Contacts of the helix formed by residues 336 - 345 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A ARG* 5.9 2.8 - - - +
334B PRO 5.9 0.4 - - - -
335B ILE* 1.3 79.2 - - - +
337B LEU* 1.3 66.9 + - - +
338B TRP* 3.9 21.7 + - + +
339B GLN* 2.9 34.7 + - + +
340B PHE 3.0 18.0 + - - -
375B TRP* 3.8 2.5 - - - -
396B TYR* 4.9 2.2 - - - -
401B ILE* 5.9 1.0 - - - +
8C A 3.6 33.9 + - - +
9C C 2.8 25.7 + - - +
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Residues in contact with LEU 337 (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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336B GLN* 1.3 70.9 - - - +
338B TRP* 1.3 64.3 + - - +
340B PHE* 2.9 12.3 + - - +
341B LEU* 3.0 22.2 + - + +
375B TRP* 3.2 54.3 - - + +
389B LEU* 3.7 26.7 - - + +
392B GLY* 4.3 4.9 - - - -
393B LEU* 3.2 45.1 - - + +
396B TYR* 3.4 12.3 + - + +
9C C 2.9 18.8 + - - +
10C A 5.8 0.9 - - - +
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Residues in contact with TRP 338 (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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201A LEU* 3.6 33.4 - - + -
336B GLN* 3.9 22.1 - - + +
337B LEU* 1.3 78.2 - - - +
339B GLN* 1.3 82.1 + - + +
341B LEU* 3.7 6.9 + - - -
342B LEU* 3.1 51.1 + - + +
396B TYR* 3.2 44.7 + + + -
401B ILE* 3.8 30.0 - - + +
402B ILE* 4.0 4.5 - - + -
414B PHE* 3.4 29.6 - + + -
416B CYS* 4.8 4.5 - - - -
418B LEU* 4.4 9.4 - - + -
421B LEU* 4.4 10.8 - - + -
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Residues in contact with GLN 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 4.2 5.2 - - + +
201A LEU* 3.4 28.0 + - + +
202A GLU* 3.5 26.9 - - + +
334B PRO 4.9 0.2 - - - +
335B ILE* 3.5 14.6 - - + -
336B GLN* 2.9 49.9 + - + +
338B TRP* 1.3 114.4 - - + +
340B PHE* 1.3 63.5 + - - +
342B LEU* 3.2 8.9 + - - +
343B GLU* 3.0 25.3 + - - +
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Residues in contact with PHE 340 (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 ILE* 3.7 9.3 - - + +
336B GLN 3.0 5.7 + - - +
337B LEU* 2.9 8.8 + - + +
339B GLN* 1.3 73.4 - - - +
341B LEU* 1.3 70.8 + - + +
343B GLU* 2.8 35.8 + - - +
344B LEU* 3.1 45.7 + - + +
371B VAL* 4.1 6.5 - - + -
374B ARG* 3.7 26.7 - - + -
375B TRP* 3.4 55.2 - + + -
378B ARG* 4.1 26.7 - - + -
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Residues in contact with LEU 341 (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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337B LEU* 3.0 26.8 + - + +
338B TRP* 3.9 5.4 - - - +
340B PHE* 1.3 87.0 - - + +
342B LEU* 1.3 58.2 + - - +
344B LEU* 3.2 10.0 + - + +
345B LEU* 2.8 37.1 + - + +
354B ILE* 4.4 13.0 - - + +
363B PHE* 4.0 22.7 - - + -
365B LEU* 4.8 3.1 - - + -
371B VAL* 4.0 27.4 - - + -
389B LEU* 4.9 5.4 - - + -
393B LEU* 3.6 32.3 - - + -
402B ILE* 4.1 9.0 - - + -
414B PHE* 4.5 5.6 - - + -
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Residues in contact with LEU 342 (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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198A LEU* 3.7 22.5 - - + +
201A LEU* 4.9 2.7 - - + -
338B TRP* 3.1 35.1 + - + +
339B GLN 3.3 7.6 - - - +
340B PHE 3.1 0.2 - - - -
341B LEU* 1.3 81.2 - - - +
343B GLU* 1.3 60.4 + - - +
345B LEU* 3.6 2.1 + - + -
346B THR* 3.2 31.5 + - + +
356B TRP* 4.2 16.6 - - + -
414B PHE* 3.9 14.1 - - + -
418B LEU* 3.7 45.3 - - + -
422B LEU* 4.5 15.7 - - + -
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Residues in contact with GLU 343 (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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198A LEU* 3.7 22.1 - - + +
199A SER* 5.6 1.7 + - - -
202A GLU* 2.7 29.7 - - - +
335B ILE* 4.5 5.4 - - - +
339B GLN 3.0 15.2 + - - +
340B PHE* 2.8 22.3 + - + +
342B LEU* 1.3 75.8 - - - +
344B LEU* 1.3 69.1 + - + +
346B THR* 2.9 18.4 + - - -
347B ASP* 3.4 10.9 + - - +
378B ARG* 5.3 6.9 + - - -
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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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340B PHE* 3.4 54.3 - - + +
341B LEU* 3.5 10.8 - - - +
343B GLU* 1.3 79.1 - - + +
345B LEU* 1.3 57.7 + - - +
346B THR 3.0 5.0 + - - -
347B ASP* 3.1 23.1 + - - +
350B CYS* 3.5 29.6 - - + +
351B GLN* 5.8 0.5 - - - +
353B PHE* 4.4 8.7 - - + -
354B ILE* 3.7 25.5 - - + +
371B VAL* 4.1 19.3 - - + -
374B ARG* 4.8 6.3 - - + +
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Residues in contact with LEU 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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341B LEU* 2.8 20.8 + - + +
342B LEU* 4.1 4.9 - - - +
343B GLU 3.3 0.2 - - - -
344B LEU* 1.3 75.7 - - - +
346B THR* 1.3 58.5 + - - +
347B ASP 3.4 2.0 - - - -
351B GLN* 6.0 2.8 - - - +
354B ILE* 3.8 18.2 - - + -
355B SER* 3.4 41.3 - - - +
356B TRP* 2.8 55.7 + - + +
363B PHE* 3.7 30.7 - - + -
414B PHE* 4.0 19.5 - - + -
433B LEU* 3.8 9.1 - - - +
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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