Contacts of the helix formed by residues 282 - 295 (chain C) in PDB entry 3IAD
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 ARG 282 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A ARG* 4.5 5.3 - - - +
515A GLU* 3.2 35.0 + - - -
279C SER* 3.0 26.2 + - - +
280C GLY 4.4 4.3 - - - +
281C ASN* 1.3 81.2 + - - +
283C PRO* 1.3 64.1 - - - +
284C LEU 3.4 0.2 - - - -
285C THR* 3.4 15.7 + - - -
286C VAL* 3.2 27.4 + - + +
313C MET* 3.7 22.5 + - - +
316C GLU* 3.3 44.0 - - - +
317C ASP* 3.2 33.5 + - - -
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Residues in contact with PRO 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C VAL* 4.5 4.3 - - + +
275C ILE* 4.3 6.1 - - + -
276C ALA* 3.9 28.7 - - + +
279C SER* 3.4 5.6 - - - +
281C ASN* 3.2 11.2 - - - +
282C ARG* 1.3 92.2 - - - +
284C LEU* 1.3 62.9 + - - +
286C VAL* 3.9 7.6 - - + -
287C ILE* 3.0 34.3 + - + +
316C GLU* 3.3 4.9 - - - +
328C ASN* 3.3 14.8 - - - +
329C ILE* 4.1 17.0 - - + -
332C ALA* 3.8 12.3 - - + -
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Residues in contact with LEU 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C PRO* 1.3 78.9 - - - +
285C THR* 1.3 57.7 + - - +
287C ILE* 6.1 0.2 - - + -
288C MET* 3.0 56.6 + - + +
312C LEU* 5.1 4.0 - - + +
315C LEU* 4.0 28.7 - - + -
316C GLU* 2.9 25.8 + - + +
319C TYR* 4.0 14.8 - - + -
328C ASN* 4.0 8.7 - - + +
331C ALA* 4.0 17.9 - - + -
332C ALA* 3.8 27.2 - - - +
335C VAL* 4.0 11.9 - - + -
364C ALA* 4.1 4.3 - - + +
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Residues in contact with THR 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ARG* 3.4 16.6 + - + -
283C PRO 3.3 0.2 - - - -
284C LEU* 1.3 76.6 - - - +
286C VAL* 1.3 63.1 + - + +
289C HIS* 3.0 37.1 + - + +
309C ILE* 4.9 7.6 - - + +
312C LEU* 3.3 42.3 + - + +
313C MET* 3.8 24.6 + - + +
316C GLU* 2.7 22.7 + - - -
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Residues in contact with VAL 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C LEU* 4.7 10.8 - - + -
262C LEU* 4.3 17.5 - - + -
275C ILE* 3.7 26.5 - - + -
279C SER* 4.1 16.2 - - - +
282C ARG* 3.2 22.8 + - + +
283C PRO* 3.6 6.3 - - + +
285C THR* 1.3 80.0 - - + +
287C ILE* 1.3 57.1 + - + +
289C HIS* 3.8 4.4 - - - +
290C THR* 2.7 38.6 + - - -
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Residues in contact with ILE 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C LEU* 4.2 12.1 - - + -
265C VAL* 4.5 7.4 - - + -
270C LEU* 4.1 15.3 - - + -
272C VAL* 4.0 19.1 - - + -
275C ILE* 4.2 19.3 - - + -
283C PRO* 3.0 21.2 + - + +
284C LEU* 4.4 0.9 - - + +
286C VAL* 1.3 74.7 - - + +
288C MET* 1.3 59.7 + - - +
290C THR* 3.4 3.1 + - - -
291C ILE* 2.9 54.4 + - + +
332C ALA* 3.8 26.0 - - + +
335C VAL* 4.8 2.7 - - + -
336C GLN* 4.0 16.8 - - + +
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Residues in contact with MET 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LEU* 3.0 43.5 + - + +
287C ILE* 1.3 76.3 - - - +
289C HIS* 1.3 57.9 + - - +
291C ILE* 3.3 5.3 + - - +
292C PHE* 2.9 59.7 + - + -
308C LEU* 5.6 1.6 - - + -
311C TYR* 5.6 2.0 - - + -
312C LEU* 3.3 35.2 - - + -
315C LEU* 5.4 1.1 - - + -
335C VAL* 3.8 22.9 - - + -
360C ILE* 3.8 17.7 - - + +
361C PHE* 5.1 10.1 - - + -
364C ALA* 3.8 22.9 - - + -
414C ILE* 5.9 1.3 - - + -
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Residues in contact with HIS 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C THR* 3.0 23.1 + - + +
286C VAL* 3.8 5.6 - - - +
288C MET* 1.3 75.5 - - - +
290C THR* 1.3 64.5 + - - +
292C PHE* 3.0 8.2 + - - +
293C GLN* 3.0 55.6 + - + +
298C LEU* 4.8 7.8 - - + +
305C VAL* 4.0 23.0 - - + +
308C LEU* 4.7 10.9 - - + +
309C ILE* 4.1 25.3 - - + +
312C LEU* 3.8 10.5 - - + +
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Residues in contact with THR 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C LEU* 3.8 28.5 - - + +
265C VAL* 4.1 29.2 - - + -
286C VAL 2.7 21.7 + - - -
287C ILE* 3.6 5.8 - - - -
289C HIS* 1.3 77.7 + - - +
291C ILE* 1.3 52.2 + - - +
293C GLN* 3.4 17.2 + - - +
294C GLU* 2.7 33.7 + - + +
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Residues in contact with ILE 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C VAL* 3.5 19.1 - - + -
287C ILE* 2.9 32.7 + - + +
288C MET* 3.6 5.4 - - - +
290C THR* 1.3 73.0 - - - +
292C PHE* 1.3 66.8 + - + +
294C GLU* 3.1 6.3 + - - +
295C ARG* 2.8 31.4 + - - +
297C LEU* 5.4 0.2 - - + -
335C VAL* 3.7 23.8 - - + -
336C GLN* 4.0 6.1 - - - -
339C HIS* 3.7 37.5 - - + +
360C ILE* 3.8 30.5 - - + -
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Residues in contact with PHE 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C MET* 2.9 51.0 + - + +
289C HIS 3.4 7.6 - - - +
291C ILE* 1.3 79.7 - - + +
293C GLN* 1.3 57.3 + - - +
295C ARG 3.5 0.2 + - - -
296C ASP* 2.8 22.9 + - - -
297C LEU* 2.9 33.6 + - + -
298C LEU* 3.6 16.0 - - + +
303C ILE* 3.5 33.2 - - + -
308C LEU* 3.9 25.8 - - + -
357C LEU* 3.8 25.6 - - + -
360C ILE* 3.9 19.1 - - + -
361C PHE* 5.6 3.8 - + + -
414C ILE* 4.9 8.5 - - + -
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Residues in contact with GLN 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C HIS* 3.0 43.3 + - + +
290C THR* 3.5 17.9 + - - +
292C PHE* 1.3 73.9 - - - +
294C GLU* 1.3 66.1 + - - +
296C ASP* 3.0 18.2 + - - +
298C LEU* 3.8 12.5 - - + +
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Residues in contact with GLU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C VAL* 4.8 11.1 - - + +
266C ASN* 3.1 38.6 + - - +
290C THR* 2.7 22.6 + - + +
291C ILE* 3.1 9.8 + - - +
293C GLN* 1.3 74.2 - - - +
295C ARG* 1.3 59.0 + - + +
296C ASP* 3.8 1.0 + - - +
339C HIS* 4.1 11.9 - - + +
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Residues in contact with ARG 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C ILE* 2.8 16.4 + - - +
294C GLU* 1.3 77.1 - - + +
296C ASP* 1.3 71.1 + - - +
297C LEU* 3.3 21.3 + - + +
300C THR* 5.0 1.2 + - - -
339C HIS* 2.8 53.5 + - + -
342C LEU* 3.4 22.9 - - - +
343C SER* 3.1 17.9 + - - +
353C ASP* 5.6 1.4 - - - +
356C ILE* 3.8 26.4 - - - +
360C ILE* 3.8 26.4 - - - +
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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