Contacts of the helix formed by residues 302 - 327 (chain 5) in PDB entry 3EXG
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 SER 302 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15 PHE* 3.7 16.9 - - - -
2965 VAL* 4.7 1.6 - - - -
3015 ALA* 1.3 74.0 - - - +
3035 VAL* 1.3 65.3 + - - +
3045 GLU* 3.4 20.4 + - - +
3055 GLU* 2.9 44.1 + - - +
3065 LEU* 3.0 13.3 + - - +
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Residues in contact with VAL 303 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2925 LYS* 4.9 16.4 - - - -
2965 VAL* 4.2 21.2 - - + +
3015 ALA 4.1 1.4 + - - -
3025 SER* 1.3 71.9 - - - +
3045 GLU* 1.3 86.8 + - + +
3065 LEU* 3.5 5.8 + - - +
3075 LYS* 3.0 30.0 + - + +
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Residues in contact with GLU 304 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3025 SER* 3.0 17.3 + - - +
3035 VAL* 1.3 98.5 - - + +
3055 GLU* 1.3 64.1 + - - +
3075 LYS* 3.3 10.7 + - - +
3085 GLU* 3.0 30.0 + - + +
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Residues in contact with GLU 305 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15 PHE* 3.1 26.2 - - - -
295 ARG* 3.5 20.1 + - - -
335 LEU* 4.5 5.3 - - + +
3015 ALA* 3.1 28.5 - - + +
3025 SER* 2.9 29.2 + - - +
3045 GLU* 1.3 75.6 - - - +
3065 LEU* 1.3 64.9 + - + +
3085 GLU* 3.0 34.1 + - - +
3095 ILE* 3.2 13.4 + - + +
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Residues in contact with LEU 306 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335 LEU* 4.1 25.4 - - + -
365 TYR* 3.7 41.7 - - + +
2925 LYS* 3.6 40.6 - - + +
2955 MET* 4.8 8.3 - - + -
2965 VAL* 4.6 12.6 - - + -
3015 ALA* 4.4 7.9 - - + -
3025 SER 3.0 10.2 + - - +
3035 VAL* 3.8 8.7 - - - +
3055 GLU* 1.3 74.8 - - - +
3075 LYS* 1.3 53.2 + - - +
3085 GLU 3.0 4.7 - - - -
3095 ILE* 2.8 12.6 + - + +
3105 ASP* 2.8 36.9 + - - +
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Residues in contact with LYS 307 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3035 VAL* 3.0 21.8 + - + +
3045 GLU* 3.6 9.9 - - - +
3065 LEU* 1.3 75.8 - - - +
3085 GLU* 1.4 55.0 + - - +
3105 ASP* 3.4 20.2 + - + +
3115 VAL* 3.2 30.5 - - + +
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Residues in contact with GLU 308 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3045 GLU* 3.0 24.6 + - - +
3055 GLU* 3.0 20.1 + - - +
3065 LEU 3.0 0.6 - - - -
3075 LYS* 1.4 73.9 - - - +
3095 ILE* 1.3 66.1 + - + +
3105 ASP 3.2 0.9 - - - -
3115 VAL* 3.3 5.9 + - - +
3125 GLU* 3.2 33.5 + - - +
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Residues in contact with ILE 309 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335 LEU* 4.2 41.5 - - + +
365 TYR* 4.8 9.0 - - + -
375 ARG* 3.4 55.4 - - + +
405 GLN* 5.8 0.9 - - + -
3055 GLU* 3.5 13.0 - - + +
3065 LEU* 2.8 20.7 + - + +
3085 GLU* 1.3 72.5 - - + +
3105 ASP* 1.3 64.7 + - - +
3125 GLU* 3.1 10.8 + - - +
3135 VAL* 3.0 26.0 + - + +
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Residues in contact with ASP 310 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365 TYR* 3.2 25.1 + - - -
405 GLN* 3.3 31.7 - - - +
445 ARG* 5.5 0.9 - - - +
2925 LYS* 6.1 0.2 - - - +
3065 LEU* 2.8 10.5 + - - +
3075 LYS* 3.4 33.3 + - + +
3095 ILE* 1.3 77.8 - - - +
3115 VAL* 1.3 59.1 + - + +
3135 VAL* 3.7 5.9 + - - +
3145 ARG* 3.2 24.8 + - - +
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Residues in contact with VAL 311 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3075 LYS* 3.2 32.1 - - + +
3085 GLU* 3.3 7.2 + - - +
3095 ILE 3.2 0.6 - - - -
3105 ASP* 1.3 76.9 - - + +
3125 GLU* 1.3 65.6 + - - +
3145 ARG* 3.3 12.4 - - + +
3155 LYS* 3.1 30.0 + - - +
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Residues in contact with GLU 312 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375 ARG* 3.2 35.5 + - - +
3085 GLU* 3.2 24.6 + - - +
3095 ILE* 3.1 12.2 + - - +
3115 VAL* 1.3 73.6 - - - +
3135 VAL* 1.3 54.5 + - - +
3155 LYS* 3.1 13.3 - - - +
3165 GLU* 2.8 35.1 + - - +
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Residues in contact with VAL 313 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375 ARG* 4.2 21.1 - - + +
405 GLN* 3.8 15.0 - - + +
415 THR* 3.6 34.1 - - + +
445 ARG* 3.4 34.3 - - + -
3095 ILE* 3.0 15.7 + - + +
3105 ASP* 3.8 9.0 - - - +
3125 GLU* 1.3 73.5 - - - +
3145 ARG* 1.3 66.3 + - - +
3165 GLU* 2.8 11.1 + - + +
3175 ILE* 2.7 27.7 + - + +
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Residues in contact with ARG 314 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445 ARG* 3.0 46.7 - - - +
3105 ASP 3.2 14.8 + - - +
3115 VAL* 3.3 20.0 - - + +
3135 VAL* 1.3 75.0 - - - +
3155 LYS* 1.3 57.2 + - - +
3175 ILE* 3.4 7.3 + - - +
3185 GLU* 2.9 31.4 + - + +
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Residues in contact with LYS 315 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3115 VAL* 3.1 18.8 + - - +
3125 GLU* 3.1 15.4 - - - +
3135 VAL 3.1 0.2 - - - -
3145 ARG* 1.3 75.9 - - - +
3165 GLU* 1.3 67.1 + - - +
3185 GLU* 3.1 6.9 + - + +
3195 ASP* 2.9 44.4 + - - +
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Residues in contact with GLU 316 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415 THR* 5.4 11.0 - - + +
1025 VAL* 5.0 9.4 - - + +
3125 GLU 2.8 17.8 + - - +
3135 VAL* 2.8 20.2 + - + +
3155 LYS* 1.3 73.8 - - - +
3175 ILE* 1.3 62.8 + - + +
3195 ASP* 3.7 5.6 + - - +
3205 ALA* 3.3 21.3 + - - +
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Residues in contact with ILE 317 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415 THR* 4.1 11.0 - - + +
445 ARG* 3.5 27.6 - - + +
455 MET* 3.8 28.7 - - + +
485 LYS* 3.8 42.0 - - + -
1025 VAL* 3.9 20.0 - - + -
1065 LEU* 4.7 2.2 - - + +
3135 VAL* 2.7 19.4 + - + +
3145 ARG* 3.6 10.1 - - - +
3165 GLU* 1.3 73.5 - - + +
3185 GLU* 1.3 60.3 - - - +
3205 ALA* 3.0 6.5 + - - +
3215 ALA* 2.8 27.0 + - - +
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Residues in contact with GLU 318 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551 GLN* 4.8 5.9 - - - +
485 LYS* 3.6 24.2 + - - -
3145 ARG* 2.9 21.9 + - + +
3155 LYS* 3.8 6.5 - - + +
3175 ILE* 1.3 73.8 - - - +
3195 ASP* 1.3 61.5 + - - +
3215 ALA* 4.6 7.4 - - - +
3225 GLN* 3.2 31.9 + - - +
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Residues in contact with ASP 319 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035 ARG* 4.3 12.6 + - - +
3155 LYS* 2.9 47.5 + - - +
3165 GLU* 4.0 6.2 - - - +
3185 GLU* 1.3 70.8 - - - +
3205 ALA* 1.3 65.1 + - - +
3225 GLN* 3.2 23.1 - - - +
3235 PHE* 3.3 8.3 + - - +
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Residues in contact with ALA 320 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025 VAL* 3.7 28.3 - - + +
1035 ARG* 3.9 29.6 - - + +
1065 LEU* 4.4 3.4 - - + -
3165 GLU 3.3 12.4 + - - +
3175 ILE 3.0 8.5 + - - +
3195 ASP* 1.3 78.5 - - - +
3215 ALA* 1.3 67.0 + - - +
3235 PHE* 2.9 7.1 + - - +
3245 ALA* 2.9 21.3 + - - +
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Residues in contact with ALA 321 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485 LYS* 3.8 36.8 - - + +
525 LEU* 4.5 7.4 - - + -
1065 LEU* 4.0 8.7 - - + +
3175 ILE 2.8 18.8 + - - +
3185 GLU* 4.2 9.4 - - - +
3205 ALA* 1.3 72.0 - - - +
3225 GLN* 1.3 58.5 + - - +
3245 ALA* 3.1 4.1 + - - +
3255 THR* 2.9 35.1 + - + +
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Residues in contact with GLN 322 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551 GLN* 3.4 53.7 + - - +
571 ILE* 3.4 23.1 - - - +
1035 ARG* 5.8 1.8 - - - +
3185 GLU* 3.2 17.2 + - - +
3195 ASP* 3.2 21.1 - - - +
3205 ALA 3.1 0.8 - - - -
3215 ALA* 1.3 77.2 - - - +
3235 PHE* 1.3 59.2 + - - +
3255 THR* 3.4 5.9 + - - -
3265 ALA* 2.8 41.9 + - - +
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Residues in contact with PHE 323 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035 ARG* 3.2 70.7 - - + +
1045 GLU 4.8 0.2 - - - -
1075 ALA* 4.1 11.9 - - + -
1145 GLY* 3.9 25.8 - - - -
3195 ASP 3.7 9.4 - - - +
3205 ALA 2.9 9.1 + - - +
3225 GLN* 1.3 89.9 - - + +
3245 ALA* 1.3 59.9 + - - +
3265 ALA* 4.5 1.3 - - + -
3275 ASP* 2.9 56.3 + - + +
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Residues in contact with ALA 324 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525 LEU* 5.5 0.9 - - + -
1035 ARG 4.7 0.7 - - - +
1065 LEU* 3.7 13.7 - - + +
1075 ALA* 3.5 39.0 - - + +
1105 THR* 2.9 27.2 + - + +
1125 ARG* 3.0 19.2 + - - +
3205 ALA 2.9 13.8 + - - +
3215 ALA* 3.1 8.0 + - - +
3235 PHE* 1.3 72.8 - - - +
3255 THR* 1.3 60.8 + - + +
3275 ASP* 5.0 0.2 - - - -
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Residues in contact with THR 325 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3221 GLN* 6.4 2.5 - - - -
3251 THR* 3.2 22.3 + - - +
525 LEU* 4.0 27.8 - - + -
575 ILE* 4.2 20.9 - - + -
1105 THR* 4.5 3.4 - - + -
1125 ARG* 2.9 20.8 + - - +
3215 ALA 2.9 17.8 + - - +
3225 GLN* 3.6 6.6 + - - -
3245 ALA* 1.3 78.6 - - - +
3265 ALA* 1.3 61.1 + - - +
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Residues in contact with ALA 326 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571 ILE* 3.3 37.7 - - + -
1121 ARG* 3.2 16.6 + - - -
3251 THR* 2.9 25.3 - - + +
3225 GLN* 2.8 28.2 + - - +
3235 PHE* 4.1 2.0 - - - +
3255 THR* 1.3 70.8 + - - +
3275 ASP* 1.3 61.4 + - - +
3285 PRO* 3.6 1.2 - - - +
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Residues in contact with ASP 327 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3251 THR 3.8 1.0 - - - +
1075 ALA* 6.0 0.2 - - + -
1125 ARG* 2.9 39.8 + - + +
1135 LYS* 3.5 12.8 + - - +
1145 GLY* 3.0 35.3 + - - -
3235 PHE* 2.9 38.3 + - + +
3245 ALA* 4.9 0.7 - - - -
3255 THR 3.3 0.2 - - - -
3265 ALA* 1.3 79.2 - - - +
3285 PRO* 1.3 75.1 - - - +
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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