Contacts of the helix formed by residues 320 - 339 (chain E) in PDB entry 1XFB
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 ASN 320 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313E ALA 3.3 19.8 - - - +
314E TRP* 3.3 25.3 - - - +
315E ARG* 4.4 4.3 - - - +
317E GLN* 3.2 18.6 + - - +
319E ASP* 1.3 89.0 + - - +
321E ALA* 1.3 63.9 + - - +
322E GLY 3.4 0.7 - - - -
323E ALA* 3.1 12.0 + - + +
324E ALA* 2.8 23.6 + - - +
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Residues in contact with ALA 321 (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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62E VAL* 3.6 13.1 - - + +
314E TRP* 4.2 12.3 - - + +
317E GLN 3.4 5.1 + - - +
318E ARG* 3.2 22.7 - - + +
319E ASP 2.9 2.6 + - - +
320E ASN* 1.3 76.4 - - - +
322E GLY* 1.3 58.3 + - - +
324E ALA* 3.1 5.0 + - - +
325E THR* 2.9 33.4 + - - +
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Residues in contact with GLY 322 (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 ASP 3.8 5.2 + - - -
320E ASN 3.4 0.4 - - - -
321E ALA* 1.3 79.6 - - - +
323E ALA* 1.3 58.0 + - - +
325E THR* 3.3 9.2 + - - -
326E GLU* 3.0 33.3 + - - +
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Residues in contact with ALA 323 (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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313E ALA* 4.4 10.3 - - + -
319E ASP 4.8 0.8 + - - -
320E ASN* 3.1 17.9 + - + +
322E GLY* 1.3 72.4 - - - +
324E ALA* 1.3 67.5 + - - +
326E GLU* 3.0 10.2 + - - +
327E GLU* 2.9 26.9 + - - +
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Residues in contact with ALA 324 (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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62E VAL* 3.3 17.5 - - + -
310E ALA* 3.2 31.8 - - - +
313E ALA* 3.8 7.3 - - - +
314E TRP* 3.5 16.6 - - + +
320E ASN 2.8 11.9 + - - +
321E ALA 3.3 9.6 - - - +
323E ALA* 1.3 77.1 - - - +
325E THR* 1.3 64.3 + - - +
327E GLU* 3.0 14.2 + - - +
328E PHE 3.1 9.4 + - - -
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Residues in contact with THR 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E VAL* 2.8 32.9 + - - +
65E SER* 3.8 9.7 + - - +
66E ALA* 3.6 30.1 - - + +
321E ALA 2.9 16.4 + - - -
322E GLY* 3.5 11.6 - - - -
324E ALA* 1.3 75.8 - - - +
326E GLU* 1.3 59.9 + - - +
328E PHE* 3.4 6.5 + - + +
329E ILE* 3.0 40.7 + - + +
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Residues in contact with GLU 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ARG* 2.5 44.6 + - - -
322E GLY 3.0 18.4 + - - +
323E ALA* 3.0 11.9 + - - +
325E THR* 1.3 76.5 - - - +
327E GLU* 1.3 71.2 + - - +
329E ILE* 3.2 7.9 + - - +
330E LYS* 2.8 29.4 + - - +
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Residues in contact with GLU 327 (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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309E SER* 3.1 37.0 - - - +
310E ALA* 3.5 14.8 - - - -
313E ALA* 4.7 6.2 - - + +
323E ALA* 2.9 16.4 + - - +
324E ALA* 3.4 9.2 - - - +
326E GLU* 1.3 78.6 - - - +
328E PHE* 1.3 60.8 + - - +
330E LYS* 3.4 29.2 + - + +
331E ARG* 3.2 28.9 + - - +
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Residues in contact with PHE 328 (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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31E LEU* 3.7 40.2 - - + -
62E VAL 5.0 0.7 - - - -
63E LEU* 3.4 48.0 - - + -
66E ALA* 3.9 17.7 - - + -
70E VAL* 4.0 17.9 - - + -
74E ILE* 4.7 3.8 - - + -
306E LEU* 3.6 30.3 - - + -
310E ALA* 3.8 12.9 - - + +
324E ALA 3.1 10.6 + - - +
325E THR* 3.5 8.7 - - - +
326E GLU 3.1 0.4 - - - -
327E GLU* 1.3 72.5 - - - +
329E ILE* 1.3 71.2 - - - +
330E LYS 2.9 2.0 + - - -
331E ARG* 2.9 4.2 + - - +
332E ALA* 2.8 35.3 + - + -
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Residues in contact with ILE 329 (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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66E ALA* 3.7 32.5 - - + -
67E ASP* 3.8 17.9 - - - +
69E ARG* 3.6 62.6 - - + +
70E VAL* 4.8 5.6 - - + +
325E THR* 3.0 22.4 + - + +
326E GLU* 3.7 6.7 - - - +
328E PHE* 1.3 75.4 - - + +
330E LYS* 1.3 62.4 + - - +
332E ALA* 3.6 8.1 - - - +
333E GLU* 2.9 30.4 + - + +
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Residues in contact with LYS 330 (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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69E ARG* 5.6 0.6 - - - +
326E GLU* 2.8 19.2 + - - +
327E GLU* 3.4 34.1 + - - +
329E ILE* 1.3 76.6 - - - +
331E ARG* 1.3 66.0 + - + +
333E GLU* 3.0 11.2 + - - +
334E VAL* 2.8 29.6 + - + +
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Residues in contact with ARG 331 (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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277E GLU* 2.8 68.6 + - - +
278E GLU* 2.5 30.3 + - - -
281E SER* 3.0 17.0 + - - -
305E ALA 3.6 3.7 + - - +
306E LEU* 3.7 19.5 - - + +
309E SER* 4.0 2.9 - - - +
327E GLU 3.2 16.4 - - - +
328E PHE 2.9 4.6 + - - +
330E LYS* 1.3 81.0 - - + +
332E ALA* 1.3 63.5 + - - +
334E VAL* 3.1 31.3 - - - +
335E ASN* 2.9 38.3 + - - +
343E TYR* 4.4 1.0 + - - -
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Residues in contact with ALA 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E VAL* 4.4 2.7 - - + -
73E CYS* 3.1 24.9 - - - +
74E ILE* 4.0 15.9 - - + -
300E PHE* 4.4 2.8 - - - -
306E LEU* 3.6 11.3 - - - +
328E PHE* 2.8 39.7 + - + +
329E ILE* 3.6 9.4 - - - +
331E ARG* 1.3 72.3 - - - +
333E GLU* 1.3 59.1 + - - +
335E ASN* 4.0 2.0 - - - +
336E GLY* 3.0 20.6 + - - -
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Residues in contact with GLU 333 (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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69E ARG* 3.2 27.3 + - - +
72E LYS* 2.7 42.4 + - - +
73E CYS* 3.7 13.4 - - - +
329E ILE* 2.9 31.0 + - + +
330E LYS* 3.0 7.2 + - - +
332E ALA* 1.3 76.0 - - - +
334E VAL* 1.3 66.7 + - - +
336E GLY* 3.0 12.0 + - - -
337E LEU* 3.0 17.4 + - + +
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Residues in contact with VAL 334 (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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281E SER* 3.7 14.1 - - - +
330E LYS* 2.8 25.5 + - + +
331E ARG* 3.1 43.3 - - - +
333E GLU* 1.3 72.0 - - - +
335E ASN* 1.3 56.9 + - - +
337E LEU* 2.9 13.0 + - - +
338E ALA* 2.8 24.1 + - - +
343E TYR* 3.3 43.5 - - + -
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Residues in contact with ASN 335 (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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281E SER* 2.7 32.5 + - - -
284E LEU* 4.0 2.0 - - + +
300E PHE* 3.5 29.0 - - + -
302E TYR* 3.5 24.6 - - - -
305E ALA 4.0 1.4 + - - -
306E LEU* 3.7 16.4 - - - +
331E ARG* 2.9 41.4 + - - +
332E ALA 4.1 0.2 - - - +
334E VAL* 1.3 73.0 - - - +
336E GLY* 1.3 61.2 + - - +
338E ALA* 3.2 6.6 + - - +
339E ALA* 2.8 30.1 + - - +
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Residues in contact with GLY 336 (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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27E GLY* 3.2 29.1 - - - -
73E CYS* 3.7 7.6 - - - -
300E PHE* 3.9 6.5 - - - -
332E ALA 3.0 12.8 + - - -
333E GLU 3.0 9.1 + - - -
335E ASN* 1.3 77.9 - - - +
337E LEU* 1.3 60.1 + - - +
339E ALA* 3.6 2.3 - - - +
340E GLN* 3.1 23.1 + - - +
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Residues in contact with LEU 337 (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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333E GLU 3.0 15.5 + - - +
334E VAL* 2.9 10.4 + - - +
336E GLY* 1.3 76.2 - - - +
338E ALA* 1.3 52.7 + - - +
339E ALA 2.9 4.9 - - - -
340E GLN* 2.7 33.0 + - - +
342E LYS* 3.1 52.0 + - + +
343E TYR* 3.8 22.0 - - + -
344E GLU 5.5 0.4 - - - +
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Residues in contact with ALA 338 (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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281E SER* 3.3 29.2 - - - +
284E LEU* 3.6 9.9 - - + +
285E ASN* 3.2 30.6 - - + +
288E ASN* 2.9 16.2 + - - -
334E VAL 2.8 12.5 + - - +
335E ASN* 3.7 12.6 - - - +
337E LEU* 1.3 77.0 - - - +
339E ALA* 1.3 56.7 + - - +
340E GLN 2.9 3.0 + - - -
341E GLY 3.1 6.6 + - - -
343E TYR* 3.7 4.4 - - + +
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Residues in contact with ALA 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E GLY* 4.3 11.1 + - - -
284E LEU* 4.1 3.8 - - - +
288E ASN* 3.2 22.8 + - - +
298E LEU 4.2 2.8 + - - +
299E THR* 3.8 32.2 - - + +
300E PHE* 4.4 4.9 - - + -
335E ASN 2.8 17.4 + - - +
336E GLY* 3.6 13.5 - - - +
337E LEU 2.9 0.4 - - - -
338E ALA* 1.3 77.1 - - - +
340E GLN* 1.3 60.8 + - - +
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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
------------------------------------------------------------
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