Contacts of the helix formed by residues 268 - 283 (chain A) in PDB entry 1DKF
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 ASP 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A PRO* 5.0 1.2 - - - +
267A ASN* 1.3 81.8 + - - +
269A PRO* 1.3 66.6 - - + +
270A VAL* 2.8 34.5 + - - +
271A THR* 2.2 33.6 + - - -
272A ASN* 2.7 39.0 + - - -
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Residues in contact with PRO 269 (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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268A ASP* 1.3 89.0 - - + +
270A VAL* 1.3 62.6 + - + +
272A ASN* 3.4 6.4 + - + +
273A ILE* 3.0 40.1 + - + +
337A VAL* 5.6 2.9 - - + -
341A SER* 3.3 40.8 - - - +
342A ALA* 5.5 0.9 - - - -
344A SER* 4.0 13.5 - - - +
345A ALA* 3.7 21.1 - - + -
444A PHE* 4.5 0.9 - - - -
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Residues in contact with VAL 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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268A ASP* 2.8 12.6 + - - +
269A PRO* 1.3 73.1 - - + +
271A THR* 1.3 60.6 + - - +
274A CYS* 3.0 47.0 + - - -
345A ALA* 4.3 13.2 - - + +
443A PHE* 3.7 26.5 - - + +
444A PHE* 3.5 25.3 - - + -
445A LYS 5.5 0.2 - - - +
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Residues in contact with THR 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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266A PRO* 3.7 26.3 - - + +
268A ASP* 2.2 37.5 + - - -
270A VAL* 1.3 79.1 - - - +
272A ASN* 1.3 57.5 + - - +
274A CYS* 3.3 4.9 + - - +
275A GLN* 2.9 65.0 + - + +
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Residues in contact with ASN 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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266A PRO 4.3 3.3 - - - +
267A ASN* 2.9 36.8 + - - +
268A ASP 2.7 33.4 + - - +
269A PRO* 3.8 6.6 - - + +
271A THR* 1.3 74.3 - - - +
273A ILE* 1.3 57.4 + - - +
275A GLN* 3.3 9.5 + - - +
276A ALA* 2.9 30.1 + - - +
331A LEU* 3.7 20.5 - - + +
333A THR* 4.7 2.0 + - - -
335A LEU* 3.7 22.3 - - + +
336A HIS 5.9 0.2 + - - -
337A VAL* 4.6 10.2 - - + +
341A SER* 5.8 1.0 + - - -
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Residues in contact with ILE 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 PRO* 3.0 33.5 + - + +
272A ASN* 1.3 76.4 - - - +
274A CYS* 1.3 59.9 + - - +
276A ALA* 3.2 3.5 + - - +
277A ALA* 2.8 28.5 + - + +
331A LEU* 4.2 18.2 - - + -
337A VAL* 4.5 24.7 - - + -
342A ALA* 6.4 1.1 - - - -
347A VAL* 5.6 5.8 - - + -
351A PHE* 5.6 3.8 - - + -
444A PHE* 3.8 29.6 - - + -
700A OLA 3.8 52.6 - - + +
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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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270A VAL* 3.0 31.8 + - - +
271A THR* 3.7 5.2 - - - +
273A ILE* 1.3 76.8 - - - +
275A GLN* 1.3 59.2 - - + +
277A ALA* 3.3 0.7 + - - +
278A ASP* 2.9 38.4 + - - +
444A PHE* 3.7 37.5 - - - -
445A LYS 3.7 17.5 - - - +
446A LEU* 3.8 13.0 - - + -
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Residues in contact with GLN 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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266A PRO* 4.4 19.6 + - - +
271A THR* 2.9 44.3 + - + +
272A ASN* 3.8 8.3 - - - +
274A CYS* 1.3 77.0 - - + +
276A ALA* 1.3 61.5 + - - +
278A ASP* 3.7 6.5 - - - +
279A LYS* 3.1 25.5 + - - +
333A THR* 4.2 12.6 - - + +
335A LEU* 5.8 2.4 - - - +
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Residues in contact with ALA 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 ASN 2.9 17.5 + - - +
273A ILE 3.6 3.6 - - - +
275A GLN* 1.3 74.5 - - - +
277A ALA* 1.3 65.3 + - - +
279A LYS* 3.7 2.4 - - - +
280A GLN* 3.2 21.5 + - - +
331A LEU* 3.5 24.0 - - + -
332A ALA* 4.1 2.9 - - - +
333A THR* 3.8 14.1 - - + +
700A OLA 3.2 32.2 - - + +
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Residues in contact with ALA 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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273A ILE* 2.8 18.6 + - + +
274A CYS 3.6 3.4 - - - +
276A ALA* 1.3 73.2 - - - +
278A ASP* 1.3 60.9 + - - +
280A GLN 3.3 1.4 + - - -
281A LEU* 2.8 33.8 + - - +
314A LEU* 3.6 12.6 - - + +
446A LEU* 3.7 29.4 - - + -
700A OLA 3.5 24.8 - - + +
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Residues in contact with ASP 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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274A CYS* 2.9 24.2 + - - +
275A GLN* 3.7 7.4 - - - +
277A ALA* 1.3 74.5 - - - +
279A LYS* 1.3 63.7 + - - +
281A LEU* 3.1 9.3 + - - +
282A PHE* 2.9 34.8 + - + -
445A LYS 5.0 1.4 - - - +
446A LEU* 3.3 13.8 - - - +
447A ILE* 2.8 41.8 + - + +
448A GLY 4.3 2.8 + - - -
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Residues in contact with LYS 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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249A PRO* 3.9 24.2 + - - +
275A GLN 3.1 15.1 + - - +
276A ALA 3.7 1.3 - - - +
278A ASP* 1.3 80.6 - - - +
280A GLN* 1.3 71.3 + - - +
282A PHE* 3.3 17.2 + - - +
283A THR* 3.6 13.5 + - + +
332A ALA* 3.3 42.3 + - + +
333A THR* 4.3 13.0 - - + +
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A VAL* 4.3 20.6 + - - +
249A PRO* 4.2 13.4 - - - +
276A ALA 3.2 9.6 + - - +
279A LYS* 1.3 85.2 + - - +
281A LEU* 1.3 65.9 + - - +
283A THR* 3.1 15.6 + - - -
284A LEU* 3.1 22.7 + - - +
314A LEU* 3.7 27.9 - - + +
317A SER* 4.7 10.7 + - - -
321A ARG* 4.0 15.8 - - - +
332A ALA* 3.6 22.6 - - + +
376A ARG* 5.4 3.8 - - - +
700A OLA 3.5 22.2 + - + +
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Residues in contact with LEU 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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277A ALA 2.8 21.7 + - - +
278A ASP* 3.3 5.4 - - - +
280A GLN* 1.3 76.6 - - - +
282A PHE* 1.3 63.2 + - - +
283A THR 3.3 0.3 + - - -
284A LEU* 3.4 23.1 + - + +
285A VAL* 4.6 2.4 + - - +
310A TRP* 3.8 37.9 - - + -
314A LEU* 4.4 4.0 - - + +
446A LEU* 4.1 24.0 - - + -
447A ILE* 3.7 28.0 - - + -
452A ILE* 4.0 21.3 - - + -
455A PHE* 3.8 19.3 - - + -
456A LEU* 5.5 8.4 - - + +
459A MET* 5.5 0.7 - - - +
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A ASP* 2.9 26.9 + - + +
279A LYS* 3.5 12.6 - - - +
280A GLN 3.1 0.2 - - - -
281A LEU* 1.3 79.3 - - - +
283A THR* 1.3 63.1 + - + +
284A LEU 3.5 0.4 + - - -
285A VAL 4.8 0.9 + - - -
286A GLU* 5.3 0.9 + - - +
447A ILE* 4.7 11.9 - - + -
455A PHE* 3.6 37.5 - + - -
459A MET* 3.4 33.3 - - + +
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Residues in contact with THR 283 (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 VAL* 2.9 42.2 + - - +
279A LYS* 3.6 13.7 + - + +
280A GLN* 3.1 19.1 + - - +
282A PHE* 1.3 82.2 - - + +
284A LEU* 1.3 58.3 + - - +
285A VAL 3.3 3.1 - - - -
286A GLU* 3.4 12.2 + - + +
287A TRP 3.0 13.3 + - - -
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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