Contacts of the helix formed by residues 284 - 301 (chain B) in PDB entry 4D1Q
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 LEU 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B PHE* 4.4 6.1 - - + +
281B THR* 3.0 31.5 + - + +
282B PRO 3.0 1.6 - - - -
283B GLU* 1.3 74.5 - - + +
285B ASN* 1.3 67.3 + - - +
286B MET 3.1 2.9 - - - -
287B PRO* 2.9 21.4 - - + +
288B ILE* 3.1 18.5 - - + +
356B ILE* 3.8 32.5 - - + -
360B MET* 3.2 37.2 - - + -
405B ASP* 4.7 9.2 - - + +
406B ILE* 4.9 4.3 - - + +
409B LEU* 3.9 24.5 - - + -
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Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 4.1 12.3 - - - +
279B GLU* 5.2 5.3 + - - +
281B THR 4.3 0.3 - - - +
282B PRO* 2.7 45.4 + - - +
284B LEU* 1.3 71.6 - - - +
286B MET* 1.3 63.4 - - - +
288B ILE* 3.3 7.2 + - - +
289B LEU* 3.0 26.5 + - - +
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Residues in contact with MET 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PRO 4.0 1.0 + - - -
283B GLU 4.0 4.6 + - - +
284B LEU 3.1 0.2 - - - -
285B ASN* 1.3 80.7 - - - +
287B PRO* 1.3 71.5 - - + +
289B LEU* 3.6 4.8 - - - +
290B ALA* 2.9 35.6 + - - +
351B HIS* 3.7 37.2 - - + +
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Residues in contact with PRO 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLU 3.8 6.7 - - - +
284B LEU* 2.9 41.3 - - + +
286B MET* 1.3 95.1 - - + +
288B ILE* 1.3 64.7 + - + +
290B ALA* 3.2 9.1 - - + +
291B CYS* 3.1 30.2 + - - -
351B HIS 5.3 0.7 - - - +
352B ILE* 4.3 3.4 - - + +
353B ASN* 4.9 15.0 - - + +
356B ILE* 5.2 11.9 - - + -
357B ILE* 4.6 16.2 - - + -
360B MET* 5.7 1.3 - - - -
405B ASP* 6.0 0.2 - - - +
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Residues in contact with ILE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 4.2 13.7 - - + -
284B LEU* 3.1 25.4 + - + +
285B ASN* 3.7 7.2 - - - +
287B PRO* 1.3 76.0 - - + +
289B LEU* 1.3 68.8 + - - +
291B CYS* 2.7 19.6 + - - +
292B LYS* 2.8 15.3 + - + +
314B GLU* 4.2 11.7 - - - +
322B THR* 3.8 33.2 - - + -
325B MET* 4.5 7.6 - - - +
326B LEU* 4.9 10.1 - - + -
357B ILE* 6.4 0.4 - - + -
360B MET* 4.2 25.4 - - + -
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASN 3.0 14.7 + - - +
286B MET* 3.6 4.9 - - - +
288B ILE* 1.3 77.5 - - - +
290B ALA* 1.3 66.7 + - - +
292B LYS* 2.9 24.0 + - + +
293B ASN* 2.8 51.2 + - - +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B MET* 2.9 22.5 + - - +
287B PRO* 3.2 15.0 - - + +
289B LEU* 1.3 79.8 - - - +
291B CYS* 1.3 58.2 + - - +
293B ASN* 3.5 8.6 + - - +
294B ILE* 3.1 28.9 + - - +
348B ARG 4.6 4.2 - - - +
351B HIS* 5.7 1.8 - - + -
352B ILE* 3.5 22.7 - - + +
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Residues in contact with CYS 291 (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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287B PRO 3.2 16.4 - - - -
288B ILE 2.7 14.0 + - - +
290B ALA* 1.3 72.2 - - - +
292B LYS* 1.3 59.1 + - - +
293B ASN 3.0 1.6 - - - -
294B ILE* 2.7 28.6 + - - +
295B VAL* 3.3 11.4 + - - +
325B MET* 3.3 19.1 - - + -
326B LEU* 3.8 17.7 - - + -
329B ILE* 3.4 23.2 - - + +
352B ILE* 3.6 19.1 - - - -
357B ILE* 3.9 15.3 - - - -
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 2.8 11.6 + - + +
289B LEU* 3.1 31.2 - - + +
291B CYS* 1.3 77.5 - - - +
293B ASN* 1.3 57.7 + - - +
295B VAL* 3.1 8.2 + - - +
296B LYS* 3.0 25.3 + - - +
313B SER* 6.3 0.9 - - - -
314B GLU* 3.5 49.4 + - + +
316B PRO* 5.4 5.6 - - - +
325B MET* 3.9 11.8 - - - +
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Residues in contact with ASN 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 2.8 50.1 + - - +
290B ALA* 3.9 7.8 + - - +
292B LYS* 1.3 76.7 - - - +
294B ILE* 1.3 63.0 + - + +
295B VAL 3.2 0.2 - - - -
296B LYS* 3.1 40.6 - - + +
297B TYR* 3.1 25.1 + - - +
348B ARG* 4.4 14.4 + - - +
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Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA 3.1 17.7 - - - +
291B CYS* 2.7 19.7 + - - +
293B ASN* 1.3 72.4 - - + +
295B VAL* 1.3 60.9 + - - +
297B TYR* 3.4 4.6 - - - +
298B PHE* 2.9 49.1 + - + -
311B LEU* 4.5 5.8 - - + -
329B ILE* 4.3 11.7 - - + -
336B VAL* 4.5 9.4 - - + -
340B LEU* 4.0 21.3 - - + -
348B ARG* 3.2 49.8 - - + +
349B ILE* 4.1 4.0 - - + +
352B ILE* 3.9 11.4 - - + -
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B CYS 3.4 10.5 - - - +
292B LYS* 3.4 15.5 - - - +
294B ILE* 1.3 74.4 - - - +
296B LYS* 1.3 67.4 + - - +
297B TYR 2.8 2.9 + - - -
298B PHE* 2.8 13.9 + - - +
299B LYS* 2.9 33.0 + - + +
304B GLN* 4.5 2.0 - - - +
311B LEU* 3.5 46.7 - - + +
312B LYS 3.7 22.2 - - - +
313B SER* 4.3 3.8 - - - +
325B MET* 4.5 6.1 - - + -
328B SER* 5.5 0.4 - - - +
329B ILE* 4.6 8.1 - - + -
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Residues in contact with LYS 296 (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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292B LYS 3.0 14.4 + - - +
293B ASN* 3.1 35.9 - - + +
295B VAL* 1.3 77.6 - - - +
297B TYR* 1.3 62.3 + - - +
299B LYS* 3.5 12.1 + - - +
300B LYS* 3.1 25.4 + - + +
348B ARG* 6.4 0.2 - - - +
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Residues in contact with TYR 297 (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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293B ASN 3.1 18.4 + - - +
294B ILE* 3.4 6.5 - - + +
295B VAL 2.8 1.2 + - - -
296B LYS* 1.3 72.4 - - - +
298B PHE* 1.3 79.0 + + - +
299B LYS 2.7 5.0 + - - -
300B LYS* 3.0 11.0 + - + -
301B ALA* 2.7 48.0 + - + +
303B LEU* 4.1 14.9 - - + +
340B LEU* 4.3 13.9 - - + -
343B ALA* 4.8 8.9 + - + +
345B GLU* 3.4 26.6 - - + +
348B ARG* 2.9 47.6 - - - +
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Residues in contact with PHE 298 (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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294B ILE* 2.9 34.0 + - + +
295B VAL 2.8 11.9 + - - +
297B TYR* 1.3 81.5 - + - +
299B LYS* 1.3 58.1 + - - +
301B ALA 4.0 0.7 - - - -
302B ASN* 3.4 0.9 + - - -
303B LEU* 2.9 49.4 + - + -
304B GLN* 3.3 24.4 + - - +
307B LEU* 3.8 31.9 - - + -
311B LEU* 3.6 17.3 - - + -
336B VAL* 3.7 22.4 - - + -
339B ILE* 4.0 23.3 - - + -
340B LEU* 3.8 24.2 - - + -
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Residues in contact with LYS 299 (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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188A LYS* 6.0 5.6 - - + +
295B VAL* 2.9 28.1 + - + +
296B LYS* 3.6 12.2 - - - +
297B TYR 2.7 4.2 + - - -
298B PHE* 1.3 72.8 - - - +
300B LYS* 1.3 65.5 + - - +
302B ASN* 3.0 24.1 + - - -
304B GLN* 4.3 22.9 - - + +
311B LEU 4.9 2.5 - - - -
313B SER* 3.1 36.4 + - - +
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Residues in contact with LYS 300 (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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296B LYS* 3.1 15.5 + - + +
297B TYR* 3.0 10.1 + - + +
299B LYS* 1.3 79.3 - - - +
301B ALA* 1.3 59.5 + - + +
302B ASN* 3.3 7.3 + - - +
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B TYR* 2.7 53.6 + - + +
300B LYS* 1.3 73.4 - - + +
302B ASN* 1.3 68.4 + - - +
303B LEU* 3.2 19.3 + - + +
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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
------------------------------------------------------------
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