Contacts of the helix formed by residues 269 - 279 (chain B) in PDB entry 1D8D
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 ASN 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A GLN* 5.1 5.3 - - - +
286A ASP* 4.9 10.1 + - - -
233B GLN* 2.9 31.3 + - - +
267B SER 4.2 0.2 + - - -
268B LEU* 1.3 69.9 - - - +
270B LEU* 1.3 60.7 + - - +
271B LYS* 3.2 12.4 + - - +
272B SER* 3.1 36.3 + - - +
273B LEU* 3.2 8.0 + - - +
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Residues in contact with LEU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B LEU* 4.4 8.1 - - + -
265B GLU* 3.6 30.7 - - + +
266B ARG* 4.7 4.0 - - + -
268B LEU* 3.1 23.4 + - + +
269B ASN* 1.3 70.6 + - - +
271B LYS* 1.3 59.3 + - - +
273B LEU* 3.6 6.2 - - + +
274B LEU* 2.9 31.4 + - - +
311B LEU* 4.0 20.9 - - + +
314B ALA* 4.0 25.4 - - + -
315B LEU* 4.3 23.0 - - + +
318B GLN* 4.3 19.1 - - - +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LYS* 5.9 2.5 - - - +
317A ASP* 4.0 5.4 + - - -
320A GLU* 3.2 38.0 + - - +
355A TYR* 4.2 10.2 + - - -
359A ILE* 4.8 4.0 - - - +
269B ASN* 3.2 9.2 + - - +
270B LEU* 1.3 78.1 - - - +
272B SER* 1.3 59.6 + - - +
274B LEU* 3.3 10.8 + - + +
275B GLN* 3.0 45.5 + - - +
315B LEU* 5.7 1.7 - - - +
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LYS* 4.8 7.6 + - - +
285A GLN* 4.2 21.0 + - - -
233B GLN* 3.5 9.4 + - - -
234B ASN 5.4 0.3 + - - -
236B GLU 4.1 2.2 - - - +
237B GLY* 3.4 16.8 - - - -
269B ASN* 3.1 35.0 + - - +
271B LYS* 1.3 78.0 - - - +
273B LEU* 1.3 60.4 + - - +
275B GLN* 3.9 7.0 - - - +
276B TRP* 3.0 29.6 + - - +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLN* 3.9 1.8 - - - +
237B GLY 3.2 20.8 + - - +
238B GLY* 4.1 5.6 - - - -
239B ILE* 4.8 2.9 - - + -
252B THR* 3.4 30.1 - - + -
256B LEU* 4.0 26.0 - - + -
268B LEU* 3.7 29.4 - - + -
269B ASN 3.2 16.2 + - - +
270B LEU* 3.6 12.6 - - + +
272B SER* 1.3 77.1 + - - +
274B LEU* 1.3 58.2 + - - +
276B TRP* 3.1 6.9 + - + +
277B VAL* 2.9 28.8 + - + +
307B LEU* 5.0 4.0 - - + -
311B LEU* 4.4 9.4 - - + -
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TYR* 3.8 21.5 - - + -
358A TYR* 3.9 24.9 - - + +
359A ILE* 5.7 0.4 - - + -
270B LEU 2.9 18.5 + - - +
271B LYS* 3.6 8.7 - - + +
273B LEU* 1.3 75.9 - - - +
275B GLN* 1.3 61.8 + - - +
277B VAL* 3.4 0.4 - - - +
278B THR* 3.0 36.6 + - + +
308B LEU* 3.9 19.7 - - + -
311B LEU* 3.7 29.6 - - + +
315B LEU* 4.3 12.8 - - + -
329B MET* 4.0 21.1 - - + -
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Residues in contact with GLN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LYS* 3.0 32.1 + - - +
313A ALA* 5.1 4.0 + - - +
317A ASP* 3.2 30.8 + - - +
355A TYR* 3.3 33.7 + - + +
356A TRP* 4.6 9.5 - - - -
271B LYS* 3.0 26.6 + - - +
272B SER* 3.9 6.5 - - - +
273B LEU 3.3 0.2 - - - -
274B LEU* 1.3 76.9 - - - +
276B TRP* 1.3 55.0 + - - +
278B THR* 3.1 13.7 + - - -
279B SER* 2.6 33.8 + - - +
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Residues in contact with TRP 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ASN* 5.5 3.6 - - - -
236B GLU* 3.3 45.4 + - + +
238B GLY* 3.6 17.3 - - - +
247B ALA* 3.7 33.3 + - + +
248B HIS 4.0 0.2 - - - -
249B GLY 3.7 7.2 - - - -
252B THR* 3.5 32.5 - - + -
272B SER 3.0 13.8 + - - +
273B LEU* 3.1 7.6 + - + +
275B GLN* 1.3 75.4 - - - +
277B VAL* 1.3 90.4 + - + +
279B SER* 3.2 7.8 + - - -
280B ARG* 3.1 61.1 + - - +
290B GLY 4.2 1.8 - - - -
291B ARG* 4.8 0.4 - - - -
292B CYS 5.1 2.0 - - - +
304B GLN* 3.4 34.8 - - - -
307B LEU* 4.3 0.2 - - + -
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B LEU* 2.9 19.8 + - + +
274B LEU* 3.4 10.8 - - - +
276B TRP* 1.3 85.9 - - + +
278B THR* 1.3 67.5 + - + +
280B ARG* 2.8 27.7 + - - +
288B PHE* 3.6 10.1 - - + -
304B GLN* 3.4 39.5 - - + +
307B LEU* 3.5 18.8 - - + -
308B LEU* 4.3 10.5 - - + -
311B LEU* 3.9 22.4 - - + -
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Residues in contact with THR 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A ARG* 2.8 36.2 + - - +
355A TYR* 3.9 22.6 - - + -
274B LEU* 3.0 36.4 + - + +
275B GLN* 3.1 13.7 + - - -
277B VAL* 1.3 75.8 - - - +
279B SER* 1.3 58.5 + - - +
280B ARG 3.3 0.9 + - - -
281B GLN* 3.4 11.1 + - - +
288B PHE* 5.0 4.3 - - - -
308B LEU* 4.0 8.3 - - + -
329B MET 3.3 26.5 - - - +
330B PHE* 5.9 1.3 - - - -
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A GLU* 3.7 24.5 + - - +
352A ARG* 3.5 24.4 + - - +
275B GLN* 2.6 28.2 + - - +
276B TRP* 3.2 7.9 + - - -
277B VAL 3.1 0.8 - - - -
278B THR* 1.3 78.9 + - - +
280B ARG* 1.3 75.1 + - - +
281B GLN 3.3 3.4 + - - +
282B MET* 5.7 0.3 - - - +
289B GLN* 4.0 2.8 - - - +
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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