Contacts of the helix formed by residues 270 - 282 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B HIS* 4.3 1.6 - - - -
269B PHE* 3.5 9.5 - - - +
134D ALA* 3.9 9.6 - - - -
263D GLU* 3.8 9.0 - - - -
266D TRP 4.1 9.4 - - - -
267D PRO 3.2 9.2 + - - -
268D GLN 3.1 4.6 - - - -
269D PHE* 1.3 84.4 - - - +
271D VAL* 1.3 67.4 + - - -
272D GLY 3.3 2.0 - - - -
273D ALA* 3.1 11.7 + - - +
274D GLU 3.4 8.5 + - - -
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Residues in contact with VAL 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 3.7 19.7 - - + -
133D ALA* 3.6 32.3 - - + -
134D ALA* 4.0 8.2 - - - +
212D HIS* 4.1 10.5 - - + +
238D MET* 3.8 23.3 - - + -
241D ILE* 4.2 9.4 - - + -
244D MET* 5.2 1.6 - - + -
263D GLU* 3.0 18.0 + - + +
270D GLY* 1.3 70.8 - - - -
272D GLY* 1.3 63.4 + - - +
273D ALA 3.2 0.2 + - - -
274D GLU* 3.3 2.9 + - - +
275D ILE* 3.2 38.7 + - + +
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Residues in contact with GLY 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D THR* 3.8 19.7 - - - -
263D GLU* 2.6 24.4 + - - +
271D VAL* 1.3 72.9 - - - +
273D ALA* 1.3 60.8 + - - +
275D ILE* 3.5 3.7 + - - +
276D CYS* 3.0 29.8 + - - -
294D ARG* 3.3 17.7 - - - -
296D THR* 5.5 0.2 - - - -
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ALA* 3.6 24.4 - - + +
274B GLU* 3.7 13.2 - - - +
277B ALA* 3.9 6.3 - - - -
269D PHE* 4.2 3.4 - - - +
270D GLY 3.1 19.0 + - - +
272D GLY* 1.3 75.7 - - - +
274D GLU* 1.3 64.0 + - - +
276D CYS* 3.4 1.9 + - - +
277D ALA* 3.1 25.6 + - - +
294D ARG* 3.6 24.1 - - - +
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Residues in contact with GLU 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B GLN* 3.8 14.4 - - + +
269B PHE* 3.2 52.4 + - + +
273B ALA* 3.7 3.8 - - - +
294B ARG* 2.8 36.0 + - - -
244D MET* 3.6 20.9 - - + -
270D GLY 3.4 1.4 + - - -
271D VAL 3.3 1.6 + - - -
272D GLY 3.3 0.4 - - - -
273D ALA* 1.3 76.3 - - - +
275D ILE* 1.3 67.8 + - - +
277D ALA* 4.4 0.2 - - - -
278D ARG* 3.0 49.9 + - + +
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Residues in contact with ILE 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D VAL* 4.3 7.2 - - + -
238D MET* 4.0 19.7 - - + -
244D MET* 3.9 21.8 - - + -
246D MET* 3.8 12.1 - - + +
249D ILE* 4.5 12.6 - - + -
259D LEU* 4.3 12.3 - - + -
261D THR* 3.7 32.1 - - + -
271D VAL* 3.2 35.4 + - + +
272D GLY* 3.8 5.2 - - - +
274D GLU* 1.3 77.6 - - - +
276D CYS* 1.3 61.7 + - - +
278D ARG* 3.2 7.5 + - - +
279D ILE* 2.9 19.9 + - - +
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Residues in contact with CYS 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B ALA* 4.4 10.3 - - - -
280B MET* 3.1 33.2 - - + +
281B GLU* 6.4 0.4 - - - -
259D LEU* 5.4 0.7 - - - -
261D THR* 4.7 8.3 - - - -
272D GLY 3.0 18.9 + - - +
273D ALA 4.0 2.5 - - - +
275D ILE* 1.3 73.6 - - - +
277D ALA* 1.3 71.5 + - - +
278D ARG 2.9 1.8 - - - -
279D ILE* 2.8 7.4 + - - +
280D MET* 2.8 26.4 + - - +
292D ALA* 4.5 13.2 - - - -
293D VAL 5.5 0.2 - - - -
294D ARG* 3.9 22.2 - - - -
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Residues in contact with ALA 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ALA* 3.8 23.3 - - + -
276B CYS* 4.0 19.7 - - + +
294B ARG* 3.9 20.0 - - - +
273D ALA 3.1 16.4 + - - +
274D GLU 3.8 3.6 - - - +
276D CYS* 1.3 79.9 - - - +
278D ARG* 1.3 62.6 + - - +
280D MET* 3.8 3.9 - - - +
281D GLU* 3.1 31.0 + - - +
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Residues in contact with ARG 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B GLN* 3.8 17.6 + - - +
294B ARG* 3.9 10.1 - - - +
349C ARG* 5.3 2.7 - - - +
244D MET* 4.6 16.9 + - - +
246D MET* 3.5 46.8 - - + +
250D GLU* 4.4 5.1 + - - +
274D GLU* 3.0 44.8 + - + +
275D ILE 3.5 4.7 - - - +
276D CYS 2.9 0.6 - - - -
277D ALA* 1.3 75.8 - - - +
279D ILE* 1.3 67.1 + - - +
281D GLU* 3.4 9.5 + - - +
282D GLY* 3.0 19.4 + - - -
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Residues in contact with ILE 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B MET* 5.7 1.3 - - + -
246D MET* 3.4 25.1 - - + -
249D ILE* 4.6 2.9 - - + -
250D GLU* 4.4 5.8 - - + -
253D VAL* 4.5 11.4 - - + -
259D LEU* 3.5 29.8 - - + -
275D ILE 2.9 9.2 + - - +
276D CYS* 2.8 13.4 + - - +
278D ARG* 1.3 72.5 - - - +
280D MET* 1.3 66.9 + - - +
282D GLY* 3.1 14.4 + - - +
284D ALA* 3.7 27.2 + - + -
285D PHE* 3.8 8.4 + - - +
288D LEU* 3.7 35.0 - - + -
292D ALA* 5.4 2.9 - - + -
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Residues in contact with MET 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B CYS* 3.3 44.4 - - + +
279B ILE* 4.6 5.2 - - + -
280B MET* 4.5 19.0 - - + +
285B PHE* 4.8 2.5 - - - -
288B LEU* 4.4 14.1 - - - -
291B PRO* 3.4 32.1 - - + +
292B ALA* 3.9 31.4 - - + +
276D CYS 2.8 13.2 + - - +
277D ALA* 3.8 4.3 - - - +
279D ILE* 1.3 78.9 - - - +
281D GLU* 1.3 60.2 + - - +
282D GLY 3.3 1.7 + - - +
285D PHE* 3.4 40.7 - - + +
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Residues in contact with GLU 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B CYS* 6.1 1.3 - - - -
291B PRO* 5.2 1.1 - - - -
292B ALA 4.2 7.6 - - - +
293B VAL* 4.2 12.8 - - + -
294B ARG* 2.9 66.3 + - + +
349C ARG* 3.1 18.3 + - - -
353C GLN* 3.1 39.9 + - + +
277D ALA* 3.1 17.8 + - - +
278D ARG* 4.0 9.3 - - - +
280D MET* 1.3 76.3 - - + +
282D GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D GLU* 4.4 3.6 - - - -
278D ARG 3.0 13.9 + - - -
279D ILE 3.1 5.6 + - - +
280D MET 3.7 4.5 - - - +
281D GLU* 1.3 81.5 - - - +
283D PRO* 1.3 71.1 - - - +
284D ALA 3.1 6.5 + - - -
285D PHE* 3.6 10.9 + - - +
286D ASN* 6.0 0.2 + - - -
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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