Contacts of the helix formed by residues 337 - 350 (chain K) in PDB entry 4UJ3
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 LYS 337 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335K PHE 4.3 1.3 - - - -
336K SER* 1.3 68.7 - - - +
338K SER* 1.3 63.6 + - - +
339K GLU* 3.2 5.7 + - + +
340K LEU* 3.3 17.6 + - + +
341K ALA* 3.3 11.3 + - - +
380K ALA 3.1 27.1 - - - +
381K LEU* 2.5 14.8 + - - +
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Residues in contact with SER 338 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335K PHE 4.2 7.9 - - - +
336K SER 3.0 10.8 + - - -
337K LYS* 1.3 69.0 - - - +
339K GLU* 1.3 65.0 + - - +
340K LEU 3.4 0.2 - - - -
341K ALA* 3.6 9.6 - - - +
342K SER* 3.4 21.8 + - - -
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Residues in contact with GLU 339 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337K LYS* 3.2 1.7 - - + -
338K SER* 1.3 77.6 + - - +
340K LEU* 1.3 66.0 + - - +
342K SER* 3.1 18.5 + - - -
343K ALA* 3.6 9.2 + - - +
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Residues in contact with LEU 340 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337K LYS* 3.3 13.9 + - + +
339K GLU* 1.3 78.6 - - - +
341K ALA* 1.3 62.1 + - - +
343K ALA* 3.3 13.1 + - + +
344K VAL* 3.1 32.5 + - + +
372K GLU* 6.5 0.9 - - + -
380K ALA* 3.4 40.4 - - + +
381K LEU* 3.4 22.4 - - + +
392K ILE* 5.2 2.9 - - + -
394K LEU* 5.4 4.3 - - + -
401K TYR* 3.4 38.1 - - + +
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Residues in contact with ALA 341 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333K LEU* 3.6 27.0 - - - +
335K PHE* 4.4 15.5 - - + +
337K LYS 3.3 10.5 + - - +
338K SER* 3.6 13.7 - - - +
339K GLU 3.2 0.4 - - - -
340K LEU* 1.3 80.2 - - - +
342K SER* 1.3 63.0 + - - +
344K VAL* 3.0 17.4 + - - +
345K LEU* 3.3 11.6 + - - +
381K LEU* 3.9 8.9 - - + +
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Residues in contact with SER 342 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338K SER 3.4 10.0 + - - -
339K GLU* 3.1 16.3 + - - -
341K ALA* 1.3 77.6 - - - +
343K ALA* 1.3 59.5 + - - +
345K LEU* 3.8 19.9 + - - +
346K GLU* 3.9 11.7 + - - +
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Residues in contact with ALA 343 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339K GLU 3.6 8.5 + - - +
340K LEU* 3.3 15.2 + - + +
341K ALA 3.1 0.2 - - - -
342K SER* 1.3 80.2 + - - +
344K VAL* 1.3 60.5 + - - +
346K GLU* 2.9 38.5 - - - +
347K ALA* 3.2 7.1 + - - +
394K LEU* 4.2 19.6 - - + +
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Residues in contact with VAL 344 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333K LEU* 4.8 13.0 - - + -
335K PHE* 6.5 0.4 - - + -
340K LEU* 3.1 21.5 + - + +
341K ALA* 3.0 10.9 + - - +
343K ALA* 1.3 75.4 - - - +
345K LEU* 1.3 59.8 + - - +
347K ALA* 3.0 7.7 + - - +
348K VAL* 2.8 45.3 + - + +
353K LEU* 4.5 11.2 - - + -
381K LEU* 4.6 10.5 - - + -
392K ILE* 4.2 22.2 - - + -
394K LEU* 4.6 8.5 - - + -
411K ILE* 4.5 15.3 - - + -
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Residues in contact with LEU 345 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316K ARG* 3.8 12.8 - - - +
325K TYR* 4.0 16.6 - - + -
329K ILE* 4.5 4.9 - - + -
330K PHE* 4.4 17.5 - - + -
333K LEU* 4.1 28.4 - - + +
341K ALA 3.3 7.6 + - - +
342K SER* 3.8 15.3 - - - +
343K ALA 3.3 0.4 - - - -
344K VAL* 1.3 79.5 - - - +
346K GLU* 1.3 64.3 + - + +
348K VAL* 3.6 2.9 + - + +
349K GLU* 3.0 66.3 + - + +
418K PHE* 5.2 2.2 - - + -
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Residues in contact with GLU 346 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342K SER 3.9 9.1 + - - +
343K ALA* 2.9 32.2 - - - +
345K LEU* 1.3 80.6 - - + +
347K ALA* 1.3 66.3 + - + +
349K GLU* 3.4 13.1 + - - +
350K ASN* 3.0 38.7 + - - +
394K LEU* 5.7 2.6 - - + +
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Residues in contact with ALA 347 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343K ALA 3.2 4.7 + - - +
344K VAL* 3.0 8.0 + - - +
346K GLU* 1.3 84.3 - - + +
348K VAL* 1.3 56.7 + - - +
350K ASN* 3.4 1.9 + - - +
351K ASN 3.1 5.0 + - - -
352K THR* 2.8 50.3 + - - +
353K LEU* 3.2 10.6 + - + -
394K LEU* 3.5 34.1 - - + -
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Residues in contact with VAL 348 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333K LEU* 5.1 8.1 - - + -
344K VAL* 2.8 36.0 + - + +
345K LEU* 3.9 6.7 - - - +
347K ALA* 1.3 76.7 - - - +
349K GLU* 1.3 64.0 + - - +
351K ASN* 3.1 13.3 + - - +
353K LEU* 4.0 12.8 - - + -
411K ILE* 4.7 4.0 - - + +
414K VAL* 4.4 5.2 - - + -
415K CYS* 3.6 37.8 - - - +
418K PHE* 3.6 37.2 - - + +
422K ARG* 4.9 2.8 + - - -
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Residues in contact with GLU 349 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314K MET* 5.1 5.4 - - + +
316K ARG* 2.4 32.3 + - - -
325K TYR* 2.6 24.4 + - - +
345K LEU* 3.0 44.7 + - + +
346K GLU* 3.6 10.8 - - - +
347K ALA 3.4 0.2 - - - -
348K VAL* 1.3 76.8 - - - +
350K ASN* 1.3 63.9 + - - +
351K ASN 3.3 0.8 + - - -
418K PHE* 3.9 24.1 - - + -
422K ARG* 4.5 13.9 + - - -
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Residues in contact with ASN 350 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346K GLU* 3.0 27.4 + - - +
347K ALA* 4.0 0.6 - - - +
348K VAL 3.1 1.0 - - - -
349K GLU* 1.3 81.7 - - - +
351K ASN* 1.3 71.3 + - - +
352K THR* 3.1 27.5 + - + +
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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