Contacts of the helix formed by residues 269 - 281 (chain A) in PDB entry 2DB3
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 THR 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A PHE* 4.0 18.6 - - + -
228A TYR* 4.5 6.5 - - + -
268A PRO* 1.3 75.1 - - - +
270A PRO* 1.3 76.1 - - + +
271A ILE* 2.9 14.6 - - - +
272A GLN* 2.7 20.8 + - - +
273A LYS* 2.9 22.0 + - - +
293A SER 2.8 33.1 + - - +
583A VAL* 6.1 0.4 - - + -
2901A ANP 3.7 28.0 - - + +
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Residues in contact with PRO 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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228A TYR* 3.7 53.8 - - + +
229A ASN* 4.8 2.5 - - - +
233A VAL* 5.1 8.3 - - + -
268A PRO 4.7 0.2 - - - +
269A THR* 1.3 88.8 - - - +
271A ILE* 1.3 63.5 + - + +
273A LYS* 3.2 14.0 + - + +
274A CYS* 3.1 25.2 + - - -
293A SER* 5.2 1.8 - - - +
455A ILE* 3.8 30.1 - - + -
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Residues in contact with ILE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A THR* 2.9 16.8 - - - +
270A PRO* 1.3 73.9 - - + +
272A GLN* 1.3 61.1 - - + +
274A CYS* 3.7 2.5 - - - +
275A SER* 2.7 50.7 + - - +
287A ALA* 4.2 10.8 - - + -
288A CYS 4.4 0.7 - - - +
289A ALA* 3.5 26.7 - - + -
293A SER* 2.9 29.6 - - - +
294A GLY 3.4 22.4 - - - +
295A LYS* 3.7 10.5 - - + +
298A ALA* 4.2 4.3 - - + -
431A PHE* 5.0 0.9 - - + -
453A VAL* 4.1 10.8 - - + -
455A ILE* 3.2 25.9 - - + +
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Residues in contact with GLN 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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244A ILE* 4.3 0.2 - - - +
247A PHE* 3.6 7.5 - - + -
265A TYR* 4.8 0.6 - - - -
268A PRO* 3.3 9.2 - - + +
269A THR* 2.7 40.2 + - - +
271A ILE* 1.3 76.6 - - - +
273A LYS* 1.3 64.2 + - - +
276A ILE* 3.1 47.4 + - + +
294A GLY* 3.0 27.6 + - - +
297A ALA* 3.4 17.7 - - - +
298A ALA* 3.8 17.7 - - - +
301A LEU* 5.7 0.2 - - - -
2901A ANP 3.0 37.4 + - - -
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Residues in contact with LYS 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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229A ASN* 5.5 9.9 + - - +
243A PRO* 3.1 12.6 - - + +
244A ILE* 3.1 46.1 + - - +
245A GLN* 3.1 37.8 + - - +
267A ILE* 4.2 16.6 - - - +
268A PRO* 3.6 26.5 - - + -
269A THR 2.9 17.5 + - - +
270A PRO* 3.4 13.5 - - + +
272A GLN* 1.3 78.0 - - - +
274A CYS* 1.3 58.9 + - - +
277A PRO* 3.4 9.0 - - - +
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Residues in contact with CYS 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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233A VAL* 4.0 28.7 - - - -
235A VAL* 4.6 9.0 - - + -
241A PRO 5.3 1.9 - - - +
243A PRO* 4.4 21.9 - - + +
270A PRO 3.1 17.6 + - - +
271A ILE* 4.1 3.8 - - - +
273A LYS* 1.3 80.7 - - - +
275A SER* 1.3 62.3 + - - +
277A PRO* 3.5 6.9 - - - +
278A VAL* 3.2 22.7 - - - +
453A VAL* 4.5 22.2 - - + -
455A ILE* 5.5 2.5 - - - -
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Residues in contact with SER 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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271A ILE* 2.7 30.5 + - - +
274A CYS* 1.3 73.0 - - - +
276A ILE* 1.3 66.5 + - - +
278A VAL* 3.2 4.2 + - - +
279A ILE* 3.0 27.0 + - - +
285A LEU* 3.4 27.7 - - - +
287A ALA* 3.9 7.1 - - - +
298A ALA* 4.0 19.3 - - - -
431A PHE* 3.7 12.0 - - - -
453A VAL* 4.3 3.5 - - - +
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Residues in contact with ILE 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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244A ILE* 4.5 13.2 - - + -
247A PHE* 4.5 16.2 - - + -
250A ALA* 4.1 26.9 - - + +
252A LEU* 4.4 10.8 - - + -
272A GLN* 3.1 37.1 + - + +
275A SER* 1.3 76.1 - - - +
277A PRO* 1.3 62.7 - - + +
280A SER* 2.9 34.3 + - - +
297A ALA 5.1 0.2 - - - +
298A ALA* 4.1 6.7 - - - +
301A LEU* 4.6 14.6 - - + -
302A PRO* 3.8 33.5 - - + +
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Residues in contact with PRO 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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241A PRO* 3.8 13.2 - - + +
242A GLN 3.3 27.8 - - - +
243A PRO* 4.3 0.4 - - + -
244A ILE* 3.3 27.1 - - + -
250A ALA 5.9 1.1 - - - +
273A LYS 3.4 19.3 - - - +
274A CYS 3.5 7.6 - - - +
276A ILE* 1.3 94.8 - - + +
278A VAL* 1.3 54.5 + - - +
280A SER* 3.4 7.6 + - - +
281A SER* 2.5 35.8 + - - -
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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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240A VAL* 3.8 27.8 - - + -
241A PRO* 3.7 13.2 - - + +
274A CYS 3.2 18.6 - - - +
275A SER* 3.2 7.9 + - - +
277A PRO* 1.3 76.5 - - - +
279A ILE* 1.3 63.0 + - - +
281A SER* 3.3 6.1 + - - -
283A ARG* 3.2 40.9 + - + +
284A ASP 4.0 2.7 - - - +
285A LEU* 3.9 23.3 - - + -
451A VAL* 3.7 20.4 - - + -
453A VAL* 5.2 2.9 - - + -
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Residues in contact with ILE 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 SER 3.0 14.1 + - - +
276A ILE 3.9 2.9 - - - +
278A VAL* 1.3 72.8 - - - +
280A SER* 1.3 67.0 + - - +
282A GLY* 2.9 12.5 + - - -
283A ARG 4.4 2.0 - - - -
285A LEU* 4.2 11.4 - - + -
298A ALA 3.4 24.7 - - - +
299A PHE* 3.8 10.1 - - + -
302A PRO* 3.7 22.0 - - + -
303A ILE* 4.0 12.1 - - + +
306A LYS* 5.2 2.2 - - + +
395A PHE* 4.4 6.9 - - + -
427A GLN* 3.0 22.4 + - - +
429A LEU* 3.7 39.0 - - + -
431A PHE* 4.2 10.8 - - + -
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Residues in contact with SER 280 (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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250A ALA 4.4 7.6 + - - -
251A ASP* 5.0 10.5 + - - -
252A LEU* 5.2 1.6 - - - +
276A ILE* 2.9 26.3 + - - +
277A PRO* 3.6 8.7 - - - -
279A ILE* 1.3 77.0 - - - +
281A SER* 1.3 60.0 + - - +
282A GLY 3.2 1.3 + - - -
302A PRO* 3.9 15.0 + - - +
305A SER* 6.1 0.3 - - - -
306A LYS* 3.0 39.7 + - - +
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Residues in contact with SER 281 (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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241A PRO* 3.3 21.2 - - - +
277A PRO 2.5 21.3 + - - -
278A VAL 3.5 7.6 - - - -
279A ILE 3.0 0.8 - - - -
280A SER* 1.3 77.7 - - - +
282A GLY* 1.3 59.9 + - - +
283A ARG* 3.3 14.7 - - - +
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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