Contacts of the helix formed by residues 269 - 281 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225D PHE* 5.0 6.6 - - - -
228D TYR* 3.9 15.6 - - - -
267D ILE 3.5 1.9 + - - -
268D PRO* 1.3 75.2 - - - +
270D PRO* 1.3 78.8 - - - +
271D ILE* 3.3 8.1 - - + +
272D GLN* 2.7 51.2 + - + +
273D LYS* 2.8 20.6 + - - +
293D SER* 2.8 33.0 + - - +
294D GLY* 5.0 0.4 - - - -
2904D ANP 4.4 7.6 - - - -
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Residues in contact with PRO 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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228D TYR* 3.5 48.2 - - + +
229D ASN* 4.8 1.3 - - - +
231D ILE 6.1 0.2 - - - +
233D VAL* 5.2 6.1 - - + -
268D PRO 4.6 1.1 - - - +
269D THR* 1.3 94.1 - - - +
271D ILE* 1.3 61.2 + - - +
273D LYS* 3.3 15.4 + - + +
274D CYS* 3.3 26.0 + - - -
293D SER* 5.8 1.8 - - - -
455D ILE* 3.8 29.4 - - + -
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Residues in contact with ILE 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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269D THR* 3.3 15.9 - - + +
270D PRO* 1.3 79.7 - - - +
272D GLN* 1.3 60.5 + - - +
274D CYS* 5.0 0.2 - - - -
275D SER* 2.7 53.8 + - - +
287D ALA* 3.6 21.3 - - + -
288D CYS 4.3 2.7 - - - +
289D ALA* 3.7 23.6 - - + -
293D SER* 3.6 11.0 - - - +
294D GLY 3.9 16.2 - - - +
295D LYS* 4.0 16.2 - - + -
298D ALA* 4.2 2.5 - - + -
431D PHE* 4.3 3.8 - - + -
453D VAL* 3.8 15.7 - - + -
455D ILE* 3.8 19.8 - - + +
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Residues in contact with GLN 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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247D PHE* 3.9 6.9 - - - -
265D TYR* 4.4 1.6 - - - -
268D PRO* 3.5 7.7 - - + +
269D THR* 2.7 46.0 + - + +
271D ILE* 1.3 75.4 - - - +
273D LYS* 1.3 66.0 + - - +
276D ILE* 3.0 44.5 + - + +
294D GLY 3.1 22.2 + - - +
297D ALA* 3.4 19.9 - - - +
298D ALA* 3.9 15.7 - - - -
301D LEU* 5.7 0.2 - - - -
2904D ANP 3.0 37.2 + - - -
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Residues in contact with LYS 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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229D ASN* 3.7 22.2 + - - +
243D PRO* 3.3 9.9 - - + +
244D ILE* 3.0 48.1 + - - +
245D GLN* 2.9 42.0 + - - +
267D ILE* 4.5 7.5 - - - +
268D PRO* 3.6 25.4 - - + +
269D THR 2.8 15.2 + - - +
270D PRO* 3.5 15.5 - - + +
272D GLN* 1.3 76.5 - - - +
274D CYS* 1.3 58.9 + - - +
277D PRO* 3.1 14.2 - - - +
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Residues in contact with CYS 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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233D VAL* 4.2 26.0 - - - -
235D VAL* 4.7 7.4 - - + -
241D PRO 5.0 1.1 - - - +
243D PRO* 4.2 23.6 - - + -
270D PRO 3.3 15.4 + - - +
271D ILE 4.2 1.3 - - - +
272D GLN 3.2 0.2 - - - -
273D LYS* 1.3 82.7 - - - +
275D SER* 1.3 62.2 + - - +
277D PRO* 3.6 8.1 - - - +
278D VAL* 3.2 23.2 - - + +
453D VAL* 3.8 26.7 - - + -
455D ILE* 4.5 2.0 - - - -
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Residues in contact with SER 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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271D ILE* 2.7 42.9 + - - +
274D CYS* 1.3 75.2 - - - +
276D ILE* 1.3 65.2 + - - +
278D VAL* 3.4 3.4 + - - +
279D ILE* 3.0 30.2 + - - +
285D LEU* 3.8 26.0 - - - +
287D ALA* 4.1 0.9 - - - +
298D ALA* 4.2 20.6 - - - -
431D PHE* 3.9 3.8 - - - -
453D VAL* 4.3 2.7 - - - +
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Residues in contact with ILE 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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244D ILE* 4.5 7.0 - - + -
247D PHE* 4.2 24.0 - - + -
250D ALA* 3.5 27.6 - - + +
252D LEU* 4.1 12.1 - - + -
272D GLN* 3.0 35.8 + - + +
275D SER* 1.3 76.1 - - - +
277D PRO* 1.3 67.3 - - + +
279D ILE 3.4 0.2 + - - -
280D SER* 3.0 29.3 + - - +
297D ALA 4.9 0.4 - - - +
298D ALA* 4.0 15.0 - - - +
301D LEU* 4.3 14.4 - - + -
302D PRO* 3.8 23.2 - - + +
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Residues in contact with PRO 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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241D PRO* 3.9 12.3 - - + +
242D GLN 3.2 27.8 - - - +
243D PRO* 4.1 0.7 - - + -
244D ILE* 4.0 20.2 - - + -
250D ALA* 5.8 1.6 - - + +
273D LYS 3.1 26.2 - - - +
274D CYS 3.6 7.6 - - - +
276D ILE* 1.3 91.5 - - + +
278D VAL* 1.3 60.2 + - - +
280D SER* 3.4 7.7 + - - +
281D SER* 2.8 30.0 + - - -
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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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240D VAL* 4.2 17.7 - - + -
241D PRO* 3.6 23.1 - - + +
274D CYS* 3.2 19.1 - - + +
275D SER* 3.4 9.6 + - - +
276D ILE 3.2 0.6 - - - -
277D PRO* 1.3 77.3 - - - +
279D ILE* 1.3 62.4 + - - +
281D SER 3.3 5.4 + - - -
283D ARG* 3.2 42.2 + - + +
284D ASP 4.3 1.3 - - - +
285D LEU* 4.0 17.0 - - + -
451D VAL* 3.8 25.4 - - + -
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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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275D SER 3.0 14.8 + - - +
278D VAL* 1.3 76.1 - - - +
280D SER* 1.3 64.6 + - - +
282D GLY* 2.9 11.8 + - - -
283D ARG 4.5 1.8 - - - -
285D LEU* 3.9 22.2 - - + -
298D ALA 3.8 22.9 - - - +
299D PHE* 3.9 10.3 - - + -
302D PRO* 3.8 22.9 - - + +
303D ILE* 4.0 11.4 - - + +
306D LYS* 5.1 2.4 - - + +
395D PHE* 4.5 7.3 - - + -
427D GLN* 3.2 17.6 + - - +
429D LEU* 3.3 39.7 - - + -
431D PHE* 4.3 1.8 - - + -
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Residues in contact with SER 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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250D ALA 4.3 9.7 + - - -
251D ASP* 5.2 7.6 + - - -
252D LEU* 5.0 1.7 - - - +
276D ILE* 3.0 23.2 + - - +
277D PRO* 3.7 7.6 - - - -
279D ILE* 1.3 76.3 - - - +
281D SER* 1.3 57.1 + - - +
282D GLY* 3.1 4.9 + - - -
302D PRO* 3.8 14.2 + - - +
306D LYS* 3.2 44.9 + - - +
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Residues in contact with SER 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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241D PRO* 3.7 17.9 - - - +
277D PRO 2.8 21.5 + - - -
278D VAL 3.6 6.3 - - - -
279D ILE 3.1 0.6 - - - -
280D SER* 1.3 76.8 - - - +
282D GLY* 1.3 60.5 + - - +
283D ARG* 3.6 17.5 + - - +
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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