Contacts of the helix formed by residues 229 - 246 (chain 1) 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 ASP 229 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91 ILE* 3.8 7.4 - - - +
101 LYS 4.9 0.5 + - - -
701 ALA* 4.2 2.2 - - - -
2261 ASP* 3.4 15.0 + - - +
2271 GLY 3.4 0.4 - - - -
2281 MET* 1.3 75.8 - - - +
2301 ILE* 1.3 57.5 + - - +
2311 LEU* 2.6 43.9 + - - +
2321 CYS* 3.0 37.5 + - - -
2331 VAL* 3.2 13.3 + - - +
2901 LEU* 5.1 7.8 - - + +
2941 ARG* 2.7 36.8 + - - -
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Residues in contact with ILE 230 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351 TYR* 4.5 26.7 - - + -
391 MET* 4.2 19.1 - - + -
701 ALA* 3.7 14.6 - - + +
731 VAL* 3.9 19.3 - - + +
741 GLY* 3.3 31.0 - - - +
2281 MET 3.3 8.6 + - - +
2291 ASP* 1.3 72.8 - - - +
2311 LEU* 1.3 65.2 + - + +
2321 CYS 3.6 0.2 - - - -
2331 VAL* 3.8 1.5 - - - +
2341 ARG* 3.0 24.2 + - + +
2871 PRO 5.2 2.0 - - - +
2901 LEU* 6.5 0.4 - - + -
2911 LEU* 3.9 37.7 - - + +
2941 ARG* 5.0 1.3 - - - +
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Residues in contact with LEU 231 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 PHE* 4.2 21.8 - - + -
91 ILE* 3.7 12.8 - - + +
251 THR* 4.4 9.4 - - + -
271 LEU* 4.3 21.3 - - + -
351 TYR* 5.0 3.1 - - + -
2291 ASP* 2.6 18.4 + - - +
2301 ILE* 1.3 87.6 - - + +
2321 CYS* 1.3 58.6 + - - +
2331 VAL 3.3 0.7 - - - -
2341 ARG* 3.7 38.2 + - + +
2351 GLU* 3.1 30.5 + - - +
2911 LEU* 5.0 4.0 - - + -
2941 ARG* 2.9 29.6 - - - +
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Residues in contact with CYS 232 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91 ILE* 3.5 26.7 - - + -
101 LYS 3.9 17.3 - - - +
121 CYS* 5.7 2.9 - - - -
2251 VAL* 3.7 19.5 - - + -
2261 ASP* 4.0 15.3 - - + +
2291 ASP* 3.0 26.6 + - - +
2311 LEU* 1.3 73.7 - - - +
2331 VAL* 1.3 62.4 + - - +
2351 GLU* 4.0 4.9 - - - -
2361 ALA* 2.7 36.2 + - - +
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Residues in contact with VAL 233 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701 ALA 3.2 28.3 - - - +
711 CYS* 3.9 2.9 - - - +
741 GLY 3.6 16.6 - - - -
751 LEU* 3.6 19.2 - - + +
2251 VAL* 4.3 5.4 - - + -
2261 ASP 3.1 23.1 - - - +
2271 GLY* 4.0 15.0 - - - +
2291 ASP 3.6 8.5 - - - +
2301 ILE 3.8 1.8 - - - +
2321 CYS* 1.3 82.7 - - - +
2341 ARG* 1.3 63.3 + - - +
2361 ALA* 3.9 1.5 - - - +
2371 THR* 2.7 26.3 + - - -
2531 MET* 5.0 0.4 - - - +
2551 LEU* 4.2 15.7 - - + -
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Residues in contact with ARG 234 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251 THR* 3.0 29.3 + - - +
261 VAL 3.7 15.4 + - - -
271 LEU* 4.2 10.5 - - - +
311 ASP* 5.3 2.6 + - - -
351 TYR* 3.4 41.5 + - - -
741 GLY 3.3 10.8 - - - +
771 ALA* 3.3 26.0 - - + -
2301 ILE* 3.0 22.0 + - + +
2311 LEU* 3.7 24.6 - - + +
2321 CYS 3.3 0.2 - - - -
2331 VAL* 1.3 76.2 - - - +
2351 GLU* 1.3 60.5 + - - +
2371 THR* 3.6 1.9 - - - -
2381 ARG* 3.1 62.3 + - - +
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Residues in contact with GLU 235 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91 ILE* 3.5 25.8 - - + -
211 PRO* 4.3 7.3 - - + +
221 PRO* 3.4 30.9 - - - +
251 THR* 3.6 24.7 + - + +
2311 LEU 3.1 19.8 + - - +
2321 CYS* 2.9 6.4 + - - +
2341 ARG* 1.3 83.3 + - - +
2361 ALA* 1.3 66.3 + - - +
2371 THR 3.1 0.9 - - - -
2381 ARG* 3.2 21.9 + - - +
2391 PHE* 2.9 23.4 + - - +
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Residues in contact with ALA 236 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121 CYS* 4.7 2.9 - - - -
211 PRO* 4.4 8.8 - - - +
2231 LEU* 4.1 13.1 - - + +
2251 VAL* 3.3 35.7 - - + -
2321 CYS 2.7 19.2 + - - +
2331 VAL 3.9 2.2 - - - +
2351 GLU* 1.3 70.7 - - - +
2371 THR* 1.3 54.2 + - - +
2391 PHE* 3.1 3.9 + - - +
2401 ALA* 2.7 36.0 + - - +
2531 MET* 3.8 15.2 - - + +
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Residues in contact with THR 237 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741 GLY 4.3 1.8 - - - -
751 LEU* 3.1 35.0 - - + +
781 GLY* 3.4 30.3 - - - +
791 ILE* 3.7 15.0 - - + -
1621 LEU* 4.7 4.7 - - + -
1901 ILE* 4.7 3.2 - - + +
2331 VAL 2.7 24.2 + - - -
2341 ARG 3.6 5.2 - - - -
2351 GLU 3.1 0.2 - - - -
2361 ALA* 1.3 75.0 - - - +
2381 ARG* 1.3 58.2 + - - +
2401 ALA* 3.2 1.4 + - - +
2411 ALA* 2.8 33.5 + - + +
2531 MET* 3.7 9.8 - - + +
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Residues in contact with ARG 238 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251 THR* 5.3 0.4 + - - -
351 TYR* 4.9 1.8 + - - -
771 ALA 3.7 9.8 + - - -
781 GLY* 3.6 24.9 - - - +
2341 ARG* 3.1 62.3 + - - +
2351 GLU* 3.2 17.9 + - - +
2371 THR* 1.3 75.5 - - - +
2391 PHE* 1.3 58.1 + - - +
2411 ALA* 3.7 1.8 - - - +
2421 ALA* 2.8 32.6 + - - +
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Residues in contact with PHE 239 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171 LEU* 3.7 30.7 - - + -
191 GLU* 3.3 24.0 - - + -
201 GLY* 3.5 27.8 - - - -
211 PRO* 3.8 16.8 - - + -
221 PRO* 5.3 4.0 - - + -
2231 LEU* 3.9 19.1 - - + -
2351 GLU* 2.9 14.1 + - - +
2361 ALA 3.4 5.8 - - - +
2381 ARG* 1.3 77.9 - - - +
2401 ALA* 1.3 60.2 + - - +
2421 ALA* 3.3 6.8 + - + +
2431 TYR* 3.1 32.7 + + + +
2511 ILE* 4.7 5.2 - - + -
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Residues in contact with ALA 240 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1901 ILE* 3.9 22.4 - - + -
2231 LEU* 4.8 3.4 - - + -
2361 ALA 2.7 19.3 + - - +
2371 THR* 3.8 2.5 - - - +
2391 PHE* 1.3 74.3 - - - +
2411 ALA* 1.3 66.9 + - - +
2431 TYR* 3.3 8.1 + - - +
2441 CYS* 3.1 27.4 + - - +
2511 ILE* 4.1 16.2 - - + +
2531 MET* 4.0 18.6 - - - -
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Residues in contact with ALA 241 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781 GLY 3.9 16.4 - - - +
791 ILE* 4.7 4.3 - - + -
1601 VAL* 4.3 6.1 - - + +
1901 ILE* 3.7 15.8 - - + +
2371 THR 2.8 22.4 + - - +
2381 ARG* 3.9 3.6 - - - +
2401 ALA* 1.3 74.3 - - - +
2421 ALA* 1.3 60.4 + - - +
2441 CYS* 3.6 3.9 + - - +
2451 ARG* 3.2 49.0 + - - +
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Residues in contact with ALA 242 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2381 ARG 2.8 19.1 + - - +
2391 PHE* 3.7 7.2 - - + +
2401 ALA 3.2 0.2 - - - -
2411 ALA* 1.3 75.5 - - - +
2431 TYR* 1.3 59.5 + - - +
2451 ARG* 3.1 9.0 + - - +
2461 SER* 2.9 29.9 + - - -
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Residues in contact with TYR 243 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171 LEU* 4.2 26.2 - - + -
2211 PRO* 3.0 27.3 - - + +
2391 PHE* 3.1 21.1 + + + +
2401 ALA* 3.4 11.4 - - - +
2421 ALA* 1.3 76.7 - - - +
2441 CYS* 1.3 62.4 + - - +
2461 SER* 3.1 22.4 + - - -
2481 LYS* 3.4 61.7 + - + +
2491 GLY 3.5 18.4 - - - -
2501 PRO 3.5 11.2 - - - -
2511 ILE* 4.3 19.1 - - + -
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Residues in contact with CYS 244 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1601 VAL* 3.8 22.2 - - + -
1881 PRO* 4.0 14.1 - - + +
1891 CYS 3.9 22.2 - - - -
1901 ILE* 4.0 15.7 - - - -
2401 ALA 3.1 19.4 + - - +
2411 ALA* 3.8 2.5 - - - +
2431 TYR* 1.3 78.0 - - - +
2451 ARG* 1.3 56.7 + - - +
2471 GLY* 3.0 20.1 + - - -
2481 LYS 4.3 0.3 + - - -
2491 GLY 3.3 24.8 + - - +
2511 ILE* 4.0 11.2 - - - -
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Residues in contact with ARG 245 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781 GLY 4.7 1.2 + - - -
791 ILE* 4.5 6.1 - - - +
801 ASN* 3.6 16.3 + - - +
831 ASP* 2.7 43.2 + - - -
1581 ASP* 3.0 56.5 + - - +
1591 GLU* 4.0 0.2 - - - +
1601 VAL* 3.7 25.1 - - + +
1881 PRO* 6.0 0.2 - - - -
2411 ALA* 3.2 29.9 + - - +
2421 ALA* 3.1 8.9 + - - +
2441 CYS* 1.3 70.3 - - - +
2461 SER* 1.3 60.0 + - - +
2471 GLY 3.1 5.5 + - - -
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Residues in contact with SER 246 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2421 ALA 2.9 14.8 + - - -
2431 TYR* 3.1 14.9 + - - -
2441 CYS 3.1 0.6 - - - -
2451 ARG* 1.3 77.7 - - - +
2471 GLY* 1.3 58.3 + - - +
2481 LYS* 3.3 27.4 + - - +
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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) + - + + + + + -
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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