Contacts of the helix formed by residues 346 - 357 (chain B) in PDB entry 4L1O
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 SER 346 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B TYR* 4.2 6.1 - - - -
344B VAL* 3.4 6.5 + - - +
345B ARG* 1.3 83.1 - - - +
347B LEU* 1.3 65.0 + - - +
348B GLU* 3.3 17.4 + - - +
349B GLU* 3.2 21.8 + - - +
350B ALA* 3.1 20.3 + - - +
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Residues in contact with LEU 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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217B TYR* 3.6 32.6 + - + +
346B SER* 1.3 73.4 - - - +
348B GLU* 1.3 65.9 + - - +
350B ALA* 3.0 5.2 + - - +
351B ILE* 2.9 38.8 + - + +
372B VAL* 3.9 39.5 - - + +
375B LYS* 4.0 29.2 - - + -
376B MET* 3.6 30.7 - - + -
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Residues in contact with GLU 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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346B SER* 3.1 19.1 - - - +
347B LEU* 1.3 84.9 + - - +
349B GLU* 1.3 64.3 + - - +
351B ILE* 3.5 10.1 + - + +
352B GLN* 3.1 24.1 + - - +
375B LYS* 3.0 36.0 - - - +
379B GLU* 5.9 0.7 - - - +
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Residues in contact with GLU 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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343B CYS 4.6 2.9 - - - +
344B VAL* 4.0 17.1 - - + +
345B ARG* 2.7 41.1 + - - +
346B SER* 3.2 18.1 + - - +
348B GLU* 1.3 78.5 - - - +
350B ALA* 1.3 58.4 + - - +
352B GLN* 3.5 14.6 + - - +
353B PHE* 2.9 31.2 + - + +
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Residues in contact with ALA 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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217B TYR* 3.6 32.3 - - + -
250B LEU* 3.9 17.2 - - + +
344B VAL* 4.1 8.2 - - + +
346B SER 3.1 10.2 + - - +
347B LEU 3.0 10.2 + - - +
349B GLU* 1.3 75.2 - - - +
351B ILE* 1.3 58.5 + - - +
353B PHE* 3.4 3.5 + - - +
354B ILE* 2.9 37.1 + - - +
376B MET* 4.3 5.6 - - + -
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Residues in contact with ILE 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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347B LEU* 2.9 36.5 + - + +
348B GLU* 3.7 9.2 - - + +
349B GLU 3.4 0.2 - - - -
350B ALA* 1.3 73.2 - - - +
352B GLN* 1.3 61.5 - - - +
354B ILE* 3.4 3.3 + - - +
355B ASN* 2.9 51.7 + - - +
375B LYS* 4.2 14.6 - - + +
376B MET* 4.1 35.2 - - + -
379B GLU* 3.9 34.3 - - + +
380B THR* 4.2 10.3 - - + -
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Residues in contact with GLN 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 GLU 3.1 18.5 + - - +
349B GLU* 3.7 14.2 - - - +
351B ILE* 1.3 75.0 - - - +
353B PHE* 1.3 60.7 + - - +
355B ASN* 3.1 7.1 + - - +
356B GLN* 2.9 64.6 + - + +
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Residues in contact with PHE 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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248B TYR* 3.5 32.1 - + - -
250B LEU* 3.8 19.5 - - + -
325B PRO* 3.8 29.4 - - + -
330B MET* 4.2 7.6 - - + -
342B VAL* 4.3 12.6 - - + -
344B VAL* 4.9 9.2 - - + -
349B GLU* 2.9 19.7 + - + +
350B ALA* 3.5 8.5 - - - +
352B GLN* 1.3 78.6 - - - +
354B ILE* 1.3 62.7 + - - +
356B GLN* 3.5 17.2 + - - +
357B ARG* 3.4 48.7 + - - -
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Residues in contact with ILE 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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215B PRO* 3.8 30.5 - - + -
217B TYR* 5.3 1.6 - - + -
248B TYR* 4.3 4.5 - - - +
250B LEU* 4.0 13.9 - - + -
350B ALA 2.9 23.0 + - - +
351B ILE* 3.7 4.7 - - - +
352B GLN 3.3 0.2 - - - -
353B PHE* 1.3 77.9 - - - +
355B ASN* 1.3 62.6 + - - +
357B ARG* 3.3 21.9 + - - +
358B GLU 4.6 2.9 - - - +
359B LYS* 5.8 0.2 - - - -
360B PRO* 4.8 13.7 - - + +
363B LEU* 3.9 28.7 - - + -
376B MET* 4.0 20.0 - - + -
380B THR* 4.1 20.4 - - + -
381B SER 5.3 2.0 - - - +
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Residues in contact with ASN 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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351B ILE* 2.9 29.8 + - - +
352B GLN* 3.1 7.6 + - - +
354B ILE* 1.3 73.4 - - - +
356B GLN* 1.3 63.3 + - + +
357B ARG 3.2 9.9 + - - +
379B GLU* 2.9 23.7 + - - +
380B THR* 3.5 23.3 - - - +
381B SER 4.6 1.7 + - - -
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Residues in contact with GLN 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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352B GLN* 2.9 53.4 + - + +
353B PHE* 4.0 10.8 - - - +
354B ILE 3.3 0.4 - - - -
355B ASN* 1.3 76.7 - - + +
357B ARG* 1.3 61.9 + - + +
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Residues in contact with ARG 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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213B LYS* 4.2 12.5 - - - +
248B TYR* 4.3 9.7 + - - +
325B PRO* 3.0 33.5 + - - +
326B GLN* 4.8 2.4 + - - -
330B MET* 2.8 31.0 + - - +
331B GLN* 3.5 11.5 - - - +
353B PHE* 3.4 53.7 + - - +
354B ILE* 3.3 15.5 + - - +
355B ASN* 3.2 8.4 - - - +
356B GLN* 1.3 85.8 - - + +
358B GLU* 1.3 71.5 + - - +
359B LYS* 3.7 2.9 + - - +
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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