Contacts of the helix formed by residues 353 - 366 (chain B) in PDB entry 1V2E
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 THR 353 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B SER* 3.8 13.8 + - - +
37B ASN* 5.7 2.5 - - + +
286B ARG* 5.1 1.3 - - - +
352B LYS* 1.3 79.0 - - - +
354B GLU* 1.3 64.3 + - - +
355B GLU* 3.5 16.4 - - + +
356B GLU* 2.6 45.7 + - - +
357B LEU* 3.2 19.1 + - - +
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Residues in contact with GLU 354 (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 ARG* 5.0 17.2 + - - +
286B ARG* 4.7 13.9 - - + +
289B LEU* 4.7 18.5 - - + +
353B THR* 1.3 70.3 - - - +
355B GLU* 1.3 78.1 + - - +
357B LEU* 2.9 21.0 + - - +
358B HIS* 2.9 26.8 + - + +
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Residues in contact with GLU 355 (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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353B THR* 3.5 17.7 - - + +
354B GLU* 1.3 86.6 - - - +
356B GLU* 1.3 64.4 + - + +
358B HIS* 2.9 8.1 + - - +
359B LEU* 2.9 26.4 + - + +
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Residues in contact with GLU 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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28B VAL* 3.7 24.3 - - + +
30B LEU* 4.6 1.9 - - - +
36B SER* 2.9 23.6 + - - -
352B LYS* 3.8 18.0 + - + +
353B THR* 2.6 46.6 + - - +
355B GLU* 1.3 80.5 - - + +
357B LEU* 1.3 61.2 + - - +
359B LEU* 4.6 6.1 - - + -
360B ALA* 3.2 24.1 + - - +
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Residues in contact with LEU 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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30B LEU* 4.5 11.9 - - + -
286B ARG* 3.6 39.0 - - + +
289B LEU* 3.6 34.3 - - + -
290B LEU* 4.4 13.6 - - + +
350B PHE* 3.8 32.8 - - + +
352B LYS* 4.4 6.5 - - + +
353B THR 3.2 15.0 + - - +
354B GLU* 2.9 9.4 + - - +
356B GLU* 1.3 74.3 - - - +
358B HIS* 1.3 70.5 + - - +
360B ALA* 3.0 14.5 + - - +
361B LEU* 3.1 17.4 + - - +
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Residues in contact with HIS 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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289B LEU* 3.8 33.3 - - + +
354B GLU* 2.9 27.7 + - + +
355B GLU* 2.9 8.8 + - - +
357B LEU* 1.3 76.0 - - - +
359B LEU* 1.3 55.5 + - - +
360B ALA 2.8 0.7 + - - -
361B LEU* 2.6 37.5 + - + +
362B GLU* 3.1 19.3 + - + +
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Residues in contact with LEU 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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28B VAL* 3.2 40.4 - - + -
355B GLU 2.9 19.9 + - - +
356B GLU* 4.3 4.3 - - + +
358B HIS* 1.3 72.6 - - - +
360B ALA* 1.3 57.1 + - - +
362B GLU* 4.0 13.2 - - + +
363B ARG* 3.0 49.3 + - + +
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Residues in contact with ALA 360 (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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28B VAL* 4.3 5.6 - - + -
30B LEU* 3.7 27.1 - - + -
290B LEU* 5.8 1.3 - - + -
328B VAL* 3.9 24.4 - - + +
356B GLU 3.2 20.1 + - - +
357B LEU 3.0 6.4 + - - +
358B HIS 2.8 1.0 + - - -
359B LEU* 1.3 76.2 - - - +
361B LEU* 1.3 62.8 + - + +
364B LEU* 2.8 33.3 + - + +
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Residues in contact with LEU 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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289B LEU* 4.7 14.6 - - + +
290B LEU* 4.1 13.7 - - + -
293B GLY* 3.9 28.7 - - - +
294B LEU* 3.3 35.0 - - + -
297B MET* 2.9 12.4 - - + +
357B LEU 3.1 17.0 + - - +
358B HIS* 2.6 22.8 + - + +
360B ALA* 1.3 69.8 - - - +
362B GLU* 1.3 61.7 + - - +
364B LEU* 2.7 12.5 + - + +
365B GLY 2.6 33.1 + - - -
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Residues in contact with GLU 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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297B MET* 5.0 2.0 - - - +
358B HIS* 3.5 18.6 - - + +
359B LEU* 4.0 17.7 - - + +
361B LEU* 1.3 79.5 - - - +
363B ARG* 1.3 58.9 + - + +
364B LEU 2.7 1.7 + - - -
365B GLY* 2.7 25.3 + - - -
366B ARG* 3.2 15.6 + - - +
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Residues in contact with ARG 363 (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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26B GLY 3.2 20.0 + - - -
27B ALA* 3.4 0.2 - - - +
28B VAL* 3.0 33.0 - - - +
326B ALA* 3.2 38.3 + - - +
327B ARG* 2.7 38.6 + - - +
328B VAL* 3.8 8.3 - - + -
359B LEU* 3.0 38.2 - - + +
360B ALA 4.1 0.2 - - - -
361B LEU 3.4 0.4 - - - -
362B GLU* 1.3 73.3 - - + +
364B LEU* 1.3 59.5 + - - +
366B ARG* 3.8 44.8 + - - +
367B VAL* 4.0 4.3 - - - +
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Residues in contact with LEU 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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290B LEU* 5.7 0.2 - - + -
294B LEU* 4.0 8.1 - - + -
297B MET* 4.0 9.7 - - + +
314B LEU* 5.4 4.5 - - + -
322B LEU* 5.1 12.6 - - + -
326B ALA* 5.2 2.0 - - + -
328B VAL* 4.7 18.8 - - + -
330B LEU* 4.8 15.5 - - + -
348B PHE* 3.9 25.1 - - + -
360B ALA* 2.8 26.7 + - + +
361B LEU* 2.7 34.4 + - + +
362B GLU 2.7 4.4 + - - -
363B ARG* 1.3 74.7 - - - +
365B GLY* 1.3 62.6 + - - +
367B VAL* 3.1 25.7 + - - +
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Residues in contact with GLY 365 (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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297B MET* 3.2 24.1 - - - +
361B LEU 2.6 14.1 + - - -
362B GLU* 2.7 5.7 + - - -
364B LEU* 1.3 67.8 - - - +
366B ARG* 1.3 50.8 + - - -
367B VAL 2.5 29.7 + - - +
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Residues in contact with ARG 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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326B ALA 5.6 0.4 + - - -
362B GLU* 3.2 12.8 + - - +
363B ARG* 3.8 46.6 + - - +
364B LEU 3.4 0.2 - - - -
365B GLY* 1.3 70.7 - - - +
367B VAL* 1.3 71.0 + - + +
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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