Contacts of the helix formed by residues 343 - 354 (chain B) in PDB entry 3RU0
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 LEU 343 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A SER 4.5 4.0 - - - +
64A GLN* 3.5 24.0 - - - +
66A ARG* 3.6 39.3 - - + +
91A LYS* 4.0 8.7 - - + -
94A LYS* 3.9 9.9 - - - +
306B LEU* 3.9 28.9 - - + -
338B CYS* 2.8 20.6 + - + +
341B LEU* 4.0 21.8 - - + +
342B GLY* 1.3 74.5 - - - +
344B LEU* 1.3 58.3 + - - +
345B GLU 3.5 2.0 - - - -
346B GLU* 3.4 15.7 + - + +
347B ALA 3.0 22.3 + - - -
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Residues in contact with LEU 344 (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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91A LYS 5.6 1.4 + - - -
92A SER* 6.5 0.4 - - - -
94A LYS 5.9 0.2 - - - +
339B ILE* 4.3 22.0 - - + +
342B GLY* 3.2 24.8 + - - +
343B LEU* 1.3 70.5 - - - +
345B GLU* 1.3 66.4 + - - +
347B ALA* 3.6 4.3 - - - +
348B LEU* 3.0 23.2 + - - +
379B LEU* 3.8 26.3 - - + +
382B HIS* 3.6 52.7 - - + +
383B GLN* 6.5 0.4 - - - -
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Residues in contact with GLU 345 (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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94A LYS* 3.3 41.7 + - + +
95A PRO* 3.4 33.2 - - + +
343B LEU 3.5 0.4 - - - -
344B LEU* 1.3 75.6 - - - +
346B GLU* 1.3 73.2 + - + +
348B LEU* 3.3 9.3 + - - +
349B PHE* 3.2 19.5 + - + +
382B HIS* 5.6 0.6 + - - -
383B GLN* 6.0 5.4 - - + -
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Residues in contact with GLU 346 (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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66A ARG* 3.6 25.2 - - - +
94A LYS* 2.6 38.7 + - - +
338B CYS* 3.6 15.9 - - - -
343B LEU* 3.4 26.3 - - + +
345B GLU* 1.3 80.4 - - + +
347B ALA* 1.3 66.7 + - - +
349B PHE* 3.0 18.2 + - - +
350B TYR* 3.1 28.8 + - + +
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Residues in contact with ALA 347 (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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335B MET* 3.6 13.1 - - + +
338B CYS* 3.5 24.1 - - + +
339B ILE* 3.8 19.7 - - + +
343B LEU 3.0 10.6 + - - +
344B LEU* 3.6 9.6 - - - +
345B GLU 3.3 0.2 - - - -
346B GLU* 1.3 76.2 - - - +
348B LEU* 1.3 51.5 + - - +
350B TYR* 3.4 0.5 + - - -
351B GLY* 2.8 34.3 + - - -
379B LEU* 3.7 18.8 - - + +
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Residues in contact with LEU 348 (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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344B LEU 3.0 13.7 + - - +
345B GLU* 3.6 11.4 - - - +
346B GLU 3.2 0.2 - - - -
347B ALA* 1.3 76.7 - - - +
349B PHE* 1.3 58.0 + - - +
351B GLY 4.5 0.2 - - - +
352B THR* 2.9 56.0 + - - +
376B VAL* 3.9 10.3 - - + +
379B LEU* 3.6 25.5 - - + +
380B GLN* 3.6 26.2 - - + -
383B GLN* 4.5 4.0 - - + -
385B MET* 3.2 41.1 - - + -
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Residues in contact with PHE 349 (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* 5.4 1.1 - - + -
345B GLU* 3.2 11.8 + - + +
346B GLU* 3.0 13.5 + - - +
348B LEU* 1.3 78.5 - - - +
350B TYR* 1.3 88.3 + + - +
352B THR* 4.3 3.0 - - - -
353B ARG* 3.5 57.7 + - - +
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Residues in contact with TYR 350 (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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306B LEU* 4.1 4.0 - - + -
310B GLN* 3.4 29.0 + - + +
313B ILE* 3.3 37.5 - - + -
331B LEU* 3.7 31.4 - - + +
334B ALA* 3.7 17.7 - - + -
335B MET* 3.9 7.4 - - - +
338B CYS* 3.9 23.1 - - - -
346B GLU* 3.1 28.1 + - + -
347B ALA 4.0 1.8 - - - +
349B PHE* 1.3 99.5 - + - +
351B GLY* 1.3 66.0 + - - +
353B ARG* 3.2 16.6 + - - +
354B THR* 3.5 11.4 - - - +
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Residues in contact with GLY 351 (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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335B MET* 3.7 25.3 - - - +
347B ALA 2.8 18.3 + - - -
348B LEU* 4.0 0.4 - - - -
350B TYR* 1.3 74.6 - - - +
352B THR* 1.3 63.8 + - - +
354B THR* 2.6 25.6 + - - -
355B MET* 3.7 1.9 + - - +
376B VAL* 3.7 17.7 - - - +
379B LEU* 5.5 0.2 - - - -
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Residues in contact with THR 352 (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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348B LEU* 2.9 41.1 + - - +
349B PHE* 4.3 3.6 - - - -
351B GLY* 1.3 74.6 - - - +
353B ARG* 1.3 64.8 + - + +
354B THR 3.2 1.0 + - - -
355B MET* 3.2 26.6 + - + +
356B GLU 4.9 0.7 + - - -
376B VAL* 4.2 6.5 - - + +
380B GLN* 4.5 6.7 + - - +
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Residues in contact with ARG 353 (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 26.3 + - - +
317B SER* 5.7 7.5 - - - +
320B LEU 5.8 0.2 + - - -
322B ASP* 2.7 52.4 + - - +
327B GLN* 4.7 5.5 - - - +
331B LEU* 3.7 20.4 - - + +
349B PHE* 3.5 54.6 + - - +
350B TYR 3.2 9.8 + - - +
351B GLY 3.1 0.8 - - - -
352B THR* 1.3 80.0 - - + +
354B THR* 1.3 60.3 + - - +
355B MET 3.4 0.2 - - - -
357B PRO* 3.6 16.8 - - - +
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Residues in contact with THR 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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328B LEU* 3.7 24.9 - - + -
331B LEU* 3.9 16.4 - - + -
332B ASP* 4.2 9.9 - - + +
350B TYR 3.5 15.5 - - - +
351B GLY* 2.6 18.9 + - - +
353B ARG* 1.3 79.0 - - - +
355B MET* 1.3 57.6 + - - +
356B GLU 3.5 0.9 - - - -
357B PRO* 3.5 2.4 - - - +
358B TYR* 2.9 34.7 + - - +
372B GLN* 3.1 35.4 + - - +
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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