Contacts of the helix formed by residues 269 - 279 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A THR* 1.3 76.8 - - - +
270A LYS* 1.3 61.7 + - - +
272A CYS* 3.1 11.0 - - - +
273A GLY* 3.0 17.2 + - - -
294A GLU 4.1 0.8 + - - -
295A LEU* 3.6 24.0 + - - +
298A GLU* 3.8 28.5 - - + -
299A GLY* 4.1 5.6 - - - +
302A LEU* 3.5 9.9 - - + +
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Residues in contact with LYS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ASP* 3.6 20.2 - - + +
268A THR* 3.1 4.2 + - - +
269A ALA* 1.3 74.3 - - - +
271A GLY* 1.3 65.6 + - - +
272A CYS 3.0 1.3 - - - -
273A GLY* 3.0 12.6 + - - -
274A ASP* 3.4 14.1 + - - +
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Residues in contact with GLY 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ASP* 3.0 27.5 + - - -
243A MET* 3.7 19.0 - - - +
267A ILE* 4.1 6.3 - - - -
270A LYS* 1.3 73.3 - - - +
272A CYS* 1.3 59.6 + - - +
274A ASP* 3.1 15.7 + - - +
275A LEU* 2.8 29.3 + - - +
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Residues in contact with CYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ILE* 4.0 3.7 - - - +
268A THR 3.2 14.0 + - - +
269A ALA* 3.1 17.3 - - - +
271A GLY* 1.3 79.0 - - - +
273A GLY* 1.3 56.5 + - - +
275A LEU* 3.1 10.5 + - - +
276A CYS* 2.8 36.8 + - - -
290A LEU* 5.0 5.6 - - - -
295A LEU* 4.2 18.6 - - + -
299A GLY* 3.8 24.5 - - - -
302A LEU* 4.4 3.4 - - + -
303A LEU* 4.0 22.9 - - - -
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Residues in contact with GLY 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ALA 3.0 9.4 + - - -
270A LYS 3.0 9.5 + - - -
272A CYS* 1.3 77.4 - - - +
274A ASP* 1.3 60.3 + - - +
276A CYS* 3.2 16.7 + - - +
277A ARG* 3.3 12.5 + - - +
280A ARG* 5.5 0.7 + - - -
302A LEU* 4.2 14.3 - - - +
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Residues in contact with ASP 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ASP* 4.3 1.9 - - - +
243A MET 4.9 0.2 - - - -
244A ALA* 4.0 29.8 + - - +
247A CYS* 3.4 24.4 - - - -
270A LYS 3.4 17.3 + - - +
271A GLY* 3.1 15.7 + - - +
273A GLY* 1.3 72.1 - - - +
275A LEU* 1.3 68.3 + - - +
277A ARG* 3.1 47.8 + - - +
278A VAL 3.6 1.7 + - - -
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A MET* 3.6 24.9 - - + -
247A CYS* 3.9 7.6 - - - -
250A LEU* 5.0 2.5 - - + -
260A LEU* 4.3 20.0 - - + -
262A ILE* 4.0 15.7 - - + -
267A ILE* 6.0 0.9 - - + -
271A GLY 2.8 12.9 + - - +
272A CYS* 3.2 15.7 - - - +
274A ASP* 1.3 77.9 - - - +
276A CYS* 1.3 58.1 + - - +
278A VAL* 3.0 23.6 + - + +
279A LEU* 3.1 33.5 + - + +
285A LEU* 5.8 0.7 - - + -
288A LEU* 4.1 10.5 - - + -
290A LEU* 3.8 31.4 - - + -
303A LEU* 5.6 1.3 - - + -
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Residues in contact with CYS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A CYS* 2.8 18.5 + - - -
273A GLY* 3.5 11.2 - - - +
274A ASP 3.1 0.6 - - - -
275A LEU* 1.3 75.0 - - - +
277A ARG* 1.3 64.1 + - - +
279A LEU* 3.9 9.0 - - - +
280A ARG* 3.2 37.6 + - - +
302A LEU* 3.8 28.9 - - + -
303A LEU* 4.1 19.3 - - - -
306A THR* 3.5 25.7 - - - +
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Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ALA* 5.7 1.0 + - - +
247A CYS* 3.9 19.2 - - - +
248A PRO* 5.5 2.4 - - - +
251A LEU* 3.5 27.7 - - + +
273A GLY 3.3 7.2 + - - +
274A ASP* 3.1 52.6 + - - +
276A CYS* 1.3 78.9 - - - +
278A VAL* 1.3 61.4 + - - +
280A ARG* 3.4 33.0 - - - +
281A ALA* 3.5 12.2 - - + +
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A CYS* 3.6 39.5 - - + +
250A LEU* 3.7 29.4 - - + +
251A LEU* 3.6 21.5 - - + -
274A ASP 3.8 2.0 - - - +
275A LEU* 3.0 12.5 + - + +
277A ARG* 1.3 75.8 - - - +
279A LEU* 1.3 61.9 + - + +
281A ALA* 3.0 2.6 + - - -
282A LYS* 2.9 43.7 + - + +
285A LEU* 4.7 14.6 - - + -
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LEU* 3.1 38.5 + - + +
276A CYS* 3.4 7.4 + - - +
278A VAL* 1.3 79.7 - - + +
280A ARG* 1.3 60.2 + - - +
281A ALA 3.4 0.7 + - - -
282A LYS* 3.8 12.3 - - - +
285A LEU* 4.1 26.5 - - + -
288A LEU* 4.2 22.2 - - + -
303A LEU* 4.2 20.4 - - + +
306A THR* 3.8 21.1 - - + -
307A LEU* 6.0 2.5 - - + -
312A CYS* 3.4 31.6 - - - -
314A LEU* 4.7 15.5 - - + -
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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