Contacts of the helix formed by residues 348 - 361 (chain O) in PDB entry 3V3K
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 TRP 348 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340O TRP* 3.4 39.2 + + + +
342O ASP* 4.5 18.2 - - + +
345O SER* 5.5 0.2 - - - -
346O GLY 4.5 2.0 - - - -
347O SER* 1.3 73.9 + - - +
349O TYR* 1.3 56.9 + - - +
351O GLU* 3.9 3.8 - - - +
352O THR* 2.7 37.5 + - - -
377O VAL* 4.3 13.0 - - + -
380O LYS* 3.5 67.6 + - + +
381O GLY* 3.9 7.0 - - - -
383O TYR 3.4 22.2 - - - -
384O LYS* 4.7 3.8 - - - -
385O GLN* 3.9 24.0 - - + +
186P LEU* 3.6 32.2 - - + +
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Residues in contact with TYR 349 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281O PHE* 3.5 11.2 - - + -
282O ILE 4.7 4.0 - - - -
283O GLN* 3.6 25.6 - - + +
330O SER* 2.6 41.6 + - - -
331O TYR 4.1 8.1 - - - -
332O SER* 3.6 30.5 - - - -
347O SER* 3.3 1.6 + - - -
348O TRP* 1.3 79.1 - - - +
350O VAL* 1.3 63.2 + - + +
352O THR* 3.3 3.5 + - - -
353O LEU* 2.8 63.2 + - + +
370O LEU* 3.9 2.4 - - + +
373O VAL* 3.9 23.0 - - + +
377O VAL* 4.3 7.0 - - - -
385O GLN* 4.2 9.5 - - - +
387O PRO* 4.2 10.8 - - + -
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Residues in contact with VAL 350 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185O ASP* 3.6 40.8 - - + +
188O LYS* 4.9 4.9 - - + +
189O LEU* 3.5 36.1 - - + -
235O LEU* 4.3 8.1 - - + -
283O GLN* 4.2 15.3 - - + -
347O SER* 3.5 11.6 + - - -
349O TYR* 1.3 87.4 - - + +
351O GLU* 1.3 60.1 + - - +
353O LEU* 4.1 6.1 - - + -
354O ASP* 2.9 29.7 + - + +
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Residues in contact with GLU 351 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185O ASP* 4.3 1.9 + - - +
188O LYS* 3.6 29.6 + - - +
345O SER* 3.0 35.9 + - - +
346O GLY 4.2 1.4 - - - +
347O SER 2.9 19.4 + - - +
348O TRP* 3.9 5.3 - - - +
350O VAL* 1.3 76.6 - - - +
352O THR* 1.3 55.6 + - - +
354O ASP* 4.3 1.0 - - - +
355O ASP* 3.2 29.6 + - + +
380O LYS* 3.6 23.1 + - - +
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Residues in contact with THR 352 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348O TRP 2.7 23.4 + - - -
349O TYR 3.8 1.1 - - - -
351O GLU* 1.3 73.3 - - - +
353O LEU* 1.3 64.8 + - - +
355O ASP* 4.0 4.9 - - + +
356O ILE* 3.3 36.6 + - + +
373O VAL* 3.8 13.7 - - - +
376O ALA* 3.4 33.0 - - + +
377O VAL* 3.5 13.5 - - + +
380O LYS* 3.8 17.5 + - - -
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Residues in contact with LEU 353 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189O LEU* 4.0 23.3 - - + -
192O ARG* 5.8 0.7 - - + -
193O PHE* 5.5 2.9 - - + -
281O PHE* 3.6 22.9 - - + -
349O TYR* 2.8 58.7 + - + +
350O VAL* 3.3 8.5 + - - +
352O THR* 1.3 72.7 - - - +
354O ASP* 1.3 59.1 + - - +
356O ILE* 3.4 1.4 + - - +
357O PHE* 3.0 68.6 + - + -
370O LEU* 4.2 7.2 - - + -
373O VAL* 3.9 10.7 - - + +
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Residues in contact with ASP 354 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188O LYS* 3.4 48.0 - - + +
189O LEU* 4.9 6.5 - - + -
192O ARG* 2.7 47.3 + - - +
350O VAL 2.9 17.0 + - - +
351O GLU 4.3 2.2 - - - +
353O LEU* 1.3 79.9 - - - +
355O ASP* 1.3 57.5 + - - +
357O PHE* 3.6 4.6 + - - +
358O GLU* 3.1 27.2 + - - +
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Residues in contact with ASP 355 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351O GLU* 3.2 19.8 + - + +
352O THR* 4.0 7.8 - - - +
353O LEU 3.3 0.2 - - - -
354O ASP* 1.3 77.4 - - - +
356O ILE* 1.3 63.2 + - - +
358O GLU* 3.5 7.7 + - - +
359O GLN* 3.2 34.6 + - - +
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Residues in contact with ILE 356 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352O THR* 3.3 26.4 + - + +
353O LEU 4.0 2.2 - - - +
355O ASP* 1.3 79.1 - - - +
357O PHE* 1.3 57.8 + - + +
359O GLN* 4.4 2.7 - - - +
360O TRP* 2.8 45.0 + - + +
369O LEU* 3.6 33.4 - - + +
372O ARG* 3.3 30.5 - - + +
373O VAL* 3.2 36.8 - - + +
376O ALA* 4.6 2.9 - - + -
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Residues in contact with PHE 357 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192O ARG* 3.9 26.9 + - + -
193O PHE* 5.0 8.1 - + - -
196O LEU* 3.9 22.1 - - + +
281O PHE* 4.7 7.2 - + - -
353O LEU* 3.0 51.3 + - + +
354O ASP* 4.0 2.5 - - - +
356O ILE* 1.3 79.8 - - + +
358O GLU* 1.3 61.1 + - - +
361O ALA* 3.0 29.4 + - + +
366O LEU* 4.3 13.7 - - + -
369O LEU* 3.6 37.5 - - + -
370O LEU* 4.9 7.2 - - + -
373O VAL* 5.3 0.7 - - + -
400O PHE* 3.5 31.2 - + - -
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Residues in contact with GLU 358 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192O ARG* 3.3 34.4 + - - +
354O ASP 3.1 18.5 + - - +
355O ASP* 3.6 8.5 - - - +
356O ILE 3.2 0.2 - - - -
357O PHE* 1.3 78.9 - - - +
359O GLN* 1.3 62.4 + - + +
362O HIS* 4.8 6.9 + - - -
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Residues in contact with GLN 359 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355O ASP* 3.2 25.3 + - - +
356O ILE* 3.2 2.5 + - - +
358O GLU* 1.3 82.5 - - + +
360O TRP* 1.3 96.0 + - + +
361O ALA 4.0 0.2 - - - -
362O HIS* 3.5 19.1 - - - -
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Residues in contact with TRP 360 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356O ILE* 2.8 26.5 + - + +
359O GLN* 1.3 115.3 + - + +
361O ALA* 1.3 57.8 + - - +
362O HIS* 3.3 5.7 + + - -
363O SER* 3.3 17.2 + - - -
364O GLU* 3.0 54.6 + - - +
369O LEU* 3.5 13.5 - - + -
372O ARG* 3.2 45.1 - - - +
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Residues in contact with ALA 361 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196O LEU* 4.7 7.4 - - + -
357O PHE* 3.0 39.5 + - + +
358O GLU 5.0 0.2 + - - -
359O GLN 4.0 0.4 - - - -
360O TRP* 1.3 76.6 - - - +
362O HIS* 1.3 60.4 + - - +
363O SER 3.4 0.2 - - - -
364O GLU 3.1 15.9 - - - +
369O LEU* 3.7 22.5 - - + +
399O PHE* 5.5 0.7 - - - -
400O PHE* 4.4 17.9 + - + +
402O THR* 4.4 13.5 - - + +
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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