Contacts of the helix formed by residues 282 - 295 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A SER* 3.1 27.6 + - - +
280A GLY 3.9 9.4 - - - +
281A ASN* 1.3 82.5 + - - +
283A PRO* 1.3 65.4 - - - +
284A LEU 3.3 2.9 + - - -
285A THR* 3.4 8.2 + - - -
286A VAL* 3.3 25.2 + - + +
313A MET* 4.0 24.2 + - - +
316A GLU* 3.0 50.0 + - - +
317A ASP* 2.7 31.3 + - - -
512C ARG* 4.5 4.2 - - - +
515C GLU* 3.0 40.5 + - - -
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Residues in contact with PRO 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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272A VAL 4.6 4.5 - - - +
275A ILE* 4.1 12.1 - - + -
276A ALA* 3.8 35.9 - - + +
279A SER* 3.4 4.7 - - - +
281A ASN* 3.1 9.4 - - - +
282A ARG* 1.3 90.3 - - - +
284A LEU* 1.3 61.0 + - - +
287A ILE* 3.1 32.8 + - + +
316A GLU* 3.3 8.1 - - - +
328A ASN* 3.5 10.8 - - - +
329A ILE* 4.1 18.8 - - + -
332A ALA* 3.7 13.9 - - + -
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Residues in contact with LEU 284 (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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283A PRO* 1.3 78.2 - - - +
285A THR* 1.3 58.9 + - - +
287A ILE* 4.3 0.4 - - + +
288A MET* 2.9 47.0 + - + +
312A LEU* 4.9 4.5 - - + +
315A LEU* 4.1 16.8 - - + -
316A GLU* 3.0 34.1 + - + +
319A TYR* 3.9 29.2 - - + -
328A ASN* 4.1 7.9 - - + +
331A ALA* 4.0 6.1 - - + -
332A ALA* 3.7 28.2 - - - +
335A VAL* 3.9 20.2 - - + -
364A ALA* 4.2 6.1 - - + +
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Residues in contact with THR 285 (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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282A ARG* 4.0 12.1 - - - -
283A PRO 3.4 0.2 - - - -
284A LEU* 1.3 78.6 - - - +
286A VAL* 1.3 64.6 + - + +
289A HIS* 2.9 31.4 + - + +
309A ILE* 4.4 19.3 - - + -
312A LEU* 3.3 41.6 - - + +
313A MET* 3.4 21.1 + - + +
316A GLU* 3.0 18.5 + - - -
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Residues in contact with VAL 286 (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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258A LEU* 4.4 10.1 - - + -
262A LEU* 4.3 17.5 - - + -
275A ILE* 3.7 24.5 - - + -
279A SER* 3.9 17.7 - - - -
282A ARG* 3.3 20.8 + - + +
283A PRO 3.7 5.2 - - - +
285A THR* 1.3 82.5 - - + +
287A ILE* 1.3 60.7 + - + +
289A HIS* 3.7 5.5 - - - +
290A THR* 2.7 39.3 + - - -
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Residues in contact with ILE 287 (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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262A LEU* 4.1 18.2 - - + -
265A VAL* 4.8 4.0 - - + -
270A LEU* 3.9 24.9 - - + -
272A VAL* 4.3 9.0 - - + -
275A ILE* 4.2 16.6 - - + -
283A PRO 3.1 19.5 + - - +
284A LEU 4.3 0.9 - - - +
286A VAL* 1.3 80.1 - - - +
288A MET* 1.3 64.3 + - - +
290A THR* 3.4 6.0 + - - -
291A ILE* 3.0 44.7 + - + +
332A ALA* 4.0 25.4 - - + +
335A VAL* 4.5 4.9 - - + -
336A GLN* 4.0 15.3 - - + -
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Residues in contact with MET 288 (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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284A LEU* 2.9 38.9 + - + +
287A ILE* 1.3 75.4 - - - +
289A HIS* 1.3 63.5 + - - +
291A ILE* 3.4 4.0 + - - +
292A PHE* 3.0 58.1 + - + -
308A LEU* 5.9 0.2 - - + -
311A TYR* 6.1 0.7 - - + -
312A LEU* 3.5 37.5 - - + -
315A LEU* 5.8 0.2 - - + -
335A VAL* 3.7 24.0 - - + -
360A ILE* 3.8 15.7 - - + -
361A PHE* 4.6 11.9 - - + -
364A ALA* 3.8 22.2 - - + -
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Residues in contact with HIS 289 (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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285A THR* 2.9 20.5 + - + +
286A VAL* 3.7 7.0 - - - +
288A MET* 1.3 76.8 - - - +
290A THR* 1.3 66.5 + - - +
292A PHE* 3.2 7.5 + - - +
293A GLN* 3.1 57.1 + - + +
298A LEU* 5.3 0.4 - - + -
305A VAL* 4.2 20.0 - - + -
308A LEU* 4.4 13.8 - - + +
309A ILE* 3.8 25.9 - - + +
312A LEU* 3.9 5.3 - - + +
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Residues in contact with THR 290 (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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262A LEU* 3.7 29.6 - - + +
265A VAL* 4.2 30.5 - - + -
286A VAL 2.7 23.1 + - - -
287A ILE* 3.8 6.3 - - - -
289A HIS* 1.3 81.1 - - - +
291A ILE* 1.3 57.6 + - - +
293A GLN* 3.6 4.5 + - - +
294A GLU* 3.0 32.4 + - + +
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Residues in contact with ILE 291 (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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265A VAL* 4.0 10.8 - - + -
287A ILE* 3.0 38.8 + - + +
288A MET* 3.9 4.0 - - - +
289A HIS 3.2 0.2 - - - -
290A THR* 1.3 76.5 - - - +
292A PHE* 1.3 59.8 + - + +
294A GLU* 3.5 5.5 - - - +
295A ARG* 3.0 29.6 + - - +
335A VAL* 3.8 17.3 - - + -
336A GLN* 4.1 4.5 - - - -
339A HIS* 3.7 47.6 - - + +
360A ILE* 3.7 35.0 - - + -
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Residues in contact with PHE 292 (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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288A MET* 3.0 56.0 + - + +
289A HIS 3.7 4.0 - - - +
291A ILE* 1.3 75.7 - - + +
293A GLN* 1.3 59.3 + - - +
295A ARG 3.5 0.5 + - - -
296A ASP* 2.8 6.4 + - - -
297A LEU* 2.8 52.9 + - + -
298A LEU* 3.7 15.3 + - + -
303A ILE* 4.2 14.8 - - + -
308A LEU* 3.9 33.4 - - + -
357A LEU* 3.7 31.0 - - + -
360A ILE* 3.8 20.0 - - + -
361A PHE* 5.5 3.1 - + + -
414A ILE* 4.8 7.2 - - + -
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Residues in contact with GLN 293 (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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289A HIS* 3.1 48.8 + - + +
290A THR* 3.9 4.7 - - - +
292A PHE* 1.3 73.0 - - - +
294A GLU* 1.3 60.1 + - - +
296A ASP* 2.7 29.2 + - - +
298A LEU* 4.0 25.0 - - + +
305A VAL* 5.1 3.6 - - - +
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Residues in contact with GLU 294 (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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265A VAL* 3.9 11.1 - - - +
266A ASN* 2.7 39.3 + - - +
290A THR* 3.0 20.3 + - + +
291A ILE* 3.5 8.7 - - - +
293A GLN* 1.3 80.3 - - - +
295A ARG* 1.3 60.2 + - + +
296A ASP* 4.8 1.9 - - - +
339A HIS* 4.4 15.3 - - + -
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Residues in contact with ARG 295 (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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291A ILE* 3.0 19.0 + - - +
294A GLU* 1.3 75.8 - - + +
296A ASP* 1.3 71.0 + - - +
297A LEU* 3.2 20.4 + - + +
300A THR* 5.1 1.2 + - - -
339A HIS* 3.1 36.3 + - + -
342A LEU* 3.4 20.8 + - - +
343A SER* 3.1 27.9 + - - +
353A ASP* 4.9 5.7 - - - +
356A ILE* 3.9 28.2 - - + +
360A ILE* 3.6 27.1 - - - +
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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