Contacts of the helix formed by residues 336 - 346 (chain F) in PDB entry 4L18
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 GLN 336 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204E LEU 5.9 1.2 + - - -
334F PRO 6.0 0.4 - - - -
335F ILE* 1.3 80.1 - - - +
337F LEU* 1.3 65.8 - - - +
338F TRP* 3.3 24.9 + - - +
339F GLN* 2.9 40.9 + - - +
340F PHE 3.0 9.9 + - - -
375F TRP* 4.2 1.8 - - - -
396F TYR* 4.8 1.4 - - - -
401F ILE* 5.4 1.9 - - - +
208G A 3.9 37.8 + - - +
209G C 3.4 21.8 + - - +
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Residues in contact with LEU 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336F GLN* 1.3 70.9 - - - +
338F TRP* 1.3 63.3 + - - +
340F PHE* 3.0 15.6 + - + +
341F LEU* 3.0 21.2 + - + +
375F TRP* 3.5 50.9 - - + +
389F LEU* 3.8 30.7 - - + +
392F GLY* 4.3 5.6 - - - -
393F LEU* 3.4 37.9 - - + +
396F TYR* 3.3 11.2 + - + +
209G C 2.8 19.8 + - - +
210G A 5.7 0.9 - - - +
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Residues in contact with TRP 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E LEU* 3.5 36.6 - - + -
336F GLN* 3.3 23.5 + - + -
337F LEU* 1.3 73.7 - - - +
339F GLN* 1.3 81.0 + - + +
341F LEU* 3.7 3.3 + - - -
342F LEU* 3.2 31.4 + - + +
396F TYR* 2.9 53.4 + + + -
401F ILE* 3.8 24.0 - - + +
402F ILE* 3.9 10.1 - - + -
414F PHE* 3.3 40.9 - + + -
416F CYS* 4.7 3.8 - - - -
418F LEU* 4.6 2.5 - - + -
421F LEU* 4.1 21.5 - - + -
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Residues in contact with GLN 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E LEU* 4.5 2.7 - - + +
201E LEU* 3.2 32.7 + - + +
202E GLU* 3.6 23.6 + - + +
334F PRO 4.9 0.2 - - - +
335F ILE* 3.5 17.6 - - + +
336F GLN* 2.9 47.4 + - - +
338F TRP* 1.3 113.1 - - + +
340F PHE* 1.3 65.6 + - - +
342F LEU* 3.2 9.2 + - - +
343F GLU* 3.0 24.4 + - - +
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Residues in contact with PHE 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335F ILE* 3.9 6.5 - - + +
336F GLN 3.0 6.5 + - - +
337F LEU* 3.0 9.3 + - + +
339F GLN* 1.3 74.7 - - - +
341F LEU* 1.3 75.2 + - + +
343F GLU* 2.9 33.4 + - - +
344F LEU* 3.1 47.7 + - + +
371F VAL* 4.2 6.7 - - + -
374F ARG* 3.7 26.7 - - + -
375F TRP* 3.7 51.6 - + + -
378F ARG* 4.0 28.9 - - + -
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Residues in contact with LEU 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337F LEU* 3.0 27.1 + - + +
338F TRP* 3.8 4.3 - - - +
340F PHE* 1.3 84.9 - - + +
342F LEU* 1.3 57.4 + - - +
344F LEU* 3.2 6.4 + - + +
345F LEU* 2.8 34.5 + - + +
354F ILE* 4.1 17.1 - - + +
363F PHE* 3.8 29.6 - - + -
365F LEU* 4.7 5.8 - - + -
371F VAL* 3.9 28.0 - - + -
389F LEU* 5.1 2.9 - - + -
393F LEU* 3.9 28.3 - - + -
402F ILE* 4.2 7.6 - - + -
414F PHE* 4.4 6.3 - - + -
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Residues in contact with LEU 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E LEU* 3.7 24.2 - - + -
201E LEU* 4.4 4.7 - - + -
338F TRP* 3.2 29.2 + - + +
339F GLN 3.3 10.1 - - - +
340F PHE 3.1 0.2 - - - -
341F LEU* 1.3 81.8 - - - +
343F GLU* 1.3 61.7 + - - +
345F LEU* 3.5 2.0 + - - -
346F THR* 3.0 33.0 + - + +
356F TRP* 4.2 14.6 - - + -
414F PHE* 3.7 22.4 - - + -
418F LEU* 3.6 36.3 - - + -
422F LEU* 4.4 15.5 - - + -
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Residues in contact with GLU 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E LEU* 3.3 25.1 - - + +
202E GLU* 2.8 27.7 - - - +
335F ILE* 4.8 1.3 - - - -
339F GLN 3.0 14.6 + - - +
340F PHE* 2.9 30.9 + - - +
342F LEU* 1.3 76.8 - - - +
344F LEU* 1.3 67.2 + - + +
346F THR* 3.0 17.3 + - - -
347F ASP* 3.5 11.0 + - - +
378F ARG* 3.8 17.0 + - - -
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Residues in contact with LEU 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340F PHE* 3.6 51.4 - - + +
341F LEU* 3.5 6.5 - - - +
343F GLU* 1.3 78.9 - - + +
345F LEU* 1.3 61.5 + - - +
346F THR 3.2 1.0 + - - -
347F ASP* 3.2 21.4 + - - +
350F CYS* 3.5 28.9 - - + +
351F GLN* 5.8 0.9 - - - +
353F PHE* 3.9 21.3 - - + -
354F ILE* 3.7 28.1 - - + +
371F VAL* 4.4 11.9 - - + -
374F ARG* 5.2 7.2 - - + +
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Residues in contact with LEU 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341F LEU 2.8 18.9 + - - +
342F LEU* 3.9 5.2 - - - +
343F GLU 3.2 0.4 - - - -
344F LEU* 1.3 77.3 - - - +
346F THR* 1.3 58.5 + - - +
347F ASP 3.4 2.0 + - - -
351F GLN* 5.7 3.6 + - + +
354F ILE* 4.0 12.1 - - + -
355F SER* 3.4 43.3 - - - +
356F TRP* 3.0 65.7 + - + +
363F PHE* 3.7 32.8 - - + -
414F PHE* 4.1 11.2 - - + -
433F LEU* 3.7 9.2 - - - +
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Residues in contact with THR 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E PHE* 3.6 48.0 - - + +
198E LEU* 3.6 17.2 - - + +
342F LEU* 3.0 27.3 + - + +
343F GLU 3.0 11.2 + - - -
345F LEU* 1.3 80.5 - - + +
347F ASP* 1.3 58.0 + - - +
348F LYS 4.2 0.2 + - - -
356F TRP* 5.3 1.8 - - + -
422F LEU* 4.9 5.2 - - + -
429F LEU* 4.5 12.6 - - + -
433F LEU* 3.7 15.9 - - - +
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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