Contacts of the helix formed by residues 337 - 350 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335W PHE* 4.3 2.4 - - - +
336W SER* 1.3 72.0 - - - +
338W SER* 1.3 63.3 + - - +
339W GLU* 3.2 4.3 + - + +
340W LEU* 3.5 10.3 + - + +
341W ALA* 3.2 22.3 + - - +
380W ALA 3.6 16.2 - - - +
381W LEU* 3.0 20.3 + - - +
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Residues in contact with SER 338 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335W PHE 4.4 6.5 - - - -
336W SER 2.9 11.3 + - - -
337W LYS* 1.3 69.6 - - - +
339W GLU* 1.3 64.7 + - - +
341W ALA* 4.0 9.3 - - - +
342W SER* 3.3 24.9 + - - -
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Residues in contact with GLU 339 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337W LYS* 3.2 2.1 - - + -
338W SER* 1.3 79.8 + - - +
340W LEU* 1.3 64.8 - - - +
341W ALA 3.5 0.2 + - - -
342W SER* 3.8 8.3 + - - -
343W ALA* 3.8 10.6 + - - +
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Residues in contact with LEU 340 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337W LYS* 3.5 12.7 + - + +
339W GLU* 1.3 76.4 - - - +
341W ALA* 1.3 64.2 + - - +
343W ALA* 3.2 9.6 + - + +
344W VAL* 3.1 28.1 + - + +
372W GLU 5.3 0.7 - - - +
380W ALA* 3.9 21.3 - - + +
381W LEU* 3.8 24.0 - - + -
392W ILE* 5.9 1.1 - - + -
394W LEU* 3.7 24.9 - - + -
401W TYR* 3.5 49.4 - - + +
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Residues in contact with ALA 341 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333W LEU* 3.9 23.7 - - - +
334W THR* 5.4 0.2 - - - -
335W PHE* 4.3 20.4 - - + +
337W LYS 3.2 17.4 + - - +
338W SER* 4.0 10.3 - - - +
339W GLU 3.3 0.2 - - - -
340W LEU* 1.3 77.7 - - - +
342W SER* 1.3 64.1 + - - +
344W VAL* 3.0 19.7 + - - +
345W LEU* 3.2 13.0 + - - +
381W LEU* 4.5 4.7 - - - +
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Residues in contact with SER 342 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338W SER 3.3 16.9 + - - -
339W GLU 4.3 3.6 - - - -
340W LEU 3.5 0.2 - - - -
341W ALA* 1.3 77.3 - - - +
343W ALA* 1.3 60.3 + - - +
345W LEU* 3.8 11.3 + - - +
346W GLU* 3.6 18.9 + - - +
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Residues in contact with ALA 343 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339W GLU 3.8 8.5 + - - +
340W LEU* 3.2 17.9 + - + +
341W ALA 3.1 0.4 - - - -
342W SER* 1.3 79.2 - - - +
344W VAL* 1.3 61.7 + - - +
346W GLU* 3.4 11.8 + - - +
347W ALA* 3.2 20.3 + - - +
394W LEU* 4.2 15.5 - - + +
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Residues in contact with VAL 344 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333W LEU* 4.6 12.1 - - + -
335W PHE* 5.6 1.8 - - + -
340W LEU* 3.2 20.2 - - + +
341W ALA* 3.3 8.3 - - - +
343W ALA* 1.3 74.1 - - - +
345W LEU* 1.3 61.4 + - - +
347W ALA* 3.0 9.3 + - - +
348W VAL* 2.9 37.4 + - + +
353W LEU* 3.4 23.1 - - + -
381W LEU* 4.3 19.1 - - + -
392W ILE* 5.1 5.4 - - + -
394W LEU* 3.9 20.2 - - + -
411W ILE* 4.2 14.4 - - + -
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Residues in contact with LEU 345 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316W ARG* 3.9 15.9 - - - +
325W TYR* 4.6 5.2 - - + -
329W ILE* 4.1 15.9 - - + -
330W PHE* 4.8 12.8 - - + -
333W LEU* 3.5 34.9 - - + +
341W ALA 3.2 8.1 + - - +
342W SER* 3.9 12.8 - - - +
344W VAL* 1.3 78.5 - - - +
346W GLU* 1.3 65.7 + - + +
348W VAL* 3.4 3.8 + - + +
349W GLU* 3.3 50.0 + - + +
418W PHE* 5.4 1.1 - - + -
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Residues in contact with GLU 346 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316W ARG* 6.2 0.2 - - - +
342W SER 3.6 9.8 + - - +
343W ALA* 3.4 12.8 + - - +
344W VAL 3.1 0.8 - - - -
345W LEU* 1.3 79.7 - - + +
347W ALA* 1.3 65.2 + - - +
349W GLU* 3.3 13.9 + - - +
350W ASN* 3.2 44.7 + - - +
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Residues in contact with ALA 347 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343W ALA 3.2 10.2 + - - +
344W VAL 3.0 9.3 + - - +
346W GLU* 1.3 78.9 - - - +
348W VAL* 1.3 58.1 + - - +
350W ASN* 3.3 1.9 + - - +
351W ASN 2.9 8.1 + - - -
352W THR* 2.8 36.9 + - - -
353W LEU* 3.3 28.8 + - + +
394W LEU* 4.0 23.6 - - + +
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Residues in contact with VAL 348 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333W LEU* 4.4 10.1 - - + -
344W VAL* 2.9 26.1 + - + +
345W LEU* 3.5 11.0 - - + +
346W GLU 3.2 0.2 - - - -
347W ALA* 1.3 76.9 - - - +
349W GLU* 1.3 62.2 + - + +
351W ASN* 3.2 13.6 + - - +
353W LEU* 3.7 22.7 - - + -
411W ILE* 4.9 2.9 - - + +
414W VAL* 4.1 11.0 - - + -
415W CYS* 4.1 23.8 - - - -
418W PHE* 3.6 40.2 - - + +
422W ARG* 5.3 3.1 + - - -
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Residues in contact with GLU 349 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314W MET* 5.8 2.4 - - - +
316W ARG* 2.9 39.7 + - - -
325W TYR* 2.8 34.7 + - - +
345W LEU* 3.3 25.3 + - + +
346W GLU* 3.8 12.5 - - - +
347W ALA 3.3 0.2 - - - -
348W VAL* 1.3 76.9 - - - +
350W ASN* 1.3 66.1 + - - +
351W ASN 3.3 1.0 + - - -
418W PHE* 4.2 19.7 - - + -
422W ARG* 4.9 11.8 + - - -
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Residues in contact with ASN 350 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346W GLU* 3.2 39.8 + - - +
347W ALA* 3.3 1.2 + - - +
349W GLU* 1.3 82.3 - - - +
351W ASN* 1.3 70.5 + - - +
352W THR* 3.0 20.2 + - - +
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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