Contacts of the helix formed by residues 269 - 281 (chain D) in PDB entry 1A4Y
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 ALA 269 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268D THR* 1.3 77.2 - - - +
270D LYS* 1.3 62.3 + - - +
272D CYS* 3.4 9.5 - - - +
273D GLY* 3.2 16.5 + - - -
294D GLU 4.2 0.4 + - - -
295D LEU* 3.8 22.6 + - - +
298D GLU* 4.1 19.1 - - + -
299D GLY* 4.0 15.7 - - - +
302D LEU* 3.5 12.3 - - + +
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Residues in contact with LYS 270 (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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240D ASP* 3.9 11.9 - - + +
268D THR* 3.0 11.1 + - - +
269D ALA* 1.3 76.6 - - - +
271D GLY* 1.3 66.4 + - - +
273D GLY* 3.0 14.2 + - - -
274D ASP* 3.6 9.4 + - - +
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Residues in contact with GLY 271 (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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240D ASP* 2.7 39.3 + - - -
243D MET* 3.7 10.9 - - - +
267D ILE* 4.0 8.3 - - - -
270D LYS* 1.3 74.1 - - - +
272D CYS* 1.3 61.7 + - - +
274D ASP* 3.0 24.9 + - - +
275D LEU* 3.1 11.8 + - - +
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Residues in contact with CYS 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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267D ILE* 3.6 5.3 - - - +
268D THR 3.0 17.9 + - - +
269D ALA* 3.4 11.7 - - - +
271D GLY* 1.3 76.6 - - - +
273D GLY* 1.3 55.0 + - - +
275D LEU* 3.5 11.1 + - - +
276D CYS* 3.0 30.5 + - - -
290D LEU* 4.8 5.2 - - + -
295D LEU* 4.1 18.2 - - + -
299D GLY* 3.8 27.6 - - - -
302D LEU* 4.6 2.7 - - - -
303D LEU* 4.0 21.5 - - - -
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Residues in contact with GLY 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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269D ALA 3.2 6.0 + - - -
270D LYS 3.0 10.9 + - - -
272D CYS* 1.3 74.3 - - - +
274D ASP* 1.3 66.2 + - - +
276D CYS* 3.1 18.8 + - - +
277D ARG* 3.4 11.2 + - - +
280D ARG* 5.2 0.9 + - - -
302D LEU* 4.0 17.2 - - - +
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Residues in contact with ASP 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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240D ASP 4.3 1.7 - - - +
243D MET* 4.7 0.4 - - + +
244D ALA* 3.8 28.3 - - - +
247D CYS* 3.8 22.3 - - - -
270D LYS 3.6 12.3 + - - +
271D GLY* 3.0 14.1 + - - +
273D GLY* 1.3 74.1 - - - +
275D LEU* 1.3 65.1 + - - +
277D ARG* 3.0 46.5 + - - +
278D VAL* 3.6 3.1 + - - +
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Residues in contact with LEU 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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243D MET* 3.1 26.2 - - + -
247D CYS* 3.9 6.7 - - - -
250D LEU* 4.9 3.8 - - + -
260D LEU* 4.3 22.4 - - + -
262D ILE* 3.9 18.6 - - + -
267D ILE* 6.3 0.2 - - + -
271D GLY 3.1 3.2 + - - +
272D CYS* 3.5 14.1 - - - +
274D ASP* 1.3 80.6 - - - +
276D CYS* 1.3 61.5 + - - +
278D VAL* 3.1 18.5 + - + +
279D LEU* 3.1 30.0 + - + +
285D LEU* 5.5 0.4 - - + -
288D LEU* 3.8 24.0 - - + -
290D LEU* 3.9 19.1 - - + -
303D LEU* 5.7 0.9 - - + -
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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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272D CYS* 3.0 20.7 + - - +
273D GLY* 3.3 12.8 - - - +
274D ASP 3.1 0.4 - - - -
275D LEU* 1.3 75.2 - - - +
277D ARG* 1.3 63.2 + - - +
279D LEU* 3.3 10.5 + - - +
280D ARG* 3.1 34.5 + - - +
302D LEU* 3.7 27.6 - - + -
303D LEU* 4.1 18.2 - - - -
306D THR* 3.2 26.7 - - - +
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Residues in contact with ARG 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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244D ALA 5.3 2.2 + - - -
247D CYS* 3.8 26.1 - - - +
248D PRO* 5.2 3.2 - - - +
251D LEU* 3.8 28.3 - - + +
273D GLY 3.4 7.8 + - - +
274D ASP* 3.0 35.4 + - - +
276D CYS* 1.3 76.8 - - - +
278D VAL* 1.3 64.3 + - - +
280D ARG* 3.0 32.9 + - - +
281D ALA* 3.4 10.4 + - - +
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Residues in contact with VAL 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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247D CYS* 3.8 44.6 - - + +
250D LEU* 4.0 26.0 - - + +
251D LEU* 3.9 16.6 - - + -
274D ASP 4.1 1.3 - - - +
275D LEU* 3.3 14.4 - - + +
277D ARG* 1.3 77.0 - - - +
279D LEU* 1.3 57.9 + - + +
281D ALA* 2.9 4.2 + - - -
282D LYS* 2.9 42.5 + - + +
285D LEU* 4.6 17.7 - - + -
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Residues in contact with LEU 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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275D LEU* 3.1 21.2 + - + +
276D CYS* 3.5 17.7 - - - +
277D ARG 3.3 0.2 - - - -
278D VAL* 1.3 81.1 - - + +
280D ARG* 1.3 59.9 + - - +
281D ALA 3.3 1.0 + - - -
282D LYS* 3.8 8.9 - - - +
285D LEU* 3.3 34.3 - - + -
288D LEU* 4.0 24.7 - - + -
303D LEU* 4.5 17.7 - - + -
306D THR* 3.6 11.4 - - + -
311D GLY 3.8 2.8 - - - +
312D CYS* 3.2 35.8 - - - -
314D LEU* 4.2 15.3 - - + -
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Residues in contact with ARG 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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273D GLY 5.2 0.6 + - - -
276D CYS* 3.1 24.1 + - - +
277D ARG* 3.0 31.4 - - - +
279D LEU* 1.3 76.7 - - - +
281D ALA* 1.3 58.2 + - + +
302D LEU 4.7 1.2 + - - -
305D GLU* 4.3 4.4 + - - +
306D THR* 2.9 38.3 + - + +
309D GLU* 2.5 48.9 + - + +
310D PRO 4.0 4.2 - - - +
311D GLY* 3.9 17.9 - - - -
312D CYS* 4.4 7.2 - - - +
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Residues in contact with ALA 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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251D LEU* 4.0 20.2 - - + -
256D ARG* 5.8 0.2 + - - -
277D ARG 3.4 10.6 + - - +
278D VAL 2.9 7.7 + - - +
280D ARG* 1.3 81.6 - - + +
282D LYS* 1.3 65.1 + - + +
283D GLU* 3.9 11.5 + - - +
311D GLY* 4.8 1.8 - - - -
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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