Contacts of the strand formed by residues 348 - 359 (chain E) in PDB entry 5IXM
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 348 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340E ARG* 2.6 41.2 + - + -
341E ILE 3.7 6.5 - - - +
342E TYR* 3.9 23.2 + - + -
346E ARG 3.9 0.8 + - - -
347E VAL* 1.3 77.9 - - - +
349E ARG* 1.3 62.1 + - - +
350E PHE 3.9 13.5 - - - +
351E ASN* 3.6 15.3 - - - +
387E PHE* 3.8 21.3 - - + -
389E ARG* 4.4 4.7 + - - +
137F ARG* 3.8 17.3 + - - -
141F THR* 5.5 0.2 + - - -
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Residues in contact with ARG 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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279E PHE* 4.4 5.5 - - - -
341E ILE* 2.9 13.3 + - + +
343E ASP* 3.6 30.5 + - + +
347E VAL* 3.2 22.7 - - + +
348E GLU* 1.3 74.8 - - - +
350E PHE* 1.3 59.8 + - + +
387E PHE* 4.3 2.5 - - - -
388E TRP* 3.4 5.7 - - - +
389E ARG* 2.5 65.7 + - + +
390E ILE 3.3 18.8 + - - -
391E ASN* 3.8 10.1 - - - +
392E ASP* 5.8 2.2 + - - -
604E C8E 3.2 58.5 + - - -
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Residues in contact with PHE 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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339E SER* 4.9 3.4 - - - -
340E ARG* 3.7 2.3 - - - -
341E ILE* 3.2 50.0 + - + -
348E GLU* 3.9 7.2 - - - +
349E ARG* 1.3 80.6 - - + +
351E ASN* 1.3 81.2 + - - +
352E VAL* 3.7 30.5 - - + -
386E THR* 4.1 9.0 - - - -
387E PHE* 3.4 18.2 - - - -
388E TRP* 3.7 19.3 - + + -
603E C8E 4.2 22.9 - - - -
604E C8E 3.7 45.3 - - - +
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Residues in contact with ASN 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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338E THR* 3.8 10.9 - - - +
339E SER 3.6 7.5 + - - +
340E ARG* 3.7 20.9 - - + +
348E GLU* 3.6 14.6 - - - +
350E PHE* 1.3 82.6 - - - +
352E VAL* 1.3 70.4 + - - +
353E SER* 3.6 16.2 + - - -
385E ASP* 3.7 15.1 - - - +
386E THR* 3.0 7.8 + - - -
387E PHE* 2.7 58.5 + - + +
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Residues in contact with VAL 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337E LEU 3.8 0.7 - - - +
338E THR* 3.4 0.9 - - - +
339E SER* 3.0 47.9 + - - +
350E PHE* 3.7 25.8 - - + -
351E ASN* 1.3 78.8 - - - +
353E SER* 1.3 73.0 + - - +
354E VAL* 4.7 10.1 - - + -
385E ASP 3.6 9.4 - - - +
386E THR* 4.4 7.6 - - - +
603E C8E 6.1 0.9 - - - +
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Residues in contact with SER 353 (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 TYR* 3.7 16.5 - - - -
337E LEU 3.3 4.0 - - - -
338E THR* 3.0 29.3 + - - +
351E ASN* 3.6 7.8 + - - -
352E VAL* 1.3 76.7 + - - +
354E VAL* 1.3 66.9 + - - +
384E GLY* 3.1 5.3 - - - -
385E ASP* 2.8 55.9 + - - +
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Residues in contact with VAL 354 (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 TYR* 3.6 3.6 - - - -
336E GLY* 3.4 0.9 - - - -
337E LEU* 2.9 35.1 + - + +
352E VAL* 4.7 12.8 - - + -
353E SER* 1.3 80.9 - - - +
355E GLY* 1.3 61.7 + - - +
382E TRP* 3.9 28.9 - - + -
383E ALA 3.7 6.7 - - - +
384E GLY* 4.9 4.0 - - - -
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Residues in contact with GLY 355 (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 TYR* 3.6 5.6 - - - -
315E LEU* 3.5 18.8 - - - -
335E THR 3.1 12.6 - - - -
336E GLY* 3.9 0.2 - - - -
354E VAL* 1.3 75.0 - - - +
356E GLN* 1.3 63.5 + - - +
382E TRP* 3.4 10.5 - - - -
383E ALA 2.9 32.4 + - - +
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Residues in contact with GLN 356 (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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315E LEU* 3.9 3.7 - - - +
333E VAL* 3.7 15.2 + - - +
334E SER* 3.4 4.7 - - - -
335E THR* 2.7 63.5 + - - +
355E GLY* 1.3 76.1 - - - +
357E ILE* 1.3 69.6 + - - +
358E TYR* 3.7 10.0 + - - +
379E SER* 2.7 31.5 + - - -
381E VAL 3.1 12.8 - - - +
382E TRP* 3.5 33.0 - - + -
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Residues in contact with ILE 357 (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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310E SER* 5.3 2.0 - - - +
314E GLY 5.2 1.3 - - - +
315E LEU* 3.6 42.4 - - + +
332E GLN* 4.1 21.1 - - + +
333E VAL 3.6 4.5 - - - +
334E SER* 3.6 16.4 - - - +
356E GLN* 1.3 83.6 - - - +
358E TYR* 1.3 61.5 + - - +
359E TYR* 3.6 38.9 - - + +
378E GLY 3.5 1.0 - - - +
379E SER* 3.3 1.7 - - - -
380E LEU 3.0 26.5 + - - -
381E VAL* 2.8 23.3 + - + -
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Residues in contact with TYR 358 (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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332E GLN* 3.3 4.7 - - - +
333E VAL* 2.9 42.6 + - + +
356E GLN* 3.7 13.3 + - - +
357E ILE* 1.3 71.2 - - - +
359E TYR* 1.3 71.4 + - - +
360E PHE* 3.6 39.2 + + - -
378E GLY* 3.6 9.6 - - - -
379E SER* 3.3 30.3 - - - +
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Residues in contact with TYR 359 (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 ASN 4.0 3.1 - - - -
332E GLN* 3.2 32.4 + - + -
357E ILE* 3.6 36.2 - - + +
358E TYR* 1.3 77.9 - - - +
360E PHE* 1.3 59.4 + - - +
361E SER 3.7 18.4 - - - +
362E ARG* 5.7 0.4 - - - -
363E SER* 3.4 22.9 - - - -
377E THR* 3.3 8.9 + - + -
378E GLY* 2.9 48.6 + - - +
380E LEU* 4.0 25.1 - - + -
381E VAL* 4.1 11.5 - - + +
405E ARG* 3.8 22.6 + - - -
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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