Contacts of the helix formed by residues 302 - 327 (chain 3) 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 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13 PHE* 3.4 16.2 - - - -
2963 VAL* 4.4 0.2 - - - -
3013 ALA* 1.3 74.3 - - - +
3033 VAL* 1.3 65.7 + - - +
3043 GLU* 3.1 15.5 + - - +
3053 GLU* 2.7 49.6 + - - +
3063 LEU* 3.2 14.6 + - - +
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Residues in contact with VAL 303 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2923 LYS* 3.8 33.0 - - + +
2963 VAL* 4.1 17.6 - - + +
3013 ALA 4.0 1.0 + - - -
3023 SER* 1.3 73.3 - - - +
3043 GLU* 1.3 81.8 + - - +
3063 LEU* 3.9 4.0 + - + +
3073 LYS* 3.1 25.2 + - + +
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Residues in contact with GLU 304 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3023 SER* 3.1 14.0 - - - +
3033 VAL* 1.3 99.6 + - - +
3053 GLU* 1.3 60.6 + - - +
3063 LEU 3.2 0.2 - - - -
3073 LYS* 3.6 7.1 - - + -
3083 GLU* 2.8 51.3 + - + +
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Residues in contact with GLU 305 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13 PHE* 3.2 11.9 - - + -
293 ARG* 3.0 26.6 + - - -
333 LEU* 4.2 11.0 - - + +
3013 ALA* 3.1 17.3 - - + +
3023 SER* 2.7 48.3 + - - +
3043 GLU* 1.3 78.2 - - - +
3063 LEU* 1.3 59.2 + - + +
3083 GLU* 3.3 9.5 + - - +
3093 ILE* 3.1 33.1 + - + +
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Residues in contact with LEU 306 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333 LEU* 4.6 5.4 - - + -
363 TYR* 3.6 41.4 + - + +
2923 LYS* 3.3 47.1 - - + +
2953 MET* 4.1 28.3 - - + -
2963 VAL* 4.7 6.5 - - + -
3013 ALA* 4.7 5.6 - - + -
3023 SER 3.2 14.4 + - - +
3033 VAL* 4.1 4.5 - - - +
3043 GLU 3.2 0.2 - - - -
3053 GLU* 1.3 76.1 - - + +
3073 LYS* 1.3 65.0 + - - +
3083 GLU 3.1 2.1 + - - -
3093 ILE* 3.3 12.3 + - + -
3103 ASP* 3.2 25.8 + - - +
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Residues in contact with LYS 307 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3033 VAL* 3.1 21.6 + - + +
3043 GLU* 3.2 9.8 + - + +
3063 LEU* 1.3 74.3 - - - +
3083 GLU* 1.3 61.5 + - + +
3103 ASP* 3.3 37.9 - - - +
3113 VAL* 3.1 26.3 - - + +
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Residues in contact with GLU 308 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3043 GLU* 2.8 37.9 + - + +
3053 GLU* 3.7 8.3 + - - +
3073 LYS* 1.3 78.5 - - + +
3093 ILE* 1.3 65.9 + - - +
3103 ASP 3.2 1.1 - - - -
3113 VAL* 3.3 17.2 + - + +
3123 GLU* 3.3 22.7 + - - +
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Residues in contact with ILE 309 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333 LEU* 4.2 27.1 - - + +
363 TYR* 4.2 21.5 - - + -
373 ARG* 3.3 60.6 - - + +
403 GLN* 5.7 0.4 - - + -
3053 GLU* 3.1 17.8 + - + +
3063 LEU* 3.3 16.3 + - + +
3083 GLU* 1.3 74.8 - - - +
3103 ASP* 1.3 68.2 + - - +
3113 VAL 3.0 0.7 + - - -
3123 GLU* 3.1 4.7 + - - +
3133 VAL* 3.0 23.7 + - + +
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Residues in contact with ASP 310 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363 TYR* 2.9 23.5 + - - -
403 GLN* 3.3 28.7 + - - +
443 ARG* 5.5 0.7 - - - +
3063 LEU 3.2 14.0 - - - +
3073 LYS* 3.3 36.2 - - - +
3093 ILE* 1.3 79.5 - - - +
3113 VAL* 1.3 52.7 + - + +
3133 VAL* 3.3 7.8 + - - +
3143 ARG* 2.8 36.2 + - - +
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Residues in contact with VAL 311 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3073 LYS* 3.1 28.5 - - + +
3083 GLU* 3.6 14.1 - - + +
3093 ILE 3.0 1.0 + - - -
3103 ASP* 1.3 78.7 - - + +
3123 GLU* 1.3 59.7 + - + +
3143 ARG* 3.5 6.8 + - + +
3153 LYS* 3.0 28.8 + - - +
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Residues in contact with GLU 312 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373 ARG* 3.2 34.8 + - - +
3083 GLU* 3.3 19.6 - - - +
3093 ILE* 3.1 5.0 + - - +
3113 VAL* 1.3 74.3 - - + +
3133 VAL* 1.3 57.2 + - - +
3153 LYS* 3.4 8.2 + - - +
3163 GLU* 2.8 33.1 + - - +
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Residues in contact with VAL 313 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373 ARG* 4.2 27.1 - - + +
403 GLN* 3.6 22.0 - - + +
413 THR* 3.4 25.6 - - + +
443 ARG* 3.4 31.9 - - + -
3093 ILE* 3.0 19.6 + - + +
3103 ASP* 3.6 6.1 - - - +
3123 GLU* 1.3 72.5 - - - +
3143 ARG* 1.3 68.0 + - - +
3163 GLU* 3.0 8.3 + - + +
3173 ILE* 2.9 25.8 + - + +
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Residues in contact with ARG 314 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443 ARG* 3.0 47.1 - - + +
3103 ASP 2.8 17.3 + - - +
3113 VAL* 3.5 10.3 - - + +
3133 VAL* 1.3 79.3 - - - +
3153 LYS* 1.3 61.9 + - - +
3173 ILE* 3.9 4.7 - - - +
3183 GLU* 3.0 43.6 + - - +
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Residues in contact with LYS 315 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3113 VAL* 3.0 16.8 + - - +
3123 GLU* 3.6 10.5 - - - +
3143 ARG* 1.3 74.2 - - - +
3163 GLU* 1.3 65.2 + - - +
3183 GLU* 3.0 7.6 + - - +
3193 ASP* 2.8 52.2 + - - +
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Residues in contact with GLU 316 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373 ARG* 6.0 0.3 + - - -
413 THR* 5.6 4.7 - - + +
1023 VAL* 5.0 12.3 - - + -
3123 GLU 2.8 18.4 + - - +
3133 VAL* 3.0 14.1 + - + +
3153 LYS* 1.3 77.3 - - - +
3173 ILE* 1.3 69.1 + - + +
3193 ASP* 3.3 8.2 + - - +
3203 ALA* 3.1 19.9 + - - +
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Residues in contact with ILE 317 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413 THR* 4.0 22.0 - - + +
443 ARG* 3.5 31.0 - - + +
453 MET* 4.2 5.4 - - + +
483 LYS* 3.6 35.4 - - + -
1023 VAL* 3.3 34.1 - - + -
1063 LEU* 4.7 3.4 - - + -
3133 VAL* 2.9 22.6 + - + +
3143 ARG* 3.9 5.8 - - - +
3163 GLU* 1.3 71.8 - - + +
3183 GLU* 1.3 64.0 + - - +
3203 ALA* 3.1 6.5 + - - +
3213 ALA* 2.7 28.8 + - - +
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Residues in contact with GLU 318 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483 LYS* 2.8 37.7 + - - -
3143 ARG* 3.0 41.2 + - - +
3153 LYS* 3.0 7.9 + - + +
3173 ILE* 1.3 83.1 - - - +
3193 ASP* 1.3 64.5 + - - +
3213 ALA* 4.2 2.9 - - - +
3223 GLN* 3.3 20.8 + - - +
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Residues in contact with ASP 319 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033 ARG* 5.5 3.6 - - - +
3153 LYS* 2.8 48.9 + - - +
3163 GLU* 3.9 10.9 - - - +
3183 GLU* 1.3 73.5 - - - +
3203 ALA* 1.3 67.7 + - - +
3223 GLN* 3.1 12.7 + - + +
3233 PHE* 2.9 23.0 + - - +
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Residues in contact with ALA 320 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023 VAL* 3.8 17.0 - - + +
1033 ARG* 3.8 44.0 - - + +
1063 LEU* 4.0 7.0 - - + -
3163 GLU 3.1 12.1 + - - +
3173 ILE 3.1 8.0 + - - +
3193 ASP* 1.3 73.6 - - - +
3213 ALA* 1.3 54.4 + - - +
3233 PHE* 2.8 7.2 + - - +
3243 ALA* 2.7 34.4 + - - +
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Residues in contact with ALA 321 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483 LYS* 3.4 43.1 - - + +
523 LEU* 4.5 6.5 - - + -
1063 LEU* 3.6 10.0 - - + +
3173 ILE 2.7 19.1 + - - +
3183 GLU* 4.2 4.3 - - - +
3203 ALA* 1.3 71.7 - - - +
3223 GLN* 1.3 57.4 + - - +
3243 ALA* 3.5 4.9 - - - +
3253 THR* 2.8 36.3 + - + +
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Residues in contact with GLN 322 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3183 GLU 3.3 13.9 + - - +
3193 ASP* 3.1 14.9 + - - +
3213 ALA* 1.3 78.3 - - - +
3233 PHE* 1.3 74.5 + - - +
3253 THR* 3.1 9.2 + - - -
3263 ALA* 3.0 40.6 + - - +
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Residues in contact with PHE 323 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033 ARG* 3.4 65.7 - - + +
1043 GLU* 5.6 0.2 - - - -
1073 ALA* 3.8 22.7 - - + -
1143 GLY* 4.6 8.7 - - - -
3193 ASP 2.9 10.8 + - - +
3203 ALA* 2.8 12.6 + - - +
3223 GLN* 1.3 84.8 - - + +
3243 ALA* 1.3 60.7 + - - +
3263 ALA* 3.8 2.2 - - + -
3273 ASP* 2.9 56.4 + - + +
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Residues in contact with ALA 324 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523 LEU* 5.4 1.3 - - + -
1033 ARG 4.8 0.2 - - - +
1063 LEU* 3.9 14.4 - - + +
1073 ALA* 3.8 23.1 - - + +
1103 THR* 3.2 31.8 + - + +
1123 ARG* 3.3 17.7 + - - +
3203 ALA 2.7 14.8 + - - +
3213 ALA* 3.5 9.0 - - - +
3223 GLN 3.1 0.2 + - - -
3233 PHE* 1.3 82.0 - - + +
3253 THR* 1.3 60.8 + - - +
3263 ALA 3.2 0.9 + - - -
3273 ASP 3.8 0.3 + - - -
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Residues in contact with THR 325 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523 LEU* 3.7 32.3 - - + -
573 ILE* 4.3 16.1 - - + +
1103 THR* 4.8 1.3 - - + -
1123 ARG* 3.1 21.3 + - - +
3213 ALA 2.8 21.4 + - - +
3223 GLN* 3.2 15.9 + - - -
3243 ALA* 1.3 71.1 - - - +
3263 ALA* 1.3 58.3 + - - +
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Residues in contact with ALA 326 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3223 GLN* 3.0 37.8 + - - +
3233 PHE* 4.0 2.7 - - + +
3253 THR* 1.3 78.7 - - - +
3273 ASP* 1.3 66.8 + - - +
3283 PRO* 3.5 3.6 - - - +
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Residues in contact with ASP 327 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123 ARG* 3.1 42.3 + - + +
1133 LYS* 3.6 6.7 + - - +
1143 GLY* 2.7 39.2 + - - -
3233 PHE* 2.9 41.6 + - + +
3243 ALA* 3.8 1.1 + - - +
3253 THR 3.6 0.6 - - - -
3263 ALA* 1.3 76.5 - - - +
3283 PRO* 1.3 75.2 - - - +
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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