ALA* 3.6 15.7 - - + +
3169D ARG* 1.3 74.4 - - - +
3171D MET* 1.3 87.0 + - + +
3173D GLN* 3.3 12.3 + - - +
3174D ALA* 2.9 27.6 + - - +
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Residues in contact with MET3171 (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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3126D LEU* 3.5 33.4 - - + -
3146D VAL* 4.5 17.0 - - + -
3149D LEU* 3.4 30.7 - - + -
3167D ALA* 2.9 20.5 + - + +
3168D ALA 3.4 2.7 + - - +
3170D MET* 1.3 82.1 - - + +
3172D SER* 1.3 65.1 + - - +
3174D ALA* 3.2 3.6 + - + +
3175D MET* 3.0 44.7 + - + +
3191D PHE* 4.9 4.9 - - + -
3211D GLY* 3.5 31.4 - - - +
3214D ALA* 4.2 6.5 - - + -
3215D LEU* 5.6 9.2 - - + +
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Residues in contact with SER3172 (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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2196D ARG* 3.4 29.7 + - - -
2210D THR* 6.0 0.5 - - - +
3168D ALA 2.9 17.9 + - - -
3169D ARG 3.5 2.5 - - - -
3171D MET* 1.3 76.8 - - - +
3173D GLN* 1.3 62.0 + - - +
3175D MET* 3.6 3.5 + - - +
3176D ARG* 3.4 27.1 + - - +
3214D ALA* 3.5 14.9 - - - +
3218D TYR* 5.0 1.6 + - - -
1009E C 3.4 30.0 + - - -
1010E T 6.0 0.4 - - - -
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Residues in contact with GLN3173 (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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2154D GLU* 3.1 36.6 - - + +
2158D GLU 3.8 7.1 - - - +
2159D ILE* 3.7 11.6 - - + +
2160D GLY* 2.8 35.5 - - - +
2161D ASP 3.0 21.3 + - - +
2163D HIS* 3.9 1.4 - - - -
3169D ARG 3.0 12.6 + - - +
3170D MET* 3.5 10.9 + - - +
3172D SER* 1.3 73.9 - - - +
3174D ALA* 1.3 64.7 + - - +
3176D ARG* 3.2 22.0 + - - +
3177D LYS* 3.2 27.1 + - + +
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Residues in contact with ALA3174 (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 ILE* 4.1 19.2 - - + +
3126D LEU* 3.8 29.6 - - + -
3170D MET 2.9 13.8 + - - +
3171D MET* 3.4 9.9 - - - +
3173D GLN* 1.3 76.5 - - - +
3175D MET* 1.3 65.0 + - + +
3177D LYS* 3.2 3.3 + - - +
3178D LEU* 2.7 41.4 + - + +
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Residues in contact with MET3175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3061D ILE* 4.1 17.9 - - - -
3171D MET* 3.0 36.6 + - - +
3172D SER 3.9 3.4 - - - +
3173D GLN 3.3 0.2 - - - -
3174D ALA* 1.3 85.8 - - + +
3176D ARG* 1.3 63.9 + - - +
3178D LEU* 4.4 6.1 - - + +
3179D ALA* 2.9 29.6 + - - +
3191D PHE* 3.8 28.0 - - + -
3214D ALA* 3.8 14.1 - - + -
3215D LEU* 3.9 24.5 - - + +
3218D TYR* 3.3 39.5 - - + -
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Residues in contact with ARG3176 (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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2147D ALA 3.3 26.9 - - - +
2148D ALA* 4.3 4.4 - - - +
2149D LEU 5.2 2.0 - - - -
2150D THR* 3.1 36.8 + - + +
2151D PRO* 4.8 3.8 - - - +
2154D GLU* 2.6 40.6 + - - -
2155D ILE* 5.4 1.6 - - - +
2167D ALA* 5.0 10.3 - - - +
2210D THR* 6.3 3.0 - - - +
3169D ARG* 4.5 1.6 + - - +
3172D SER* 3.4 13.0 + - - +
3173D GLN* 3.2 31.5 + - - +
3175D MET* 1.3 80.0 - - - +
3177D LYS* 1.3 60.3 + - + +
3179D ALA* 4.2 7.1 + - - +
3180D GLY 4.5 3.5 + - - -
3218D TYR* 3.6 12.7 + - - +
1008E C 6.0 3.8 - - - -
1009E C 3.5 22.4 + - - -
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Residues in contact with LYS3177 (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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2150D THR* 4.6 8.1 - - + -
2154D GLU* 3.5 19.3 - - + +
2155D ILE* 3.2 38.7 + - - +
2157D GLY 2.8 21.8 + - - +
2158D GLU* 4.1 1.3 - - - +
2159D ILE* 3.9 20.6 - - + +
3127D GLU* 3.5 15.8 + - - -
3130D ASP* 3.4 28.8 + - - +
3134D ARG* 5.1 1.0 - - - +
3173D GLN* 3.2 16.8 + - + +
3174D ALA* 3.2 7.7 + - - +
3176D ARG* 1.3 77.1 - - - +
3178D LEU* 1.3 63.9 + - - +
3180D GLY* 4.2 1.2 + - - -
3181D ASN* 3.7 23.6 + - - +
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Residues in contact with LEU3178 (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 ILE* 5.2 2.0 - - + -
3061D ILE* 4.9 2.7 - - + -
3126D LEU* 4.5 9.0 - - + +
3129D CYS* 4.1 11.7 - - + +
3130D ASP* 3.6 42.8 - - + +
3133D ALA* 4.8 4.9 - - + -
3174D ALA* 2.7 37.7 + - + +
3175D MET* 4.1 6.5 - - + +
3177D LYS* 1.3 70.8 - - + +
3179D ALA* 1.3 67.3 + - - +
3180D GLY 3.2 2.5 - - - -
3181D ASN* 3.0 3.9 + - - -
3182D LEU* 2.8 37.6 + - + +
3189D LEU* 3.8 24.7 - - + -
3191D PHE* 4.4 11.9 - - + -
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Residues in contact with ALA3179 (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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2095D ALA 5.1 2.2 - - - +
2096D GLU 4.2 15.0 - - - +
2097D HIS* 4.0 10.5 - - + +
2148D ALA* 6.1 0.4 - - + -
3059D GLY 4.6 2.1 - - - +
3061D ILE* 4.4 13.8 - - + +
3175D MET 2.9 17.9 + - - +
3176D ARG 4.5 3.4 - - - +
3177D LYS 3.6 0.2 - - - -
3178D LEU* 1.3 76.0 - - - +
3180D GLY* 1.3 62.1 + - - +
3182D LEU* 3.5 4.3 + - - +
3183D LYS* 3.2 22.2 + - - +
3218D TYR* 4.0 22.7 - - + -
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Residues in contact with GLY3180 (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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2097D HIS* 3.7 29.0 - - - -
3176D ARG 4.5 4.2 + - - -
3177D LYS 4.2 3.5 + - - -
3178D LEU 3.2 0.8 - - - -
3179D ALA* 1.3 75.9 - - - +
3181D ASN* 1.3 66.3 + - - +
3183D LYS* 3.4 3.1 + - - +
3184D GLN* 3.1 32.0 + - - +
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Residues in contact with ASN3181 (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 ILE* 6.2 2.6 - - - +
3130D ASP* 2.8 27.1 - - - +
3133D ALA* 4.0 18.8 - - + +
3134D ARG* 3.2 31.4 - - + +
3177D LYS* 3.7 9.2 + - - +
3178D LEU 3.0 7.4 + - - +
3180D GLY* 1.3 76.4 - - - +
3182D LEU* 1.3 60.0 + - - +
3184D GLN* 3.7 6.7 + - - +
3185D SER* 2.9 30.1 + - - -
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Residues in contact with LEU3182 (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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3059D GLY* 3.3 10.4 - - - +
3060D ARG 4.9 0.9 - - - +
3061D ILE* 3.7 23.6 - - + -
3133D ALA* 4.0 15.5 - - + -
3141D ILE* 4.8 3.1 - - + -
3178D LEU* 2.8 29.9 + - + +
3179D ALA 3.8 3.6 - - - +
3181D ASN* 1.3 75.2 - - - +
3183D LYS* 1.3 60.3 + - - +
3185D SER 3.4 0.3 + - - -
3186D ASN 3.0 7.6 + - - -
3187D THR* 2.9 68.3 + - + +
3189D LEU* 3.7 39.9 - - + -
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Residues in contact with LYS3183 (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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2097D HIS* 3.7 27.4 + - + +
2098D ALA 4.8 0.2 - - - +
2099D LEU 4.9 5.1 + - - -
2118D GLN* 3.7 29.7 - - - +
3034D SER* 3.6 29.8 + - - +
3035D MET* 4.9 8.3 + - - +
3036D ASP 6.2 0.2 - - - -
3058D MET 4.6 5.4 - - - -
3059D GLY* 3.6 19.4 + - - +
3060D ARG* 3.6 33.4 - - - +
3179D ALA 3.2 14.9 + - - +
3180D GLY 3.4 4.2 + - - +
3182D LEU* 1.3 80.2 - - - +
3184D GLN* 1.3 65.3 + - + +
3186D ASN* 3.1 18.6 + - - +
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Residues in contact with GLN3184 (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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2097D HIS* 3.9 25.7 + - - -
2118D GLN* 4.1 10.3 + - - +
2120D ASP* 3.4 25.8 + - - +
3034D SER* 6.4 2.5 - - - -
3180D GLY* 3.1 17.9 + - - +
3181D ASN* 4.4 6.9 + - - +
3183D LYS* 1.3 77.5 - - + +
3185D SER* 1.3 59.1 + - - +
3186D ASN* 5.3 0.2 - - - -
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Residues in contact with SER3185 (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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3133D ALA 2.5 30.0 + - - -
3134D ARG* 4.2 5.4 + - - -
3136D GLY* 4.0 21.6 + - - +
3138D VAL 4.9 2.3 - - - +
3139D ASP* 5.6 1.6 - - - +
3181D ASN 2.9 15.9 + - - -
3182D LEU 4.1 0.2 - - - -
3183D LYS 3.1 0.2 - - - -
3184D GLN* 1.3 77.7 - - - +
3186D ASN* 1.3 69.4 + - - +
3187D THR* 3.1 16.3 + - - -
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Residues in contact with ASN3186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3034D SER 5.6 1.6 - - - +
3036D ASP 5.4 3.6 - - - +
3038D GLU* 3.2 28.2 + - - +
3058D MET* 3.4 50.9 - - - +
3059D GLY* 3.6 7.3 + - - -
3138D VAL 5.4 0.2 - - - -
3139D ASP* 4.1 3.6 - - - +
3182D LEU 3.0 7.4 + - - -
3183D LYS* 3.1 14.9 + - - +
3184D GLN 3.4 0.8 - - - +
3185D SER* 1.3 80.9 - - - +
3187D THR* 1.3 57.9 + - - +
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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
------------------------------------------------------------
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