Contacts of the helix formed by residues 320 - 339 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H ALA 3.3 20.0 - - - +
314H TRP* 3.3 24.7 - - - +
315H ARG* 4.4 4.5 - - - +
317H GLN* 3.2 19.2 + - - +
319H ASP* 1.3 90.0 + - - +
321H ALA* 1.3 65.0 + - - +
322H GLY 3.4 0.4 - - - -
323H ALA* 3.1 13.9 + - + +
324H ALA* 2.8 22.9 + - - +
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Residues in contact with ALA 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H VAL* 3.6 12.4 - - + +
314H TRP* 4.2 12.6 - - + +
317H GLN 3.4 5.3 + - - +
318H ARG* 3.2 22.4 - - + +
319H ASP 2.9 2.4 + - - +
320H ASN* 1.3 75.3 - - - +
322H GLY* 1.3 58.7 + - - +
324H ALA* 3.1 6.2 + - - +
325H THR* 2.9 33.0 + - - +
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Residues in contact with GLY 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H ASP 3.8 5.4 + - - -
320H ASN 3.4 0.4 - - - -
321H ALA* 1.3 77.9 - - - +
323H ALA* 1.3 57.1 + - - +
325H THR* 3.3 8.8 + - - -
326H GLU* 3.0 33.9 + - - +
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Residues in contact with ALA 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H ALA* 4.4 10.8 - - + -
319H ASP 4.8 1.2 + - - +
320H ASN* 3.1 17.3 + - + +
322H GLY* 1.3 72.4 - - - +
324H ALA* 1.3 66.8 + - - +
326H GLU* 3.0 11.5 + - - +
327H GLU* 2.9 26.5 + - - +
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Residues in contact with ALA 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H VAL* 3.3 18.4 - - + -
310H ALA* 3.2 32.2 - - - +
313H ALA* 3.8 7.4 - - - +
314H TRP* 3.5 15.9 - - + +
320H ASN 2.8 12.6 + - - +
321H ALA 3.3 9.2 - - - +
323H ALA* 1.3 76.4 - - - +
325H THR* 1.3 63.3 + - - +
327H GLU* 3.0 14.4 + - - +
328H PHE* 3.1 9.7 + - - +
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Residues in contact with THR 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H VAL* 2.8 32.9 + - - +
65H SER* 3.8 9.6 + - - +
66H ALA* 3.6 31.0 - - + +
67H ASP 5.1 0.2 - - - +
321H ALA 2.9 15.8 + - - -
322H GLY* 3.5 11.9 - - - -
324H ALA* 1.3 75.7 - - - +
326H GLU* 1.3 60.2 + - - +
328H PHE* 3.4 5.7 + - + +
329H ILE* 3.0 40.9 + - + +
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Residues in contact with GLU 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H ARG* 2.5 44.4 + - - -
322H GLY 3.0 20.4 + - - +
323H ALA* 3.0 12.1 + - - +
325H THR* 1.3 76.7 - - - +
327H GLU* 1.3 70.0 + - - +
329H ILE* 3.2 7.9 + - - +
330H LYS* 2.8 30.5 + - - +
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Residues in contact with GLU 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H SER* 3.1 38.0 - - - +
310H ALA* 3.5 14.4 - - - -
313H ALA* 4.7 6.4 - - + +
323H ALA* 2.9 15.6 + - - +
324H ALA* 3.0 9.8 + - - +
326H GLU* 1.3 78.9 - - - +
328H PHE* 1.3 61.3 - - - +
330H LYS* 3.4 30.3 + - - +
331H ARG* 3.2 28.5 + - - +
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Residues in contact with PHE 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 3.7 38.4 - - + -
62H VAL 5.0 0.7 - - - -
63H LEU* 3.4 46.7 - - + -
66H ALA* 3.9 17.5 - - + -
70H VAL* 4.0 19.1 - - + -
74H ILE* 4.7 4.9 - - + -
306H LEU* 3.6 30.7 - - + -
310H ALA* 3.8 12.3 - - + +
324H ALA 3.1 10.2 + - - +
325H THR* 3.5 8.3 - - - +
326H GLU 3.1 0.6 - - - -
327H GLU* 1.3 72.9 - - - +
329H ILE* 1.3 72.3 + - - +
330H LYS 2.9 2.2 + - - -
331H ARG* 2.9 4.0 + - - +
332H ALA* 2.8 35.3 + - + -
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Residues in contact with ILE 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H ALA* 3.7 32.5 - - + -
67H ASP* 3.8 18.6 - - - +
69H ARG* 3.6 62.4 - - + +
70H VAL* 4.8 5.2 - - + +
325H THR* 3.0 22.9 + - + +
326H GLU* 3.7 7.2 - - - +
328H PHE* 1.3 76.4 - - + +
330H LYS* 1.3 62.1 + - - +
332H ALA* 3.6 7.9 - - - +
333H GLU* 2.9 29.8 + - + +
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Residues in contact with LYS 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H ARG* 5.6 1.1 - - - +
326H GLU* 2.8 18.2 + - - +
327H GLU* 3.4 33.8 + - - +
328H PHE 3.0 0.2 - - - -
329H ILE* 1.3 76.2 - - - +
331H ARG* 1.3 65.8 + - + +
333H GLU* 3.0 12.8 + - - +
334H VAL* 2.8 29.7 + - + +
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Residues in contact with ARG 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H GLU* 2.8 67.1 + - - +
278H GLU* 2.5 30.3 + - - -
281H SER* 3.0 16.6 + - - -
305H ALA 3.6 3.7 + - - +
306H LEU* 3.7 20.2 - - + +
309H SER* 4.0 3.1 - - - +
327H GLU 3.2 16.8 - - - +
328H PHE 2.9 4.8 + - - +
330H LYS* 1.3 80.3 - - + +
332H ALA* 1.3 63.7 + - - +
334H VAL* 3.1 31.6 - - - +
335H ASN* 2.9 38.6 + - - +
343H TYR* 4.4 1.0 + - - -
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Residues in contact with ALA 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H VAL* 4.4 2.5 - - + -
73H CYS* 3.1 25.1 - - - +
74H ILE* 4.0 14.8 - - + -
300H PHE* 4.4 3.4 - - - -
306H LEU* 3.6 10.7 - - - +
328H PHE* 2.8 40.7 + - + +
329H ILE* 3.6 9.0 - - - +
331H ARG* 1.3 72.0 - - - +
333H GLU* 1.3 59.8 + - - +
335H ASN* 4.0 1.6 - - - +
336H GLY* 3.0 21.0 + - - -
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Residues in contact with GLU 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H ARG* 3.2 28.2 + - - +
72H LYS* 2.7 42.1 + - - +
73H CYS* 3.7 12.2 - - - +
329H ILE* 2.9 30.5 + - + +
330H LYS* 3.5 7.5 - - - +
332H ALA* 1.3 74.8 - - - +
334H VAL* 1.3 65.7 + - - +
336H GLY* 3.0 11.3 + - - -
337H LEU* 3.0 17.5 + - + +
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Residues in contact with VAL 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H SER* 3.7 14.1 - - - +
330H LYS* 2.8 25.5 + - + +
331H ARG* 3.1 43.7 - - - +
333H GLU* 1.3 72.6 - - - +
335H ASN* 1.3 57.0 + - - +
337H LEU* 2.9 12.8 + - - +
338H ALA* 2.8 23.9 + - - +
343H TYR* 3.3 43.8 - - + +
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Residues in contact with ASN 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H SER* 2.7 32.1 + - - -
284H LEU* 4.0 2.4 - - + +
300H PHE* 3.5 29.0 - - + -
302H TYR* 3.5 24.7 + - - -
305H ALA 4.0 1.6 + - - -
306H LEU* 3.7 16.0 - - - +
331H ARG* 2.9 42.0 + - - +
332H ALA 4.1 0.4 - - - +
334H VAL* 1.3 73.2 - - - +
336H GLY* 1.3 60.8 + - - +
338H ALA* 3.7 6.6 - - - +
339H ALA* 2.8 29.6 + - - +
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Residues in contact with GLY 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H GLY* 3.2 30.3 - - - -
73H CYS* 3.7 7.2 - - - -
300H PHE* 3.9 6.5 - - - -
332H ALA 3.0 12.8 + - - -
333H GLU 3.0 9.1 + - - -
335H ASN* 1.3 78.8 - - - +
337H LEU* 1.3 60.1 + - - +
339H ALA* 3.6 2.1 - - - +
340H GLN* 3.1 22.4 + - - +
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Residues in contact with LEU 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333H GLU* 3.0 15.0 + - + +
334H VAL* 2.9 10.2 + - - +
336H GLY* 1.3 76.4 - - - +
338H ALA* 1.3 53.8 + - - +
339H ALA 2.9 4.9 - - - -
340H GLN* 2.7 32.2 + - - +
342H LYS* 3.1 51.8 + - + +
343H TYR* 3.8 22.0 - - + -
344H GLU 5.5 0.4 - - - +
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Residues in contact with ALA 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H SER* 3.3 29.4 - - - +
284H LEU* 3.6 9.9 - - + +
285H ASN* 3.2 29.4 - - + +
288H ASN* 2.9 16.5 + - - -
334H VAL 2.8 12.3 + - - +
335H ASN* 3.7 12.6 - - - +
337H LEU* 1.3 76.6 - - - +
339H ALA* 1.3 56.5 + - - +
340H GLN 3.0 2.6 + - - -
341H GLY 3.1 6.9 + - - -
343H TYR* 3.7 5.5 - - + +
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Residues in contact with ALA 339 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H GLY* 4.3 10.9 + - - -
284H LEU* 4.2 3.6 - - - -
288H ASN* 3.2 22.6 + - - +
298H LEU 4.2 3.0 + - - +
299H THR* 3.8 32.6 - - + +
300H PHE* 4.4 4.9 - - + -
335H ASN 2.8 16.5 + - - +
336H GLY* 3.6 13.0 - - - +
337H LEU 2.9 0.6 - - - -
338H ALA* 1.3 75.5 - - - +
340H GLN* 1.3 61.9 + - - +
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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