Contacts of the helix formed by residues 284 - 301 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278G PHE* 4.3 4.0 - - + -
281G THR* 3.3 28.4 + - + +
282G PRO 2.7 1.4 + - - -
283G GLU* 1.3 83.6 - - - +
285G ASN* 1.3 66.0 + - - +
286G MET 2.7 5.1 + - - -
287G PRO* 2.9 26.2 - - + +
288G ILE* 3.0 20.1 + - + +
356G ILE* 3.5 31.6 - - + -
360G MET* 3.4 34.1 - - + -
405G ASP* 4.2 18.8 - - + +
406G ILE* 5.5 2.9 - - + +
409G LEU* 4.2 16.2 - - + -
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Residues in contact with ASN 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G PHE 5.1 4.7 + - - +
279G GLU* 5.1 5.5 + - - +
281G THR 4.0 2.7 + - - -
282G PRO* 2.6 45.7 + - + +
284G LEU* 1.3 70.2 - - - +
286G MET* 1.3 54.1 + - - +
288G ILE* 3.7 12.5 - - - +
289G LEU* 2.9 32.9 + - - +
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Residues in contact with MET 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G PRO 4.0 1.4 + - - +
283G GLU 4.9 3.6 - - - +
284G LEU 2.7 4.4 + - - -
285G ASN* 1.3 72.9 - - - +
287G PRO* 1.4 92.8 - - + +
288G ILE 2.8 10.3 + - - -
289G LEU* 3.0 5.0 + - - +
290G ALA* 2.8 30.1 + - + +
351G HIS* 3.0 35.7 - - + +
352G ILE* 4.5 1.3 - - + -
353G ASN 5.6 0.7 - - - +
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Residues in contact with PRO 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G GLU 3.8 6.1 - - - +
284G LEU* 2.9 46.9 - - + +
286G MET* 1.4 99.2 - - + +
288G ILE* 1.3 56.8 + - + +
290G ALA* 4.0 1.3 - - + -
291G CYS* 3.3 26.3 + - - +
352G ILE* 3.4 30.3 - - + +
353G ASN 5.4 0.4 - - - +
356G ILE* 4.9 14.4 - - + -
357G ILE* 4.2 15.1 - - + +
360G MET* 5.6 1.6 - - - -
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Residues in contact with ILE 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G PHE* 4.1 32.5 - - + -
284G LEU* 3.0 24.1 + - + +
285G ASN* 3.7 11.4 - - - +
286G MET 2.8 4.9 + - - -
287G PRO* 1.3 71.4 - - - +
289G LEU* 1.3 56.0 + - + +
290G ALA 3.1 4.0 - - - -
291G CYS* 3.1 4.8 + - - +
292G LYS* 2.6 41.6 + - + +
314G GLU* 4.0 20.4 - - - +
322G THR* 4.5 17.3 - - + -
325G MET* 4.9 2.9 - - - +
326G LEU* 5.0 9.0 - - + -
360G MET* 4.6 13.2 - - + -
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Residues in contact with LEU 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G ASN 2.9 20.5 + - - +
286G MET* 4.0 3.6 - - - +
288G ILE* 1.3 78.2 - - + +
290G ALA* 1.3 59.1 + - - +
292G LYS* 3.9 23.0 - - + +
293G ASN* 3.3 32.4 + - - +
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Residues in contact with ALA 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G MET* 2.8 23.9 + - + +
287G PRO* 4.0 4.5 - - + +
289G LEU* 1.3 74.4 - - - +
291G CYS* 1.3 65.2 + - - +
293G ASN* 3.4 13.4 + - - +
294G ILE* 3.4 18.0 - - - +
348G ARG* 4.9 4.2 - - - +
351G HIS* 5.5 3.6 - - + +
352G ILE* 3.6 27.3 - - + +
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Residues in contact with CYS 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G PRO 3.3 20.0 + - - +
288G ILE* 3.1 5.7 + - - +
290G ALA* 1.3 76.1 - - - +
292G LYS* 1.3 54.2 + - - +
293G ASN 2.8 15.2 + - - -
294G ILE* 2.9 24.1 + - - +
295G VAL* 3.7 4.0 + - - +
325G MET* 3.7 12.0 - - + +
326G LEU* 5.3 4.5 - - + -
329G ILE* 3.4 35.1 - - + +
333G TRP* 5.4 3.6 - - - -
352G ILE* 3.9 21.5 - - - -
357G ILE* 4.6 19.3 - - - -
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Residues in contact with LYS 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G ILE* 2.6 24.4 + - + +
289G LEU* 4.0 25.7 - - + +
290G ALA 3.4 0.2 - - - -
291G CYS* 1.3 71.1 - - - +
293G ASN* 1.3 63.0 + - - +
295G VAL* 3.8 7.8 - - - +
296G LYS* 3.6 20.9 + - - +
313G SER* 5.7 3.1 - - - +
314G GLU* 3.5 44.0 + - + +
316G PRO* 5.0 6.4 - - - +
325G MET* 3.9 17.6 - - + +
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Residues in contact with ASN 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G LEU* 3.3 22.0 + - - +
290G ALA* 3.4 11.6 + - - +
291G CYS 2.8 2.0 + - - -
292G LYS* 1.3 81.4 - - - +
294G ILE* 1.3 65.1 + - + +
295G VAL 3.0 2.2 - - - -
296G LYS* 3.8 32.4 - - - +
297G TYR* 2.9 27.1 + - - +
348G ARG* 4.2 23.7 + - - +
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Residues in contact with ILE 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G ALA 3.4 14.1 - - - +
291G CYS* 2.9 18.8 + - - +
293G ASN* 1.3 74.3 - - + +
295G VAL* 1.3 58.2 + - - +
297G TYR* 4.0 5.6 - - + +
298G PHE* 3.1 43.4 + - + -
311G LEU* 4.4 7.6 - - + -
329G ILE* 4.7 13.7 - - + -
336G VAL* 3.8 29.2 - - + -
340G LEU* 4.3 9.2 - - + -
348G ARG* 3.7 40.4 - - + +
349G ILE* 4.3 8.3 - - + +
352G ILE* 4.2 8.7 - - + -
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Residues in contact with VAL 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G CYS 3.7 5.8 + - - +
292G LYS* 3.8 11.0 - - - +
293G ASN 3.0 0.4 - - - -
294G ILE* 1.3 73.4 - - - +
296G LYS* 1.3 60.1 + - - +
297G TYR 3.0 0.9 - - - -
298G PHE* 2.6 31.1 + - - +
299G LYS* 3.1 43.3 + - + +
304G GLN* 5.8 0.2 - - - +
311G LEU* 3.5 29.8 - - + +
312G LYS 3.4 28.9 - - - +
313G SER* 4.1 5.8 - - - +
325G MET* 4.8 6.5 - - + -
328G SER* 5.0 0.2 - - - +
329G ILE* 5.0 8.5 - - + -
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Residues in contact with LYS 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G LYS* 3.6 12.1 + - - +
293G ASN* 3.3 35.6 + - - +
295G VAL* 1.3 81.5 - - - +
297G TYR* 1.3 61.6 + - - +
299G LYS* 3.9 9.5 - - - +
300G LYS* 3.3 28.9 + - + +
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Residues in contact with TYR 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293G ASN* 2.9 17.5 + - - +
294G ILE* 4.0 8.3 - - + +
295G VAL 2.7 3.8 + - - -
296G LYS* 1.3 75.0 - - - +
298G PHE* 1.3 71.6 - + - +
300G LYS* 3.5 9.9 + - + +
301G ALA* 2.9 47.6 + - + +
303G LEU* 6.5 0.4 - - + -
340G LEU* 4.5 17.7 - - + -
343G ALA* 4.5 11.1 + - + +
345G GLU* 3.3 39.7 - - + +
348G ARG* 3.6 35.0 - - + +
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Residues in contact with PHE 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294G ILE* 3.1 29.3 + - + +
295G VAL* 2.6 12.6 + - - +
297G TYR* 1.3 85.6 - + - +
299G LYS* 1.3 58.3 + - - +
301G ALA 4.3 1.6 - - - -
302G ASN* 3.8 0.9 + - - -
303G LEU* 3.3 53.4 + - + +
304G GLN* 3.4 44.1 + - - +
307G LEU* 4.4 20.6 - - + -
311G LEU* 3.9 13.0 - - + -
336G VAL* 3.7 30.5 - - + -
339G ILE* 4.1 25.1 - - + -
340G LEU* 4.8 8.7 - - + -
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Residues in contact with LYS 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295G VAL* 3.1 29.8 + - + +
296G LYS* 3.9 10.3 - - - +
298G PHE* 1.3 73.2 - - - +
300G LYS* 1.3 70.4 + - - +
302G ASN* 3.5 21.0 + - - +
304G GLN* 3.8 26.0 - - + +
311G LEU 4.3 4.3 - - - -
312G LYS* 5.4 0.2 - - - +
313G SER* 3.0 35.9 - - - +
188H LYS* 5.9 2.4 - - - +
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Residues in contact with LYS 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296G LYS* 3.3 21.0 + - + +
297G TYR* 3.7 10.1 - - + +
299G LYS* 1.3 80.6 - - - +
301G ALA* 1.3 57.6 + - + +
302G ASN* 3.0 16.3 + - - -
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Residues in contact with ALA 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297G TYR* 2.9 43.7 + - + +
298G PHE* 3.9 4.0 - - - +
300G LYS* 1.3 70.8 - - + +
302G ASN* 1.3 51.1 + - - +
303G LEU* 2.7 28.5 + - - +
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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