Contacts of the helix formed by residues 282 - 295 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B SER* 3.0 28.3 + - - +
280B GLY 3.9 5.8 - - - +
281B ASN* 1.3 81.9 + - - +
283B PRO* 1.3 65.3 - - - +
284B LEU 3.4 2.4 + - - -
285B THR* 3.5 11.3 + - - -
286B VAL* 3.1 28.1 + - + +
313B MET* 3.6 25.8 + - - +
316B GLU* 3.3 41.5 + - - +
317B ASP* 2.9 36.8 + - - -
512D ARG* 4.4 5.1 - - - +
515D GLU* 2.8 43.8 + - - +
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Residues in contact with PRO 283 (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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272B VAL* 4.5 5.6 - - + +
275B ILE* 4.3 13.0 - - + -
276B ALA* 3.7 34.1 - - + +
279B SER* 3.3 6.7 - - - +
281B ASN* 3.2 8.5 - - - +
282B ARG* 1.3 88.3 - - - +
284B LEU* 1.3 65.8 + - - +
287B ILE* 3.0 34.2 + - + +
316B GLU* 3.2 8.1 - - - +
328B ASN* 3.6 9.2 - - - +
329B ILE* 4.1 18.2 - - + -
332B ALA* 3.8 11.2 - - + -
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Residues in contact with LEU 284 (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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283B PRO* 1.3 79.2 - - - +
285B THR* 1.3 63.1 + - - +
287B ILE* 4.2 0.6 - - + +
288B MET* 3.0 46.9 + - + +
312B LEU* 4.7 5.2 - - + +
315B LEU* 4.1 30.1 - - + -
316B GLU* 3.0 33.8 + - + +
319B TYR* 4.2 15.3 - - + -
328B ASN* 4.0 8.5 - - + +
331B ALA* 3.8 10.5 - - + +
332B ALA* 3.6 31.3 - - - +
335B VAL* 4.2 8.1 - - + -
364B ALA* 4.4 4.5 - - + +
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Residues in contact with THR 285 (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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282B ARG* 3.7 13.5 - - - -
283B PRO 3.4 0.2 - - - -
284B LEU* 1.3 78.2 - - - +
286B VAL* 1.3 61.8 + - + +
289B HIS* 3.0 33.4 + - + +
309B ILE* 4.3 15.7 - - + -
312B LEU* 3.6 24.2 - - + +
313B MET* 3.6 38.9 + - + -
316B GLU* 2.6 23.7 + - - -
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 3.9 18.6 - - + -
262B LEU* 3.3 35.4 - - + -
275B ILE* 4.6 4.0 - - + -
279B SER* 3.7 19.5 - - - +
282B ARG* 3.1 23.3 + - + +
283B PRO* 4.2 2.5 - - + +
285B THR* 1.3 79.8 - - + +
287B ILE* 1.3 61.3 + - - +
289B HIS* 3.6 5.7 + - - +
290B THR* 2.9 28.1 + - - +
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Residues in contact with ILE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU* 4.4 11.4 - - + -
265B VAL* 4.6 3.8 - - + -
270B LEU* 4.2 15.5 - - + -
272B VAL* 4.1 18.2 - - + -
275B ILE* 4.4 21.3 - - + -
283B PRO 3.0 23.3 + - - +
284B LEU 4.2 1.3 - - - +
286B VAL* 1.3 72.3 - - - +
288B MET* 1.3 67.5 + - - +
290B THR* 3.3 8.3 + - - -
291B ILE* 3.0 42.7 + - + +
332B ALA* 3.8 23.3 - - + +
335B VAL* 4.4 7.0 - - + -
336B GLN* 4.0 18.2 - - + -
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Residues in contact with MET 288 (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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284B LEU* 3.0 33.8 + - + +
287B ILE* 1.3 78.2 - - + +
289B HIS* 1.3 57.6 + - - +
291B ILE* 3.3 4.2 + - - +
292B PHE* 2.9 60.9 + - + -
311B TYR* 5.9 0.2 - - + -
312B LEU* 3.3 40.8 - - + -
315B LEU* 5.6 0.2 - - + -
335B VAL* 3.6 33.2 - - + -
360B ILE* 3.6 18.8 - - + +
361B PHE* 5.0 10.5 - - + -
364B ALA* 3.8 16.6 - - + -
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Residues in contact with HIS 289 (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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285B THR* 3.0 22.3 + - + +
286B VAL* 3.6 6.2 - - - +
288B MET* 1.3 77.2 - - - +
290B THR* 1.3 63.1 + - - +
292B PHE* 3.3 5.0 + - - +
293B GLN* 3.1 51.6 + - + +
298B LEU* 5.1 0.2 - - + -
305B VAL* 4.3 13.9 - - + +
308B LEU* 4.4 17.3 - - + -
309B ILE* 4.8 20.9 - - + +
312B LEU* 4.0 8.7 - - + +
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Residues in contact with THR 290 (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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262B LEU* 3.7 31.9 - - + +
265B VAL* 4.0 29.4 - - + -
286B VAL 2.9 15.8 + - - -
287B ILE* 3.5 9.9 - - - -
289B HIS* 1.3 76.9 + - - +
291B ILE* 1.3 61.6 + - - +
293B GLN* 3.5 4.5 + - - +
294B GLU* 3.1 26.8 + - + +
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Residues in contact with ILE 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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265B VAL* 4.1 10.8 - - + -
287B ILE* 3.0 37.6 + - + +
288B MET* 3.7 4.5 - - - +
290B THR* 1.3 76.0 - - - +
292B PHE* 1.3 59.3 + - + +
294B GLU* 3.9 4.1 - - - +
295B ARG* 3.0 31.5 + - - +
335B VAL* 3.7 21.5 - - + -
336B GLN* 4.1 4.9 - - - -
339B HIS* 3.7 46.9 - - + +
360B ILE* 3.7 34.5 - - + -
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Residues in contact with PHE 292 (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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288B MET* 2.9 55.4 + - + +
289B HIS 3.3 4.0 + - - +
291B ILE* 1.3 79.1 - - + +
293B GLN* 1.3 56.5 + - - +
295B ARG 3.6 0.3 + - - -
296B ASP 2.8 6.2 + - - -
297B LEU* 2.8 55.7 + - + +
298B LEU* 3.8 13.6 - - + +
303B ILE* 4.1 13.9 - - + -
308B LEU* 3.8 37.0 - - + -
357B LEU* 3.6 32.3 - - + -
360B ILE* 3.8 19.3 - - + -
361B PHE* 5.7 2.5 - + - -
414B ILE* 4.9 7.4 - - + -
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Residues in contact with GLN 293 (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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289B HIS* 3.1 49.1 + - + +
290B THR* 3.9 4.9 - - - +
292B PHE* 1.3 72.3 - - - +
294B GLU* 1.3 60.9 + - - +
296B ASP* 2.8 30.5 + - - +
298B LEU* 3.7 24.4 - - + +
305B VAL* 4.9 8.9 - - - +
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Residues in contact with GLU 294 (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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265B VAL* 3.7 12.5 - - - +
266B ASN* 2.9 43.1 + - - +
290B THR* 3.1 18.3 + - + +
291B ILE* 3.9 3.8 - - - +
293B GLN* 1.3 78.7 - - - +
295B ARG* 1.3 61.4 + - - +
296B ASP* 3.4 2.9 + - - +
339B HIS* 3.6 17.3 + - - -
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Residues in contact with ARG 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ILE* 3.0 20.8 + - - +
294B GLU* 1.3 75.9 - - + +
296B ASP* 1.3 70.3 + - - +
297B LEU* 3.2 20.7 + - + +
300B THR* 4.7 1.9 + - - -
339B HIS* 3.0 51.6 + - + -
342B LEU* 3.2 19.5 + - - +
343B SER* 3.2 15.1 + - - +
353B ASP* 5.6 2.3 - - - +
356B ILE* 3.9 34.7 - - - +
360B ILE* 3.7 26.6 - - - +
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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