Contacts of the helix formed by residues 320 - 339 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313L ALA 3.3 20.0 - - - +
314L TRP* 3.3 24.6 - - - +
315L ARG* 4.4 4.9 - - - +
317L GLN* 3.2 17.8 + - - +
319L ASP* 1.3 90.6 + - - +
321L ALA* 1.3 63.3 + - - +
322L GLY 3.4 0.7 - - - -
323L ALA* 3.1 13.5 + - + +
324L ALA* 2.8 23.0 + - - +
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Residues in contact with ALA 321 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62L VAL* 3.6 13.4 - - + +
314L TRP* 4.2 12.3 - - + +
317L GLN 3.4 4.9 + - - +
318L ARG* 3.2 22.2 - - + +
319L ASP 2.9 2.4 + - - +
320L ASN* 1.3 76.0 - - - +
322L GLY* 1.3 57.7 + - - +
324L ALA* 3.1 5.6 + - - +
325L THR* 2.9 33.8 + - - +
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Residues in contact with GLY 322 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319L ASP 3.8 5.4 + - - -
320L ASN 3.4 0.4 - - - -
321L ALA* 1.3 78.6 - - - +
323L ALA* 1.3 57.0 + - - +
325L THR* 3.3 8.8 + - - -
326L GLU* 3.0 33.9 + - - +
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Residues in contact with ALA 323 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313L ALA* 4.4 11.0 - - + -
319L ASP 4.8 1.0 + - - +
320L ASN* 3.1 17.5 + - + +
322L GLY* 1.3 71.5 - - - +
324L ALA* 1.3 66.4 + - - +
326L GLU* 3.0 11.1 + - - +
327L GLU* 2.9 26.4 + - - +
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Residues in contact with ALA 324 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62L VAL* 3.3 18.4 - - + -
310L ALA* 3.2 32.3 - - - +
313L ALA* 3.8 7.1 - - - +
314L TRP* 3.5 16.4 - - + +
320L ASN 2.8 13.0 + - - +
321L ALA 3.3 9.4 - - - +
323L ALA* 1.3 76.0 - - - +
325L THR* 1.3 63.3 + - - +
327L GLU* 3.0 14.9 + - - +
328L PHE* 3.1 9.5 + - - +
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Residues in contact with THR 325 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62L VAL* 2.8 32.2 + - - +
63L LEU 4.9 0.2 - - - +
65L SER* 3.8 9.9 + - - +
66L ALA* 3.6 30.5 - - + +
67L ASP 5.1 0.4 - - - +
321L ALA* 2.9 16.5 + - - +
322L GLY* 3.5 11.6 - - - -
323L ALA 3.2 0.2 - - - -
324L ALA* 1.3 75.5 - - - +
326L GLU* 1.3 60.3 + - - +
328L PHE* 3.4 5.4 + - + +
329L ILE* 3.0 41.0 + - + +
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Residues in contact with GLU 326 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L ARG* 2.5 44.4 + - - -
322L GLY 3.0 19.2 + - - +
323L ALA* 3.0 12.1 + - - +
325L THR* 1.3 75.6 - - - +
327L GLU* 1.3 70.2 + - - +
329L ILE* 3.2 7.0 + - - +
330L LYS* 2.8 30.2 + - - +
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Residues in contact with GLU 327 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309L SER* 3.1 38.0 - - - +
310L ALA* 3.5 15.5 - - - +
313L ALA* 4.7 6.2 - - + +
323L ALA* 2.9 15.9 + - - +
324L ALA* 3.0 9.6 + - - +
326L GLU* 1.3 79.0 - - - +
328L PHE* 1.3 60.6 + - - +
330L LYS* 3.4 30.1 + - - +
331L ARG* 3.2 28.9 + - - +
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Residues in contact with PHE 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L LEU* 3.7 39.0 - - + -
62L VAL 5.0 1.3 - - - -
63L LEU* 3.4 46.4 - - + -
66L ALA* 3.9 17.7 - - + -
70L VAL* 4.0 17.7 - - + -
74L ILE* 4.7 4.5 - - + -
306L LEU* 3.6 29.6 - - + -
307L GLN* 5.4 0.2 - - - -
310L ALA* 3.8 12.3 - - + +
324L ALA 3.1 10.2 + - - +
325L THR* 3.5 8.5 - - - +
326L GLU 3.1 0.4 - - - -
327L GLU* 1.3 72.4 - - - +
329L ILE* 1.3 72.7 + - - +
330L LYS 2.9 2.6 + - - -
331L ARG* 2.9 3.8 + - - +
332L ALA* 2.8 33.9 + - + -
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Residues in contact with ILE 329 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L ALA* 3.7 33.0 - - + -
67L ASP* 3.8 19.1 - - - +
69L ARG* 3.6 60.3 - - + +
70L VAL* 4.8 3.8 - - + +
325L THR* 3.0 24.4 + - + +
326L GLU* 3.7 6.5 - - - +
328L PHE* 1.3 75.9 - - + +
330L LYS* 1.3 61.8 + - - +
332L ALA* 3.6 7.6 - - + +
333L GLU* 2.9 31.8 + - + +
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Residues in contact with LYS 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L ARG* 5.6 1.1 - - - +
326L GLU* 2.8 18.8 + - - +
327L GLU* 3.4 33.9 + - - +
328L PHE 2.9 0.2 + - - -
329L ILE* 1.3 75.8 - - - +
331L ARG* 1.3 67.4 + - + +
333L GLU* 3.0 11.9 + - - +
334L VAL* 2.8 29.6 + - + +
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Residues in contact with ARG 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L GLU* 2.8 68.0 + - - +
278L GLU* 2.5 30.5 + - - -
281L SER* 3.0 17.4 + - - -
305L ALA 3.6 3.7 + - - +
306L LEU* 3.7 19.5 - - + +
309L SER* 4.0 3.4 - - - +
327L GLU 3.2 16.6 - - - +
328L PHE 2.9 4.6 + - - +
330L LYS* 1.3 80.9 - - + +
332L ALA* 1.3 62.8 + - - +
334L VAL* 3.1 31.8 - - - +
335L ASN* 2.9 38.6 + - - +
343L TYR* 4.4 0.6 + - - -
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Residues in contact with ALA 332 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70L VAL* 4.4 2.9 - - + -
73L CYS* 3.1 24.6 - - - +
74L ILE* 4.0 14.6 - - + -
300L PHE* 4.4 3.2 - - - -
306L LEU* 3.6 12.0 - - - +
328L PHE* 2.8 39.6 + - + +
329L ILE* 3.6 9.2 - - - +
331L ARG* 1.3 71.9 - - - +
333L GLU* 1.3 57.9 + - - +
335L ASN* 4.0 1.2 - - - +
336L GLY 3.0 20.8 + - - -
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Residues in contact with GLU 333 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L ARG* 3.2 27.8 + - - +
72L LYS* 2.7 42.1 + - - +
73L CYS* 3.7 13.1 - - - +
329L ILE* 2.9 30.4 + - + +
330L LYS* 3.0 7.7 + - - +
332L ALA* 1.3 75.6 - - - +
334L VAL* 1.3 66.5 + - - +
336L GLY* 3.0 11.6 + - - -
337L LEU* 3.0 18.3 + - + +
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Residues in contact with VAL 334 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L SER* 3.7 14.4 - - - +
330L LYS* 2.8 24.9 + - + +
331L ARG* 3.1 43.3 - - - +
333L GLU* 1.3 73.0 - - - +
335L ASN* 1.3 57.2 + - - +
337L LEU* 2.9 12.7 + - - +
338L ALA* 2.8 23.9 + - - +
343L TYR* 3.3 43.5 - - + -
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Residues in contact with ASN 335 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281L SER* 2.7 32.1 + - - -
284L LEU* 4.0 1.7 - - + +
300L PHE* 3.5 27.4 - - + -
302L TYR* 3.5 25.4 + - - -
305L ALA 4.0 1.2 + - - -
306L LEU* 3.7 15.9 - - + +
331L ARG* 2.9 41.8 + - - +
332L ALA 4.1 0.2 - - - +
334L VAL* 1.3 72.7 - - - +
336L GLY* 1.3 61.2 + - - +
338L ALA* 3.7 6.5 - - - +
339L ALA* 2.8 30.5 + - - +
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Residues in contact with GLY 336 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L GLY* 3.2 30.2 - - - -
73L CYS* 3.7 7.9 - - - -
300L PHE* 3.9 6.9 - - - -
332L ALA 3.0 12.3 + - - -
333L GLU 3.0 10.4 + - - -
335L ASN* 1.3 78.0 - - - +
337L LEU* 1.3 58.7 + - - +
339L ALA* 3.6 2.1 - - - +
340L GLN* 3.1 22.8 + - - +
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Residues in contact with LEU 337 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333L GLU* 3.0 15.0 + - + +
334L VAL* 2.9 10.8 + - - +
336L GLY* 1.3 75.1 - - - +
338L ALA* 1.3 53.4 + - - +
339L ALA 2.9 4.9 - - - -
340L GLN* 2.7 32.1 + - - +
341L GLY 3.2 7.1 + - - -
342L LYS* 3.2 45.4 + - + +
343L TYR* 3.8 21.8 - - + -
344L GLU 5.5 0.7 - - - +
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Residues in contact with ALA 338 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281L SER* 3.3 29.6 - - - +
284L LEU* 3.6 9.5 - - + +
285L ASN* 3.2 29.0 - - + +
288L ASN* 2.9 15.9 + - - -
334L VAL 2.8 11.9 + - - +
335L ASN* 3.2 12.5 + - - +
337L LEU* 1.3 77.2 - - - +
339L ALA* 1.3 56.6 + - - +
340L GLN 2.9 2.8 + - - -
341L GLY 3.1 6.6 + - - -
343L TYR* 3.7 5.5 - - + +
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Residues in contact with ALA 339 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C LYS* 5.0 2.6 + - - -
27L GLY* 4.3 11.9 + - - -
284L LEU* 4.1 3.8 - - - +
288L ASN* 3.2 23.1 + - - +
298L LEU 4.2 3.4 + - - +
299L THR* 3.8 32.0 - - + +
300L PHE* 4.4 4.5 - - + -
335L ASN 2.8 17.0 + - - +
336L GLY* 3.6 12.6 - - - +
337L LEU 2.9 0.8 - - - -
338L ALA* 1.3 75.2 - - - +
340L GLN* 1.3 61.5 + - - +
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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
------------------------------------------------------------
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