Contacts of the helix formed by residues 374 - 386 (chain B) in PDB entry 4I5L
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 TYR 374 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ARG* 4.0 24.0 - - - -
263B THR* 3.8 18.4 - - + -
264B THR* 2.7 29.7 + - - +
316B PHE* 4.0 0.9 - - - -
319B ILE* 3.8 16.8 - - + +
320B TYR* 3.7 29.3 + + - +
323B PHE* 3.4 56.5 - + + -
332B LEU* 3.5 20.3 + - + -
373B SER* 1.3 72.5 - - - +
375B ALA* 1.3 65.2 + - - +
377B PHE* 3.0 6.7 + + - +
378B VAL* 3.0 38.1 + - + +
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLN* 5.0 2.0 - - - +
263B THR* 4.4 8.0 - - + +
267B GLN* 3.7 34.4 - - - +
373B SER* 3.4 8.8 + - - +
374B TYR* 1.3 81.4 - - - +
376B ASP* 1.3 63.6 + - - +
378B VAL* 3.2 12.8 + - - +
379B TRP* 3.2 22.1 - - - -
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Residues in contact with ASP 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B VAL 5.2 0.7 - - - +
361B THR* 3.9 28.3 - - + +
366B VAL* 4.4 6.8 - - - +
372B ILE* 3.8 22.1 - - + +
373B SER* 3.3 28.4 + - - +
375B ALA* 1.3 74.1 - - - +
377B PHE* 1.3 65.1 + - - +
379B TRP* 3.1 21.8 + - - +
380B PHE* 3.1 12.0 + - - +
395B TYR* 4.7 2.1 + - - -
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Residues in contact with PHE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ILE* 3.8 10.8 - - + -
322B LYS* 3.9 14.8 - - + -
323B PHE* 3.5 56.1 - + + -
326B LEU* 3.7 22.2 - - + -
334B ILE* 4.8 3.1 - - + -
339B LEU* 3.8 22.2 - - + -
342B HIS* 4.6 5.6 - - - -
372B ILE* 4.1 13.6 - - + +
373B SER 3.0 13.0 + - - +
374B TYR* 3.0 14.0 + + - +
376B ASP* 1.3 78.1 - - - +
378B VAL* 1.3 58.6 + - - +
380B PHE* 3.2 15.2 + + - +
381B LEU* 2.8 45.1 + - + +
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B THR* 4.4 16.6 - - + +
267B GLN* 3.7 24.7 - - + -
319B ILE* 3.9 18.2 - - + -
374B TYR* 3.0 49.7 + - + +
375B ALA* 3.4 10.3 - - - +
376B ASP 3.2 0.2 - - - -
377B PHE* 1.3 76.3 - - - +
379B TRP* 1.3 57.3 + - + +
381B LEU* 4.7 0.2 - - - -
382B ILE* 3.0 51.5 + - + +
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Residues in contact with TRP 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLN* 4.8 2.0 - - - +
267B GLN* 2.9 36.1 + - + +
270B PHE* 3.9 18.6 - - + -
271B TYR* 3.6 58.0 - + - -
274B ASN* 5.2 7.9 - - - -
277B TRP* 4.5 32.5 - + - -
362B ARG* 5.7 9.2 - - - -
375B ALA 3.2 24.5 - - - -
376B ASP* 3.1 14.4 + - - +
378B VAL* 1.3 74.4 - - + +
380B PHE* 1.3 62.9 + - - +
383B SER* 2.7 34.0 + - - -
391B THR* 3.9 16.6 - - + -
395B TYR* 4.1 15.5 - + + -
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Residues in contact with PHE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 3.6 38.4 - - + -
342B HIS* 3.8 29.4 - + + -
347B LEU* 3.5 33.0 - - + -
352B ILE* 4.7 2.2 - - + -
355B ILE* 4.0 22.2 - - + -
372B ILE* 5.0 5.4 - - + -
376B ASP 3.1 11.0 + - - +
377B PHE* 3.2 26.7 + + + +
379B TRP* 1.3 77.1 - - - +
381B LEU* 1.3 64.4 + - - +
383B SER* 3.2 3.5 + - - -
384B GLU* 2.8 35.9 + - + +
395B TYR* 3.4 17.4 + - - +
396B TRP* 3.9 11.1 - + - -
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Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B VAL* 5.0 0.4 - - + -
319B ILE* 3.7 29.4 - - + +
322B LYS* 3.6 34.1 - - + -
342B HIS* 3.6 31.6 - - + +
343B ASN* 5.8 0.2 - - - +
377B PHE* 2.8 29.6 + - + +
378B VAL* 4.1 3.8 - - - +
380B PHE* 1.3 81.4 - - - +
382B ILE* 1.3 56.7 + - - +
384B GLU* 3.3 4.4 + - + +
385B GLU* 2.9 49.0 + - + +
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Residues in contact with ILE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ARG* 3.6 37.5 - - + +
271B TYR* 3.7 38.3 + - + -
315B HIS* 4.7 5.4 - - + +
319B ILE* 4.2 16.8 - - + -
378B VAL* 3.0 41.3 + - + +
381B LEU* 1.3 74.9 - - - +
383B SER* 1.3 61.1 + - - +
385B GLU* 3.6 14.7 + - - +
386B ASP* 3.3 25.9 + - + +
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Residues in contact with SER 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TYR* 2.8 22.8 + - - -
379B TRP 2.7 23.0 + - - -
380B PHE 3.5 3.1 - - - -
382B ILE* 1.3 76.7 - - - +
384B GLU* 1.3 59.9 + - - +
386B ASP 3.2 8.1 - - - +
387B LYS* 3.3 4.9 - - - +
392B SER* 2.9 22.6 + - - -
395B TYR* 3.5 31.4 - - - +
396B TRP* 3.0 21.0 + - - -
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Residues in contact with GLU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B HIS* 4.1 23.7 - - + +
343B ASN* 4.1 9.0 + - - +
346B ALA* 5.3 0.3 - - - +
347B LEU* 3.1 23.1 - - - +
380B PHE* 2.8 25.2 + - + +
381B LEU* 3.9 6.5 - - + +
383B SER* 1.3 76.4 - - - +
385B GLU* 1.3 64.4 + - - +
386B ASP 3.4 0.2 + - - -
387B LYS* 2.9 45.6 + - - +
396B TRP* 3.8 14.0 - - + +
473B ASN* 2.9 11.2 + - - -
476B LYS* 2.9 37.0 + - - +
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Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B HIS* 3.0 32.8 + - - -
318B VAL* 4.1 20.3 - - - +
319B ILE* 4.8 1.3 - - - +
381B LEU* 2.9 39.1 + - + +
382B ILE* 3.9 17.9 + - - +
384B GLU* 1.3 73.3 - - + +
386B ASP* 1.3 62.3 + - + +
387B LYS 4.3 0.2 - - - -
476B LYS* 4.2 12.4 + - - +
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Residues in contact with ASP 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TYR* 4.8 0.2 + - - -
382B ILE* 3.3 14.9 + - + +
383B SER 3.2 4.2 - - - +
384B GLU 3.3 1.0 - - - -
385B GLU* 1.3 83.0 - - + +
387B LYS* 1.3 58.1 + - - +
388B LYS* 2.8 39.3 + - - +
389B THR* 4.1 18.1 + - - +
392B SER* 3.0 20.4 + - - -
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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