Contacts of the helix formed by residues 355 - 371 (chain B) in PDB entry 7V3X
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 GLY 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ARG* 4.0 17.3 - - - +
216B ARG 5.0 7.1 + - - -
354B ALA* 1.3 77.5 - - - +
356B LEU* 1.3 65.7 + - - -
357B GLU* 3.3 6.7 - - - -
358B ASP* 3.2 22.9 + - - +
359B HIS* 3.2 11.9 + - - -
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Residues in contact with LEU 356 (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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217B ARG* 6.0 4.5 - - - +
351B PRO 5.8 1.3 - - - +
354B ALA 5.6 0.7 - - - +
355B GLY* 1.3 67.7 - - - -
357B GLU* 1.3 67.9 + - - +
359B HIS* 3.1 19.5 + - + +
360B LEU* 2.9 22.7 + - - +
383B LEU* 3.8 28.7 - - + +
387B VAL* 3.6 28.9 - - + -
391B ALA* 3.5 39.7 - - + +
392B PHE* 3.8 5.4 - - + +
395B PHE* 3.8 28.4 - - + -
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Residues in contact with GLU 357 (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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216B ARG 4.4 4.2 - - - +
217B ARG* 4.0 23.2 - - - +
218B ARG* 3.0 38.4 + - - +
236B PRO* 4.3 16.7 - - + +
237B PHE 2.9 31.0 + - - +
238B THR* 4.3 8.3 + - + +
355B GLY* 4.5 6.1 - - - -
356B LEU* 1.3 77.1 - - - +
358B ASP* 1.3 89.1 + - - +
360B LEU* 3.3 9.7 + - - +
361B GLN* 3.2 20.1 + - - +
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Residues in contact with ASP 358 (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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216B ARG 5.4 2.3 - - - +
238B THR* 2.9 31.0 - - + +
354B ALA* 3.6 15.8 - - + +
355B GLY* 3.2 24.5 + - - +
356B LEU 3.2 0.4 - - - -
357B GLU* 1.3 85.9 - - - +
359B HIS* 1.3 66.3 + - - +
361B GLN* 2.9 9.5 + - - +
362B ILE* 2.9 30.5 + - + +
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Residues in contact with HIS 359 (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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317B TYR* 3.6 26.8 + + - +
349B ALA* 4.9 5.3 - - + +
350B TYR 3.8 15.0 - - - -
351B PRO* 2.8 29.5 + - + +
353B SER* 4.2 7.2 - - - -
354B ALA* 3.3 14.8 + - + +
355B GLY 3.2 24.8 + - - -
356B LEU* 3.1 13.4 + - + +
358B ASP* 1.3 76.8 - - - +
360B LEU* 1.3 54.0 - - - +
362B ILE* 2.9 12.6 + - - +
363B ILE* 2.7 43.3 + - + +
383B LEU* 4.3 11.0 - - + -
395B PHE* 4.0 14.4 - - + -
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Residues in contact with LEU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PHE* 4.8 18.2 - - + -
356B LEU 2.9 11.1 + - - +
357B GLU* 3.5 12.8 - - - +
359B HIS* 1.3 75.0 - - - +
361B GLN* 1.3 52.0 + - - +
363B ILE* 3.5 4.3 + - + +
364B LYS* 2.8 41.1 + - + +
394B GLN 5.5 0.2 - - - +
395B PHE* 3.8 28.0 - - + +
398B GLY* 4.3 19.1 - - - +
399B VAL* 3.7 29.4 - - + +
402B TYR* 5.7 4.3 - - + -
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Residues in contact with GLN 361 (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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238B THR* 4.2 19.3 - - + +
240B THR* 5.6 6.1 - - + -
245B ASN* 6.5 0.2 - - + -
357B GLU 3.2 8.6 + - - +
358B ASP* 2.9 12.0 + - - +
360B LEU* 1.3 74.3 - - - +
362B ILE* 1.3 56.7 + - + +
364B LYS* 3.0 7.6 + - - +
365B SER* 2.5 40.5 + - - -
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Residues in contact with ILE 362 (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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315B PHE* 5.4 1.1 - - + -
317B TYR* 6.1 0.4 - - - +
347B VAL* 4.4 22.2 - - + -
358B ASP* 2.9 29.0 + - + +
359B HIS* 3.4 12.3 - - - +
361B GLN* 1.3 72.5 - - + +
363B ILE* 1.3 56.1 + - + +
365B SER* 3.2 7.1 + - - -
366B GLU* 2.8 37.4 + - + +
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Residues in contact with ILE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B PHE* 3.8 30.7 - - + -
317B TYR* 3.2 30.1 - - + +
359B HIS 2.7 22.6 + - - +
360B LEU* 3.7 6.3 - - + +
362B ILE* 1.3 73.5 - - + +
364B LYS* 1.3 61.5 - - - +
366B GLU* 3.3 2.1 + - - +
367B ILE* 2.9 45.9 + - + +
375B ILE* 5.2 0.9 - - + -
383B LEU* 5.2 0.9 - - + -
395B PHE* 3.9 28.5 - - + -
399B VAL* 4.2 26.7 - - + -
402B TYR* 6.2 0.2 - - + -
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Residues in contact with LYS 364 (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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360B LEU* 2.8 28.8 + - + +
361B GLN* 3.5 4.9 - - - +
363B ILE* 1.3 74.0 - - - +
365B SER* 1.3 61.7 + - - +
367B ILE* 3.4 5.2 + - - +
368B ASN* 3.2 32.4 + - - +
402B TYR* 4.2 30.1 - - + -
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Residues in contact with SER 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B GLN* 2.5 28.8 + - - -
362B ILE* 3.4 8.5 - - - -
364B LYS* 1.3 71.6 - - - +
366B GLU* 1.3 53.1 + - - +
368B ASN* 2.9 22.5 + - - +
369B ASP* 2.5 28.6 + - - +
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Residues in contact with GLU 366 (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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313B ILE* 3.7 5.4 - - + +
315B PHE* 4.1 19.5 - - + -
347B VAL* 4.5 12.6 - - + -
362B ILE* 2.8 23.1 + - + +
363B ILE 3.8 3.4 - - - +
365B SER* 1.3 72.1 - - - +
367B ILE* 1.3 59.8 - - - +
369B ASP* 3.8 6.8 + - - +
370B PHE* 3.4 28.1 + - - +
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Residues in contact with ILE 367 (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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313B ILE* 4.0 7.2 - - + -
315B PHE* 4.4 0.9 - - + -
363B ILE* 2.9 40.5 + - + +
364B LYS 3.6 4.9 - - - +
365B SER 3.1 0.4 - - - -
366B GLU* 1.3 76.5 - - - +
368B ASN* 1.3 59.2 + - - +
371B LYS* 3.0 24.3 + - - -
372B PRO* 3.2 10.4 - - + +
375B ILE* 3.4 31.6 - - + -
399B VAL* 5.9 2.2 - - + -
402B TYR* 4.1 29.4 - - + -
403B ALA* 5.9 5.4 - - + +
406B GLU* 5.2 2.0 - - + -
408B ILE* 3.6 29.8 - - + -
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Residues in contact with ASN 368 (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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364B LYS* 3.2 15.6 + - - +
365B SER* 2.9 10.9 + - - +
367B ILE* 1.3 81.5 + - - +
369B ASP* 1.3 64.7 + - - +
371B LYS* 4.2 7.6 + - - +
402B TYR* 2.6 30.6 + - - -
406B GLU* 5.3 3.8 + - - -
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Residues in contact with ASP 369 (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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311B ARG* 5.5 0.7 + - - -
365B SER* 2.5 37.9 + - - +
366B GLU* 3.8 6.8 + - - +
368B ASN* 1.3 78.1 - - - +
370B PHE* 1.3 62.1 + - + +
371B LYS* 3.6 3.3 + - - +
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Residues in contact with PHE 370 (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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311B ARG* 3.2 54.5 + - + +
312B ALA 3.4 21.1 - - - -
313B ILE* 3.7 24.5 - - + -
342B ASN* 3.5 35.2 - - + -
344B LEU 3.8 14.4 - - - -
345B LYS* 3.9 20.0 - - + -
366B GLU 3.4 16.4 + - - +
369B ASP* 1.3 77.8 - - + +
371B LYS* 1.3 70.9 + - - +
372B PRO* 4.4 2.2 - - + -
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Residues in contact with LYS 371 (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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311B ARG* 3.8 21.8 + - - +
367B ILE 3.0 15.2 + - - -
368B ASN 4.2 6.5 + - - +
369B ASP 3.4 4.7 - - - +
370B PHE* 1.3 80.5 - - - +
372B PRO* 1.4 67.3 - - - +
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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