Contacts of the helix formed by residues 338 - 351 (chain E) in PDB entry 1UW9
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 GLU 338 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331E VAL* 5.1 0.2 - - - -
336E GLU* 4.9 0.4 - - - +
337E GLY* 1.3 70.7 - - - +
339E ARG* 1.3 78.2 + - - +
340E GLU* 3.0 28.7 + - - +
341E VAL* 3.0 37.5 + - + +
342E THR* 2.8 28.1 + - - -
471E THR* 3.9 32.7 - - + +
473E ASP* 4.2 11.3 + - - +
474E LYS* 5.7 5.4 - - + -
475E LEU* 4.8 4.8 + - - +
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Residues in contact with ARG 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E VAL* 4.0 26.0 - - + +
337E GLY 3.6 2.4 + - - -
338E GLU* 1.3 79.4 - - - +
340E GLU* 1.3 71.7 + - - +
342E THR* 3.5 1.7 - - - -
343E LEU* 2.9 57.4 + - + +
389E ALA* 6.2 0.4 - - - +
392E GLU* 2.8 43.0 + - - -
393E ILE* 3.5 27.3 - - + +
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Residues in contact with GLU 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E GLU* 3.0 20.6 + - - +
339E ARG* 1.3 96.1 + - + +
341E VAL* 1.3 66.8 + - - +
343E LEU* 3.5 5.7 + - - +
344E GLY 3.1 17.8 + - - -
359E SER* 3.7 19.2 + - - +
360E ARG* 3.0 48.1 + - - +
475E LEU* 4.6 4.9 - - + -
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Residues in contact with VAL 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E HIS* 3.4 36.8 - - + +
312E ARG* 4.4 1.7 + - - +
337E GLY* 6.1 0.7 - - - -
338E GLU* 3.0 31.1 + - + +
339E ARG 3.4 0.2 - - - -
340E GLU* 1.3 75.1 - - - +
342E THR* 1.3 62.1 - - - +
344E GLY* 3.3 2.9 + - - -
345E PHE* 3.2 34.9 + - + -
360E ARG 4.1 10.5 - - - +
473E ASP* 4.1 23.8 - - - +
474E LYS 5.0 0.2 - - - -
475E LEU* 3.8 32.3 - - + +
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Residues in contact with THR 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E SER 3.8 20.7 + - - +
329E GLY* 5.1 1.9 - - - +
331E VAL* 3.9 19.1 - - + +
337E GLY* 3.6 18.9 + - - -
338E GLU 2.8 21.6 + - - -
339E ARG 3.5 3.8 - - - -
341E VAL* 1.3 73.8 - - - +
343E LEU* 1.3 59.7 + - - +
344E GLY 3.2 0.2 + - - -
345E PHE* 3.3 19.7 + - + -
346E VAL* 2.9 44.3 + - + +
393E ILE* 5.2 3.4 - - + -
394E PHE* 4.4 11.0 - - + -
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Residues in contact with LEU 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E ARG* 2.9 52.6 + - + +
340E GLU* 3.9 7.0 - - - +
342E THR* 1.3 76.0 - - + +
344E GLY* 1.3 62.2 + - - +
346E VAL* 3.5 9.8 + - + +
347E ASP* 3.2 28.8 + - - +
360E ARG* 3.4 41.1 - - - +
393E ILE* 3.5 40.2 - - + +
394E PHE* 6.3 0.2 - - + -
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Residues in contact with GLY 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312E ARG* 6.2 0.4 - - - -
340E GLU 3.1 10.8 + - - -
341E VAL 3.3 4.5 + - - -
342E THR 3.1 0.2 - - - -
343E LEU* 1.3 76.0 - - - +
345E PHE* 1.3 61.4 + - - +
347E ASP* 3.3 9.1 + - - +
348E LEU* 3.2 22.7 + - - +
360E ARG* 3.8 23.3 - - - +
362E ILE* 3.8 19.1 - - - +
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Residues in contact with PHE 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295E ARG* 4.6 2.5 - - - -
310E HIS* 4.1 12.8 - + - -
311E PHE* 3.6 39.9 - + + -
312E ARG* 3.7 27.9 - - + +
315E ALA* 4.9 2.9 - - + -
328E SER* 3.2 36.1 - - - -
337E GLY* 6.1 2.0 - - - -
341E VAL* 3.2 38.6 + - + -
342E THR* 3.6 29.2 - - + -
344E GLY* 1.3 72.1 - - - +
346E VAL* 1.3 65.1 + - + +
348E LEU* 3.2 10.7 + - + +
349E MET* 2.9 40.2 + - - +
360E ARG 4.9 0.2 + - - -
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Residues in contact with VAL 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E SER* 4.1 14.6 - - - -
342E THR* 2.9 29.3 + - + +
343E LEU* 3.8 12.8 - - + +
345E PHE* 1.3 78.4 - - + +
347E ASP* 1.3 63.8 + - - +
349E MET* 3.1 9.0 + - - +
350E ARG* 3.0 59.9 + - - +
376E PRO* 4.4 9.9 - - + -
393E ILE 5.9 0.7 - - - +
394E PHE* 3.9 30.3 - - + -
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Residues in contact with ASP 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E LEU 3.2 17.5 + - - +
344E GLY* 3.4 11.0 - - - +
345E PHE 3.2 0.2 - - - -
346E VAL* 1.3 78.1 - - - +
348E LEU* 1.3 57.4 + - - +
350E ARG* 4.5 12.4 + - - -
351E ASP* 2.9 57.7 + - - +
354E VAL* 3.6 18.2 - - + +
360E ARG* 4.2 15.1 + - - -
362E ILE* 5.3 1.8 - - + +
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Residues in contact with LEU 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ASP* 5.0 1.1 - - - +
312E ARG* 4.1 28.7 - - + +
315E ALA* 6.1 2.0 - - + -
316E LYS* 3.8 38.5 - - + +
319E ARG* 2.8 19.9 + - - -
344E GLY 3.2 15.9 + - - +
345E PHE* 3.2 11.6 + - + +
347E ASP* 1.3 78.4 - - - +
349E MET* 1.3 56.3 + - + +
354E VAL* 3.8 30.3 - - + -
362E ILE* 4.1 23.1 - - + -
366E GLN* 3.9 15.7 - - + -
368E TRP* 2.9 17.1 + - - +
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Residues in contact with MET 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E PHE* 4.8 1.6 - - - -
315E ALA* 3.9 22.7 - - + +
319E ARG* 3.1 23.0 + - + +
326E LEU* 3.6 48.2 - - + +
328E SER* 4.4 9.4 - - - -
345E PHE* 2.9 34.2 + - - +
346E VAL* 3.1 11.6 + - - +
348E LEU* 1.3 79.2 - - - +
350E ARG* 1.3 57.4 + - + +
374E VAL* 2.8 39.7 + - + +
376E PRO* 3.6 20.4 - - + -
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Residues in contact with ARG 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E ILE* 3.8 15.1 - - + +
319E ARG* 3.9 1.0 + - - -
346E VAL* 3.0 36.8 + - - +
347E ASP* 4.5 9.9 + - - -
349E MET* 1.3 80.0 - - + +
351E ASP* 1.3 73.6 + - - +
373E GLY* 3.6 19.7 + - - -
374E VAL 3.6 16.2 - - - +
376E PRO* 3.6 17.2 - - + +
393E ILE 5.3 1.6 + - - -
394E PHE* 2.8 29.9 + - - +
397E ASP* 2.8 47.4 + - - +
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Residues in contact with ASP 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E ARG* 2.8 25.6 + - - -
347E ASP* 2.9 46.7 + - - +
350E ARG* 1.3 88.8 + - - +
352E ASP* 1.3 61.3 + - - +
353E TYR 4.2 7.9 - - - +
354E VAL* 3.9 12.5 - - + +
368E TRP* 3.2 8.1 - - - -
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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