Contacts of the helix formed by residues 336 - 345 (chain H) in PDB entry 3WTW
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334H PRO 4.3 6.3 - - - +
335H ILE* 1.3 75.9 - - - +
337H LEU* 1.3 61.1 + - - +
338H TRP* 3.4 31.3 + - + +
339H GLN* 2.9 27.6 + - - +
340H PHE* 2.9 23.9 + - - +
375H TRP* 3.2 13.3 - - - -
396H TYR* 5.3 0.7 - - - -
399H LYS* 5.7 1.2 + - - -
7I A 3.5 33.0 + - - +
8I C 2.9 29.0 + - - +
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Residues in contact with LEU 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H GLN* 1.3 70.3 - - - +
338H TRP* 1.3 63.8 + - - +
339H GLN 2.9 6.4 + - - -
340H PHE* 4.9 0.9 - - + -
341H LEU* 3.1 33.9 + - + +
375H TRP* 3.4 40.6 - - + +
389H LEU* 3.4 55.2 - - + +
392H GLY* 4.2 6.3 - - - -
393H LEU* 3.7 22.4 - - + +
396H TYR* 3.5 11.6 + - + +
8I C 3.0 17.1 + - - +
9I A 5.5 2.0 - - - +
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Residues in contact with TRP 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H GLN* 3.4 30.4 - - + +
337H LEU* 1.3 72.4 - - - +
339H GLN* 1.3 88.8 + - + +
341H LEU* 5.0 1.3 - - - -
342H LEU* 3.4 25.9 + - + +
396H TYR* 2.8 41.2 + + + +
401H ILE* 3.9 24.7 - - + -
402H ILE* 4.0 17.5 - - + -
414H PHE* 3.5 16.0 - + - -
416H CYS* 4.3 17.5 - - - -
418H LEU* 4.8 13.2 - - + -
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Residues in contact with GLN 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H PRO 4.4 2.4 + - - -
335H ILE* 2.9 34.9 - - + +
336H GLN* 2.9 32.9 + - - +
337H LEU 2.9 1.8 - - - -
338H TRP* 1.3 117.2 + - + +
340H PHE* 1.3 66.5 + - - +
341H LEU 3.2 1.3 - - - -
342H LEU* 3.0 10.6 + - - +
343H GLU* 2.9 21.4 + - - +
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Residues in contact with PHE 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335H ILE* 4.0 9.1 - - + +
336H GLN 2.9 20.2 + - - +
337H LEU* 3.9 2.9 - - + +
339H GLN* 1.3 71.8 - - - +
341H LEU* 1.3 74.3 + - + +
343H GLU* 2.9 25.1 + - - +
344H LEU* 3.0 48.9 - - + +
371H VAL* 3.8 8.5 - - + -
374H ARG* 3.2 38.1 - - + -
375H TRP* 3.3 41.5 - + + -
378H ARG* 4.0 29.6 - - + -
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Residues in contact with LEU 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337H LEU* 3.1 28.4 + - + +
338H TRP* 4.8 2.0 - - - +
340H PHE* 1.3 81.0 - - + +
342H LEU* 1.3 55.0 + - - +
343H GLU 2.6 16.2 + - - -
344H LEU* 2.7 18.7 + - + +
345H LEU* 3.2 13.6 + - + +
354H ILE* 4.0 15.0 - - + +
363H PHE* 4.1 25.6 - - + -
365H LEU* 4.7 7.0 - - + -
371H VAL* 3.3 33.9 - - + -
389H LEU* 4.8 5.6 - - + -
393H LEU* 4.1 29.6 - - + -
402H ILE* 4.9 3.4 - - + -
414H PHE* 5.2 2.9 - - + -
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Residues in contact with LEU 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338H TRP* 3.4 24.1 + - + +
339H GLN* 3.0 8.1 + - - +
341H LEU* 1.3 78.3 - - - +
343H GLU* 1.3 52.4 + - - +
345H LEU* 3.8 10.3 + - + +
346H THR* 2.7 37.6 + - + +
356H TRP* 5.9 7.9 - - + -
414H PHE* 3.5 33.1 - - + -
418H LEU* 3.9 28.3 - - + -
422H LEU* 5.8 1.3 - - + -
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Residues in contact with GLU 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335H ILE* 5.8 5.6 - - - +
339H GLN 2.9 9.7 + - - +
340H PHE* 3.0 27.4 - - - +
341H LEU 2.6 5.9 + - - -
342H LEU* 1.3 74.9 - - - +
344H LEU* 1.3 65.7 + - + +
345H LEU 3.1 1.3 - - - -
346H THR* 2.9 20.8 + - - +
347H ASP* 3.6 10.7 + - - +
378H ARG* 5.4 4.9 + - - -
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Residues in contact with LEU 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340H PHE* 3.0 49.1 - - + +
341H LEU* 2.7 13.2 + - + +
343H GLU* 1.3 78.8 - - + +
345H LEU* 1.3 58.8 + - - +
347H ASP* 3.1 24.6 - - - +
350H CYS* 3.6 31.3 - - + +
351H GLN* 4.6 1.4 + - - +
353H PHE* 4.5 10.5 - - + -
354H ILE* 4.2 18.4 - - + +
371H VAL* 3.6 33.9 - - + -
374H ARG* 4.6 6.5 - - + -
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Residues in contact with LEU 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341H LEU 3.2 11.2 + - - +
342H LEU* 4.1 11.9 - - + +
343H GLU 3.1 0.8 - - - -
344H LEU* 1.3 75.1 - - - +
346H THR* 1.3 56.7 + - - +
347H ASP 3.1 8.3 + - - -
348H LYS* 5.8 0.2 - - - +
351H GLN* 4.4 8.2 + - + -
354H ILE* 3.9 17.0 - - + +
355H SER* 3.3 44.9 - - - +
356H TRP* 3.0 50.4 + - + +
363H PHE* 3.6 29.2 - - + -
414H PHE* 4.6 9.9 - - + -
433H LEU* 3.6 14.4 - - - +
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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
------------------------------------------------------------
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