Contacts of the helix formed by residues 270 - 282 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138F HIS* 4.1 3.1 - - - -
269F PHE* 3.6 7.7 - - - -
134H ALA* 3.9 10.1 - - - -
263H GLU* 3.7 7.2 - - - -
266H TRP 4.0 7.2 - - - -
267H PRO 3.3 13.7 + - - -
268H GLN 3.1 2.0 - - - -
269H PHE* 1.3 82.9 - - - +
271H VAL* 1.3 67.1 + - - +
272H GLY 3.3 2.5 - - - -
273H ALA* 3.3 15.5 + - - +
274H GLU 3.5 3.5 + - - -
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Residues in contact with VAL 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F PHE* 3.6 21.3 - - + -
131H CYS* 6.1 0.7 - - - -
133H ALA* 3.8 29.2 - - + -
134H ALA* 4.2 9.6 - - + +
212H HIS* 4.2 9.9 - - - +
238H MET* 4.0 32.8 - - + -
241H ILE* 4.5 8.1 - - + -
244H MET* 4.4 3.8 - - + -
263H GLU* 2.8 21.4 + - + +
270H GLY* 1.3 71.7 - - - -
272H GLY* 1.3 64.8 + - - +
274H GLU* 3.1 14.0 + - - +
275H ILE* 3.2 14.5 + - + +
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Residues in contact with GLY 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261H THR* 3.6 26.2 - - - -
263H GLU* 2.4 23.4 + - - +
271H VAL* 1.3 71.5 - - - +
273H ALA* 1.3 65.2 + - - +
275H ILE* 3.1 5.8 + - - +
276H CYS* 3.0 27.0 + - - -
294H ARG* 3.5 10.1 - - - -
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Residues in contact with ALA 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269F PHE* 5.8 0.2 - - - -
273F ALA* 4.0 6.9 - - + +
274F GLU* 3.8 28.7 - - - +
277F ALA* 3.8 5.8 - - - -
269H PHE* 4.3 2.2 - - - +
270H GLY 3.3 19.5 + - - +
271H VAL 3.2 0.8 - - - -
272H GLY* 1.3 75.6 - - - +
274H GLU* 1.3 64.5 + - - +
276H CYS* 3.1 2.1 + - - +
277H ALA* 2.9 23.9 + - - +
294H ARG* 3.3 31.1 - - - +
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Residues in contact with GLU 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268F GLN* 3.2 16.5 - - - +
269F PHE* 2.7 59.1 + - + +
273F ALA* 3.8 5.2 - - - +
294F ARG* 3.1 26.3 + - - -
244H MET* 3.6 22.0 - - + -
270H GLY 3.5 1.2 + - - -
271H VAL 3.1 2.9 + - - +
273H ALA* 1.3 78.7 - - - +
275H ILE* 1.3 57.2 + - - +
277H ALA* 3.4 0.9 + - - +
278H ARG* 2.9 57.7 + - - +
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Residues in contact with ILE 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H VAL* 4.1 13.2 - - + -
238H MET* 3.8 35.2 - - + -
244H MET* 3.9 20.0 - - + -
246H MET* 3.8 14.3 - - + +
249H ILE* 4.5 10.1 - - + -
259H LEU* 4.5 12.1 - - + -
261H THR* 3.7 27.8 - - + -
271H VAL* 3.7 13.2 - - + +
272H GLY* 3.1 8.9 + - - +
274H GLU* 1.3 77.9 - - - +
276H CYS* 1.3 57.5 + - - +
278H ARG* 3.5 7.0 + - - +
279H ILE* 3.1 25.5 + - - +
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Residues in contact with CYS 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277F ALA* 4.1 15.0 - - - -
280F MET* 3.7 19.6 - - + +
281F GLU* 5.9 1.6 - - - -
259H LEU* 5.8 0.7 - - - -
261H THR* 4.9 10.1 - - - -
272H GLY 3.0 15.6 + - - +
273H ALA 3.5 6.7 - - - +
275H ILE* 1.3 75.3 - - - +
277H ALA* 1.3 68.1 + - - +
278H ARG 3.0 0.9 - - - -
279H ILE* 3.0 15.4 + - - +
280H MET* 3.1 14.7 + - - +
292H ALA* 4.0 27.6 - - - -
293H VAL 5.3 0.2 - - - -
294H ARG* 4.0 20.4 - - - -
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Residues in contact with ALA 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273F ALA* 3.7 15.7 - - + -
276F CYS* 4.1 18.4 - - + +
294F ARG* 3.5 34.5 - - - +
273H ALA 2.9 12.3 + - - +
274H GLU 3.5 7.9 - - - +
276H CYS* 1.3 76.3 - - - +
278H ARG* 1.3 56.3 + - - +
280H MET* 3.3 2.6 + - - +
281H GLU* 3.0 35.6 + - - +
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Residues in contact with ARG 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268F GLN* 3.2 24.7 + - - +
294F ARG* 4.1 6.7 - - - +
349G ARG* 5.8 3.4 - - - +
244H MET* 3.6 37.4 + - - +
246H MET* 3.5 35.5 - - - +
250H GLU* 3.7 4.9 - - - +
274H GLU* 2.9 48.0 + - + +
275H ILE* 3.7 5.8 - - - +
276H CYS 3.0 0.2 - - - -
277H ALA* 1.3 74.6 - - - +
279H ILE* 1.3 65.8 + - - +
281H GLU* 4.1 9.5 - - - +
282H GLY* 3.1 20.3 + - - -
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Residues in contact with ILE 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280F MET* 5.1 6.1 - - + -
246H MET* 3.8 17.5 - - + -
249H ILE* 4.3 1.6 - - + -
250H GLU* 4.2 8.1 - - + +
253H VAL* 4.3 11.9 - - + -
259H LEU* 3.4 32.3 - - + -
275H ILE 3.1 15.7 + - - +
276H CYS* 3.0 9.3 + - - +
278H ARG* 1.3 78.0 - - - +
280H MET* 1.3 66.8 + - + +
282H GLY* 3.2 10.0 + - - -
284H ALA* 3.9 22.7 - - + -
285H PHE* 3.6 19.0 + - - -
288H LEU* 3.8 30.5 - - + -
292H ALA* 5.4 1.1 - - + -
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Residues in contact with MET 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276F CYS* 3.2 46.2 - - + +
279F ILE* 4.8 2.5 - - + -
280F MET* 4.4 17.0 - - + -
285F PHE* 4.7 10.8 - - - -
288F LEU* 4.8 5.2 - - - -
291F PRO* 3.6 18.6 - - + +
292F ALA* 3.7 41.1 - - + +
276H CYS 3.1 11.2 + - - +
277H ALA* 3.7 3.1 - - - +
279H ILE* 1.3 76.9 - - - +
281H GLU* 1.3 65.4 + - + +
282H GLY 3.2 1.9 + - - +
285H PHE* 3.4 46.3 - - + +
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Residues in contact with GLU 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276F CYS* 6.3 1.1 - - - -
291F PRO* 5.2 1.6 - - - -
292F ALA 4.2 16.4 - - - +
293F VAL* 4.6 1.6 - - - -
294F ARG* 2.9 53.9 + - + +
349G ARG* 3.0 38.3 + - - +
353G GLN* 3.1 33.9 + - + +
277H ALA* 3.0 18.1 + - - +
278H ARG* 4.1 10.6 - - - +
280H MET* 1.3 77.6 - - + +
282H GLY* 1.3 58.8 + - - +
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Residues in contact with GLY 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H GLU* 3.7 4.0 - - - -
278H ARG 3.1 17.6 + - - -
279H ILE 3.2 1.3 + - - -
280H MET 3.1 7.5 - - - +
281H GLU* 1.3 81.2 - - - +
283H PRO* 1.3 71.5 - - - +
284H ALA 3.2 6.9 + - - -
285H PHE* 3.6 10.2 + - - +
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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
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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