Contacts of the helix formed by residues 270 - 282 (chain L) 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 GLY 270 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138J HIS* 4.0 2.0 - - - -
269J PHE* 3.5 9.4 - - - +
134L ALA* 3.8 9.0 - - - -
263L GLU* 4.1 4.5 - - - -
266L TRP 4.0 17.0 - - - -
267L PRO 3.5 5.9 + - - -
268L GLN 3.2 3.6 - - - -
269L PHE* 1.3 82.0 - - - +
271L VAL* 1.3 66.0 + - - -
272L GLY 3.3 2.2 - - - -
273L ALA* 3.2 11.6 + - - +
274L GLU 3.4 8.5 + - - -
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Residues in contact with VAL 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J PHE* 3.4 21.0 - - + -
133L ALA* 3.8 28.0 - - + -
134L ALA* 4.0 9.1 - - + +
212L HIS* 4.3 7.2 - - + +
238L MET* 3.8 36.1 - - + -
241L ILE* 4.7 7.9 - - + -
244L MET* 5.2 1.6 - - + -
263L GLU* 3.4 21.4 + - + +
270L GLY* 1.3 71.0 - - - -
272L GLY* 1.3 63.6 + - - +
274L GLU* 3.1 12.1 + - - +
275L ILE* 3.1 18.1 + - + +
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Residues in contact with GLY 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261L THR* 3.5 25.2 + - - -
263L GLU* 2.7 23.3 + - - -
271L VAL* 1.3 74.5 - - - +
273L ALA* 1.3 62.2 + - - +
275L ILE* 3.6 4.1 + - - +
276L CYS* 3.1 29.5 + - - -
294L ARG* 3.5 11.9 - - - -
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Residues in contact with ALA 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273J ALA* 3.8 18.7 - - + +
274J GLU* 3.5 25.4 - - - +
277J ALA* 3.9 15.0 - - + -
267L PRO 5.1 0.2 + - - -
269L PHE* 4.3 2.5 - - - +
270L GLY 3.2 19.6 + - - +
272L GLY* 1.3 76.8 - - - +
274L GLU* 1.3 56.8 + - - +
276L CYS* 3.3 3.1 + - - +
277L ALA* 3.0 26.3 + - - +
294L ARG* 3.7 10.4 - - - +
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Residues in contact with GLU 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268J GLN* 3.8 12.0 - - - +
269J PHE* 3.0 51.6 + - + +
273J ALA* 3.7 2.9 - - - +
294J ARG* 2.8 42.6 + - - -
244L MET* 3.7 22.7 - - + -
270L GLY 3.4 2.2 + - - -
271L VAL 3.1 3.2 + - - -
273L ALA* 1.3 74.8 - - - +
275L ILE* 1.3 66.5 + - - +
277L ALA* 3.3 1.1 + - - +
278L ARG* 3.0 45.0 + - - +
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Residues in contact with ILE 275 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210L VAL* 3.7 27.8 - - + -
238L MET* 3.8 21.1 - - + -
244L MET* 4.3 18.2 - - - -
246L MET* 4.0 14.6 - - + +
249L ILE* 4.6 10.5 - - + -
259L LEU* 4.3 13.7 - - + -
261L THR* 3.8 29.6 - - + -
271L VAL* 3.1 17.0 + - + +
272L GLY 3.9 6.5 - - - +
274L GLU* 1.3 75.1 - - - +
276L CYS* 1.3 57.3 - - - +
278L ARG* 3.4 5.2 + - - +
279L ILE* 3.1 26.3 + - - +
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Residues in contact with CYS 276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277J ALA* 3.8 22.2 - - + -
280J MET* 3.6 30.2 - - + +
281J GLU* 6.1 0.9 - - - -
259L LEU* 5.9 0.4 - - - -
261L THR* 4.9 6.3 - - - -
272L GLY 3.1 19.6 + - - +
273L ALA 3.5 8.1 - - - +
274L GLU 3.1 0.2 - - - -
275L ILE* 1.3 74.1 - - - +
277L ALA* 1.3 65.3 + - - +
278L ARG 3.0 1.3 - - - -
279L ILE* 3.2 3.8 + - - +
280L MET* 3.1 21.3 + - - +
292L ALA* 4.2 19.7 - - - -
294L ARG* 4.1 17.7 - - - -
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Residues in contact with ALA 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273J ALA* 3.8 11.9 - - + -
276J CYS* 4.2 15.2 - - + +
294J ARG* 3.4 38.4 - - - +
273L ALA 3.0 14.1 + - - +
274L GLU 3.8 2.7 - - - +
276L CYS* 1.3 79.2 - - - +
278L ARG* 1.3 61.8 + - - +
280L MET* 3.7 2.4 + - - +
281L GLU* 3.0 31.6 + - - +
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Residues in contact with ARG 278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268J GLN* 3.4 19.2 + - - -
294J ARG* 4.2 1.8 - - - +
349K ARG* 5.1 4.9 - - - +
244L MET* 4.4 20.4 + - - +
246L MET* 3.6 49.4 - - + +
250L GLU* 3.9 2.8 - - - +
274L GLU* 3.0 43.0 + - + +
275L ILE* 3.9 0.9 - - - +
276L CYS 3.0 0.2 - - - -
277L ALA* 1.3 76.5 - - - +
279L ILE* 1.3 58.4 + - - +
281L GLU* 3.3 14.3 + - - +
282L GLY* 2.8 34.3 + - - -
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Residues in contact with ILE 279 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280J MET* 4.8 8.5 - - + -
246L MET* 3.6 22.4 - - + -
249L ILE* 4.9 0.4 - - + -
250L GLU* 4.3 4.0 - - + -
253L VAL* 4.4 17.0 - - + -
259L LEU* 3.5 28.5 - - + -
275L ILE 3.1 12.2 + - - +
276L CYS* 3.2 6.3 + - - +
278L ARG* 1.3 78.5 - - - +
280L MET* 1.3 65.5 + - - +
282L GLY* 3.4 6.6 + - - +
284L ALA* 3.4 28.5 - - + -
285L PHE* 3.7 16.5 + - + +
288L LEU* 3.5 29.6 - - + -
292L ALA* 5.1 2.5 - - + -
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Residues in contact with MET 280 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276J CYS* 3.3 52.5 - - + +
279J ILE* 5.0 2.7 - - + -
280J MET* 4.4 18.2 - - + +
285J PHE* 5.2 1.6 - - - -
288J LEU* 4.5 9.6 - - - -
291J PRO* 3.4 33.4 - - + +
292J ALA* 3.8 27.4 - - + +
276L CYS 3.1 13.2 + - - +
277L ALA* 4.0 3.6 - - - +
279L ILE* 1.3 80.5 - - - +
281L GLU* 1.3 60.4 + - - +
282L GLY 3.5 1.6 + - - +
285L PHE* 3.7 35.6 - - + +
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Residues in contact with GLU 281 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276J CYS* 6.0 0.9 - - - -
291J PRO* 5.3 2.2 - - - -
292J ALA 3.9 17.3 - - - +
293J VAL* 5.9 0.9 - - - -
294J ARG* 2.9 67.4 + - + +
349K ARG* 3.1 22.7 + - - +
353K GLN* 3.5 35.5 + - + +
277L ALA* 3.0 15.7 + - - +
278L ARG* 3.9 8.4 - - - +
280L MET* 1.3 76.2 - - + +
282L GLY* 1.3 61.2 + - - +
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Residues in contact with GLY 282 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250L GLU* 3.4 12.8 - - - -
278L ARG 2.8 15.0 + - - -
279L ILE 3.4 1.9 + - - -
280L MET 3.3 6.4 - - - +
281L GLU* 1.3 77.1 - - - +
283L PRO* 1.3 71.5 - - - +
284L ALA 3.1 5.7 + - - -
285L PHE* 3.7 9.7 + - - +
286L ASN* 5.4 0.7 + - - -
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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