Contacts of the helix formed by residues 284 - 301 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278H PHE* 4.0 9.6 - - + -
281H THR* 3.4 30.7 - - + +
282H PRO 2.5 5.7 + - - -
283H GLU* 1.3 80.9 - - - +
285H ASN* 1.3 65.3 + - - +
286H MET 2.9 4.9 + - - -
287H PRO* 3.0 19.9 - - + +
288H ILE* 3.2 20.6 + - + +
356H ILE* 4.1 24.2 - - + -
360H MET* 3.8 37.5 - - + -
405H ASP* 4.8 11.2 - - + +
406H ILE* 5.5 4.3 - - + -
409H LEU* 3.9 21.8 - - + -
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Residues in contact with ASN 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H PHE 4.7 6.9 - - - +
279H GLU* 5.6 2.8 + - - +
281H THR 4.6 1.6 - - - +
282H PRO* 2.8 44.6 + - - +
284H LEU* 1.3 70.5 - - - +
286H MET* 1.3 65.5 + - - +
288H ILE* 3.4 13.4 + - - +
289H LEU* 2.8 24.0 + - - +
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Residues in contact with MET 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282H PRO 4.2 2.0 + - - +
283H GLU 5.4 2.5 - - - +
284H LEU 2.9 5.0 + - - -
285H ASN* 1.3 77.4 - - - +
287H PRO* 1.4 63.3 - - + +
288H ILE 2.6 13.7 + - - -
289H LEU* 2.8 11.7 + - - +
290H ALA* 2.9 13.9 + - + +
351H HIS* 3.6 51.4 - - + +
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Residues in contact with PRO 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H GLU 4.3 4.3 - - - +
284H LEU* 3.0 28.0 - - + +
286H MET* 1.4 89.1 - - + +
288H ILE* 1.3 60.1 + - + +
290H ALA* 3.9 9.6 - - + -
291H CYS* 3.0 28.9 + - - +
351H HIS 4.8 4.3 - - - +
352H ILE* 3.9 17.2 - - + +
353H ASN* 5.0 4.0 - - + +
356H ILE* 4.5 26.0 - - + -
357H ILE* 4.1 18.9 - - + +
360H MET* 5.8 1.1 - - - -
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Residues in contact with ILE 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H PHE* 4.2 25.8 - - + -
284H LEU* 3.2 18.4 + - + +
285H ASN* 3.6 15.7 - - - +
286H MET 2.6 5.5 + - - -
287H PRO* 1.3 72.3 - - + +
289H LEU* 1.3 62.3 + - + +
291H CYS* 2.7 28.0 + - - +
292H LYS* 2.9 28.9 + - + +
322H THR* 4.1 29.2 - - + +
325H MET* 4.7 1.1 - - - +
326H LEU* 5.1 5.6 - - + -
357H ILE* 5.7 0.9 - - + -
360H MET* 4.3 17.5 - - + -
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Residues in contact with LEU 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285H ASN 2.8 16.8 + - - +
286H MET* 2.8 9.8 + - - +
288H ILE* 1.3 75.2 - - + +
290H ALA* 1.3 61.8 + - - +
292H LYS* 2.9 27.6 + - + +
293H ASN* 2.9 40.4 + - - +
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Residues in contact with ALA 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286H MET* 2.9 17.1 + - + +
287H PRO* 4.1 2.0 - - + -
289H LEU* 1.3 76.8 - - - +
291H CYS* 1.3 59.4 + - - +
293H ASN* 3.4 9.9 + - - +
294H ILE* 3.1 30.0 + - - +
348H ARG 5.1 8.3 - - - +
351H HIS* 5.0 9.4 - - + +
352H ILE* 3.4 26.9 - - + -
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Residues in contact with CYS 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287H PRO 3.0 13.0 + - - +
288H ILE 2.7 18.2 + - - +
290H ALA* 1.3 68.9 - - - +
292H LYS* 1.3 61.9 + - - +
293H ASN 3.0 1.8 - - - -
294H ILE* 3.1 10.9 + - - -
295H VAL* 3.4 9.0 + - - +
325H MET* 3.4 20.1 - - + +
326H LEU* 4.2 7.4 - - + -
329H ILE* 3.4 36.2 - - + +
352H ILE* 3.4 23.6 - - - -
357H ILE* 4.0 24.2 - - - -
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Residues in contact with LYS 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288H ILE* 2.9 31.1 + - + +
289H LEU* 3.5 25.2 - - + +
291H CYS* 1.3 76.1 - - - +
293H ASN* 1.3 60.3 + - - +
295H VAL* 3.7 9.4 + - + +
296H LYS* 3.1 26.7 + - - +
314H GLU* 3.6 37.2 + - + +
316H PRO* 5.5 2.8 - - - +
325H MET* 3.5 25.6 - - - -
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Residues in contact with ASN 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H LEU* 2.9 33.8 + - - +
290H ALA* 3.7 9.9 - - - +
291H CYS 3.0 0.4 - - - -
292H LYS* 1.3 80.2 - - - +
294H ILE* 1.3 65.0 + - + +
295H VAL 3.3 1.6 - - - -
296H LYS* 3.3 35.2 - - - +
297H TYR* 3.2 23.0 + - - +
348H ARG* 4.4 16.1 + - + +
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Residues in contact with ILE 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290H ALA 3.1 18.6 - - - +
291H CYS* 3.1 11.1 + - - +
293H ASN* 1.3 76.9 - - + +
295H VAL* 1.3 68.0 + - - +
297H TYR* 3.6 4.3 + - + +
298H PHE* 3.1 37.5 + - + -
311H LEU* 3.9 16.2 - - + -
329H ILE* 4.4 14.4 - - + -
336H VAL* 5.1 8.1 - - + -
340H LEU* 4.8 12.8 - - + -
348H ARG* 3.7 32.5 - - + -
349H ILE* 4.3 11.7 - - + +
352H ILE* 4.2 10.5 - - + -
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Residues in contact with VAL 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291H CYS 3.4 8.3 + - - +
292H LYS* 3.8 13.2 - - - +
293H ASN 3.3 0.2 - - - -
294H ILE* 1.3 76.7 - - - +
296H LYS* 1.3 71.4 + - - +
298H PHE* 2.7 17.3 + - - +
299H LYS* 3.1 21.5 + - + +
304H GLN* 5.8 0.4 - - - -
311H LEU* 3.3 45.5 - - + +
312H LYS 3.4 14.8 - - - +
313H SER* 3.5 29.6 - - - -
325H MET* 5.0 3.6 - - + -
329H ILE* 5.2 4.9 - - + -
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Residues in contact with LYS 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292H LYS* 3.1 13.3 + - - +
293H ASN* 3.3 29.8 - - + +
295H VAL* 1.3 83.5 - - + +
297H TYR* 1.3 57.3 + - - +
299H LYS* 3.4 9.7 + - - +
300H LYS* 3.2 29.8 + - + +
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Residues in contact with TYR 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293H ASN 3.2 16.4 + - - +
294H ILE* 3.8 6.1 - - + +
295H VAL 2.8 4.4 + - - -
296H LYS* 1.3 76.5 - - - +
298H PHE* 1.3 75.1 + + - +
299H LYS 3.2 0.7 - - - -
300H LYS* 4.9 12.8 - - + -
301H ALA* 3.2 38.8 + - + +
303H LEU* 3.7 20.5 - - + +
340H LEU* 4.0 21.3 - - + +
343H ALA* 4.9 6.0 + - + +
345H GLU* 3.2 29.5 - - + +
348H ARG* 3.2 38.8 - - + +
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Residues in contact with PHE 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294H ILE* 3.1 36.0 + - + +
295H VAL* 2.7 14.1 + - - +
297H TYR* 1.3 81.6 - + - +
299H LYS* 1.3 57.8 + - - +
301H ALA 4.3 0.7 - - - -
302H ASN* 3.8 1.4 + - - -
303H LEU* 3.2 50.0 + - + -
304H GLN* 3.5 20.5 + - + +
307H LEU* 3.5 33.2 - - + -
311H LEU* 4.3 13.2 - - + -
336H VAL* 3.9 27.8 - - + -
339H ILE* 3.9 23.3 - - + -
340H LEU* 4.0 22.0 - - + -
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Residues in contact with LYS 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188G LYS* 6.0 1.6 - - - +
295H VAL* 3.1 19.8 + - + +
296H LYS* 3.6 11.7 - - - +
298H PHE* 1.3 76.4 - - - +
300H LYS* 1.3 67.7 + - - +
302H ASN* 3.7 15.6 + - - +
304H GLN* 3.4 25.3 + - - +
311H LEU 4.7 5.1 + - - -
312H LYS* 5.8 0.2 - - - +
313H SER* 3.5 35.5 + - - +
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Residues in contact with LYS 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296H LYS* 3.2 16.0 + - + +
297H TYR* 4.4 13.9 - - + +
299H LYS* 1.3 77.0 - - - +
301H ALA* 1.3 56.9 + - + +
302H ASN* 2.7 26.0 + - - -
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Residues in contact with ALA 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297H TYR* 3.2 37.0 + - + +
298H PHE 4.1 0.9 - - - -
300H LYS* 1.3 78.8 - - + +
302H ASN* 1.3 65.3 + - - +
303H LEU* 2.9 29.5 + - + +
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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
------------------------------------------------------------
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