Contacts of the helix formed by residues 336 - 347 (chain A) in PDB entry 2IBI
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 PRO 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A LEU* 4.2 8.7 - - + -
270A ARG 3.6 19.5 - - - +
272A LEU* 3.9 12.1 - - + -
275A THR* 5.7 0.2 - - - +
278A MET* 4.1 13.2 - - + -
279A ASN* 3.8 22.9 - - - +
282A LEU* 4.2 2.0 - - + -
321A LEU* 3.7 34.1 - - + -
334A VAL 3.5 9.8 - - - +
335A SER* 1.4 80.5 - - - +
337A SER* 1.3 62.5 + - - +
338A GLU 3.3 2.5 - - - -
339A PHE* 3.1 6.0 + - + +
340A LYS* 2.9 20.8 + - - +
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Residues in contact with SER 337 (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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270A ARG* 5.9 1.3 - - - -
272A LEU* 3.4 24.5 - - - +
335A SER* 3.1 21.3 + - - -
336A PRO* 1.3 76.8 - - - +
338A GLU* 1.3 61.1 + - - +
340A LYS* 3.4 4.0 + - - +
341A THR* 3.2 28.6 + - - -
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Residues in contact with GLU 338 (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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317A GLU* 3.3 35.3 - - - +
335A SER 4.7 1.9 + - - +
336A PRO 3.3 0.6 - - - -
337A SER* 1.3 80.1 + - - +
339A PHE* 1.3 64.3 + - - +
341A THR* 3.6 11.7 + - - +
342A GLN* 3.4 36.4 + - - +
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Residues in contact with PHE 339 (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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278A MET* 3.7 26.7 - - + -
282A LEU* 3.8 18.6 - - + -
314A LEU* 4.1 11.9 - - + -
317A GLU* 4.1 18.6 + - + +
318A PHE* 3.8 39.3 - + + -
321A LEU* 4.0 24.2 - - + -
336A PRO 3.1 7.6 + - - +
338A GLU* 1.3 77.8 - - - +
340A LYS* 1.3 67.4 + - - +
342A GLN* 3.0 4.5 + - - +
343A ILE* 2.9 28.7 + - + -
361A PHE* 4.0 13.7 - + - -
365A LEU* 3.5 35.2 - - + -
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Residues in contact with LYS 340 (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 LEU* 4.1 17.5 - - + -
275A THR* 4.0 15.0 - - + -
277A PHE* 6.3 1.8 - - - -
278A MET* 4.1 20.2 - - + -
336A PRO 2.9 12.5 + - - +
337A SER 3.6 9.4 - - - +
338A GLU 3.4 0.2 - - - -
339A PHE* 1.3 80.4 - - - +
341A THR* 1.3 62.4 + - - +
343A ILE* 3.2 11.5 + - + +
344A GLN* 2.5 57.5 + - + +
350A PHE* 3.3 8.9 + - + +
352A GLY 2.8 33.2 + - - +
353A TYR* 3.6 27.9 + - + +
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Residues in contact with THR 341 (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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337A SER 3.2 12.0 + - - -
338A GLU* 3.7 19.4 + - - +
339A PHE 3.3 0.2 - - - -
340A LYS* 1.3 77.2 - - - +
342A GLN* 1.3 69.0 + - - +
344A GLN* 3.4 15.4 + - - +
345A ARG* 2.6 60.5 + - - +
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Residues in contact with GLN 342 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A ALA 4.4 9.4 - - - +
311A HIS* 5.0 3.5 + - - -
313A ALA* 2.9 30.9 - - - +
314A LEU* 3.9 23.0 + - + +
317A GLU* 3.7 20.4 - - + +
338A GLU* 3.4 22.2 + - - +
339A PHE* 3.0 10.4 + - - +
341A THR* 1.3 92.2 + - - +
343A ILE* 1.3 64.0 + - - +
345A ARG* 3.3 12.9 + - - +
346A TYR* 3.2 20.6 + - - +
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Residues in contact with ILE 343 (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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278A MET* 4.4 5.2 - - - -
314A LEU* 3.8 21.2 - - + +
339A PHE* 2.9 29.9 + - + +
340A LYS* 3.2 20.8 + - + +
342A GLN* 1.3 71.7 - - - +
344A GLN* 1.3 55.4 + - + +
346A TYR* 3.6 11.4 - - + -
347A ALA* 2.6 35.9 + - + +
350A PHE* 4.6 11.7 - - + -
361A PHE* 3.7 34.5 - - + -
364A PHE 4.4 0.9 - - - +
365A LEU* 3.8 38.1 - - + +
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Residues in contact with GLN 344 (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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340A LYS* 2.5 55.2 + - + +
341A THR* 3.4 21.0 + - - +
343A ILE* 1.3 75.8 - - - +
345A ARG* 1.3 83.8 + - - +
347A ALA 3.6 7.0 - - - -
348A PRO* 3.1 29.5 - - - +
350A PHE* 3.4 8.8 - - + +
351A VAL* 3.7 35.8 - - + +
352A GLY 5.0 1.6 - - - +
353A TYR* 5.8 1.0 + - - -
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Residues in contact with ARG 345 (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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310A ALA 5.6 2.5 - - - +
311A HIS* 3.9 18.0 - - + +
341A THR* 2.6 45.0 + - - +
342A GLN* 3.3 18.6 + - - +
343A ILE 3.2 0.2 - - - -
344A GLN* 1.3 110.8 - - - +
346A TYR* 1.3 65.6 + - - +
348A PRO* 3.9 9.4 - - - +
351A VAL* 4.7 7.5 - - - +
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Residues in contact with TYR 346 (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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311A HIS* 3.6 43.7 + + + +
314A LEU* 4.2 13.7 - - + -
342A GLN 3.2 10.0 + - - +
343A ILE* 3.2 10.7 + - + +
345A ARG* 1.3 82.1 - - - +
347A ALA* 1.3 64.7 + - + +
348A PRO* 3.3 8.7 - - - +
364A PHE* 3.5 33.8 - + - -
367A ASP* 2.3 30.7 + - - -
368A GLY* 3.3 21.4 - - - -
371A ASN* 2.8 22.2 + - + -
372A GLU* 5.4 1.8 - - - -
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Residues in contact with ALA 347 (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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343A ILE* 2.6 16.9 + - + +
344A GLN* 3.2 8.9 - - - +
346A TYR* 1.3 77.1 - - + +
348A PRO* 1.3 67.7 - - - +
349A ARG* 2.8 8.0 + - - +
350A PHE* 2.9 33.5 + - + -
364A PHE* 3.8 32.8 - - + -
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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