Contacts of the helix formed by residues 320 - 339 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313J ALA 3.3 19.1 - - - +
314J TRP* 3.3 25.1 - - - +
315J ARG* 4.4 4.3 - - - +
317J GLN* 3.2 19.4 + - - +
319J ASP* 1.3 88.8 + - - +
321J ALA* 1.3 65.5 + - - +
322J GLY 3.4 0.7 - - - -
323J ALA* 3.1 12.9 + - + +
324J ALA* 2.8 22.9 + - - +
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Residues in contact with ALA 321 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J VAL* 3.6 11.9 - - + +
314J TRP* 4.2 13.0 - - + +
317J GLN 3.5 5.7 + - - +
318J ARG* 3.2 22.4 - - + +
319J ASP 2.9 2.2 + - - +
320J ASN* 1.3 75.1 - - - +
322J GLY* 1.3 57.8 + - - +
324J ALA* 3.1 5.8 + - - +
325J THR* 2.9 33.0 + - - +
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Residues in contact with GLY 322 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319J ASP 3.8 5.4 + - - -
320J ASN 3.4 0.4 - - - -
321J ALA* 1.3 78.3 - - - +
323J ALA* 1.3 57.6 + - - +
325J THR* 3.3 9.1 + - - -
326J GLU* 3.0 32.9 + - - +
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Residues in contact with ALA 323 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313J ALA* 4.4 11.2 - - + -
319J ASP 4.8 1.2 + - - +
320J ASN* 3.1 17.0 + - + +
322J GLY* 1.3 71.3 - - - +
324J ALA* 1.3 66.8 + - - +
326J GLU* 3.0 11.3 + - - +
327J GLU* 2.9 26.4 + - - +
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Residues in contact with ALA 324 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J VAL* 3.3 18.6 - - + -
310J ALA* 3.2 31.5 - - - +
313J ALA* 3.8 7.3 - - - +
314J TRP* 3.5 16.6 - - + +
320J ASN 2.8 12.4 + - - +
321J ALA 3.3 9.4 - - - +
323J ALA* 1.3 76.4 - - - +
325J THR* 1.3 62.6 + - - +
327J GLU* 3.0 14.2 + - - +
328J PHE* 3.1 9.9 + - - +
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Residues in contact with THR 325 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62J VAL* 2.8 32.6 + - - +
65J SER* 3.8 9.8 + - - +
66J ALA* 3.6 31.0 - - + +
67J ASP 5.1 0.2 - - - +
321J ALA* 2.9 15.4 + - - +
322J GLY* 3.5 12.3 - - - -
324J ALA* 1.3 76.3 - - - +
326J GLU* 1.3 60.2 + - - +
328J PHE* 3.4 5.3 + - + +
329J ILE* 3.0 40.7 + - + +
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Residues in contact with GLU 326 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J ARG* 2.5 43.6 + - - -
322J GLY 3.0 19.6 + - - +
323J ALA* 3.0 12.5 + - - +
325J THR* 1.3 77.9 - - - +
327J GLU* 1.3 69.5 + - - +
328J PHE 3.1 0.2 + - - -
329J ILE* 3.2 7.6 + - - +
330J LYS* 2.8 29.5 + - - +
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Residues in contact with GLU 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309J SER* 3.1 38.5 - - - +
310J ALA* 3.5 15.3 - - - +
313J ALA* 4.7 6.6 - - + +
323J ALA* 2.9 16.0 + - - +
324J ALA* 3.4 9.9 - - - +
326J GLU* 1.3 79.7 - - - +
328J PHE* 1.3 60.8 + - - +
330J LYS* 3.4 29.6 + - - +
331J ARG* 3.2 28.7 + - + +
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Residues in contact with PHE 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J LEU* 3.7 38.8 - - + -
62J VAL 5.0 0.9 - - - -
63J LEU* 3.4 48.9 - - + -
66J ALA* 3.9 17.3 - - + -
70J VAL* 4.0 18.4 - - + -
74J ILE* 4.7 4.5 - - + -
306J LEU* 3.6 29.8 - - + -
310J ALA* 3.8 12.5 - - + +
324J ALA 3.1 10.7 + - - +
325J THR* 3.5 8.3 - - - +
326J GLU 3.1 0.4 - - - -
327J GLU* 1.3 72.2 - - - +
329J ILE* 1.3 71.8 + - - +
330J LYS 2.9 2.6 + - - -
331J ARG* 2.9 4.2 + - - +
332J ALA* 2.8 35.7 + - + -
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Residues in contact with ILE 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J ALA* 3.7 32.3 - - + -
67J ASP* 3.8 18.4 - - - +
69J ARG* 3.6 61.5 - - + +
70J VAL* 4.8 5.4 - - + +
325J THR* 3.0 22.6 + - + +
326J GLU* 3.7 7.0 - - - +
328J PHE* 1.3 76.9 - - + +
330J LYS* 1.3 62.5 + - - +
332J ALA* 3.6 7.5 - - - +
333J GLU* 2.9 31.0 + - + +
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Residues in contact with LYS 330 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J ARG* 5.6 1.1 - - - +
326J GLU* 2.8 18.6 + - - +
327J GLU* 3.4 35.3 + - - +
328J PHE 3.0 0.2 - - - -
329J ILE* 1.3 76.4 - - - +
331J ARG* 1.3 65.3 + - + +
333J GLU* 3.0 12.4 + - - +
334J VAL* 2.8 29.5 + - + +
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Residues in contact with ARG 331 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J GLU* 2.8 67.6 + - - +
278J GLU* 2.5 30.0 + - - -
281J SER* 3.0 17.0 + - - -
305J ALA 3.6 4.0 + - - +
306J LEU* 3.7 19.5 - - + +
309J SER* 4.0 3.1 - - - +
327J GLU 3.2 16.4 - - - +
328J PHE 2.9 4.6 + - - +
330J LYS* 1.3 80.6 - - + +
332J ALA* 1.3 63.5 + - - +
334J VAL* 3.1 31.5 - - - +
335J ASN* 2.9 38.4 + - - +
343J TYR* 4.4 1.0 + - - -
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Residues in contact with ALA 332 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J VAL* 4.4 2.7 - - + -
73J CYS* 3.1 24.7 - - - +
74J ILE* 4.0 14.6 - - + -
300J PHE* 4.4 3.4 - - - -
306J LEU* 3.6 11.1 - - + +
328J PHE* 2.8 39.9 + - + +
329J ILE* 3.6 8.7 - - - +
331J ARG* 1.3 73.2 - - - +
333J GLU* 1.3 58.7 + - - +
335J ASN* 4.0 2.0 - - - +
336J GLY* 3.0 20.6 + - - -
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Residues in contact with GLU 333 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J ARG* 3.2 28.1 + - - +
72J LYS* 2.7 41.8 + - - +
73J CYS* 3.7 12.9 - - - +
329J ILE* 2.9 30.7 + - + +
330J LYS* 3.5 7.3 - - - +
332J ALA* 1.3 75.6 - - - +
334J VAL* 1.3 66.7 + - - +
336J GLY* 3.0 11.4 + - - -
337J LEU* 3.0 17.3 + - + +
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Residues in contact with VAL 334 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281J SER* 3.7 14.4 - - - +
330J LYS* 2.8 24.9 + - + +
331J ARG* 3.1 44.4 - - - +
333J GLU* 1.3 72.4 - - - +
335J ASN* 1.3 56.7 + - - +
337J LEU* 2.9 13.0 + - - +
338J ALA* 2.8 23.6 + - - +
343J TYR* 3.3 43.5 - - + -
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Residues in contact with ASN 335 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281J SER* 2.7 31.7 + - - -
284J LEU* 4.0 1.7 - - - +
300J PHE* 3.5 28.8 - - + -
302J TYR* 3.5 25.7 + - - -
305J ALA 4.0 1.2 + - - -
306J LEU* 3.7 16.2 - - - +
331J ARG* 2.9 42.2 + - - +
332J ALA 4.1 0.4 - - - +
334J VAL* 1.3 73.2 - - - +
336J GLY* 1.3 60.6 + - - +
338J ALA* 3.7 6.1 - - - +
339J ALA* 2.8 30.0 + - - +
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Residues in contact with GLY 336 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J GLY* 3.2 30.1 - - - -
73J CYS* 3.7 7.4 - - - -
300J PHE* 3.9 6.7 - - - -
332J ALA 3.0 12.8 + - - -
333J GLU 3.0 9.8 + - - -
335J ASN* 1.3 78.4 - - - +
337J LEU* 1.3 60.1 + - - +
339J ALA* 3.6 1.9 - - - +
340J GLN* 3.1 22.6 + - - +
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Residues in contact with LEU 337 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333J GLU* 3.0 15.0 + - + +
334J VAL* 2.9 11.1 + - - +
336J GLY* 1.3 75.8 - - - +
338J ALA* 1.3 52.6 + - - +
339J ALA 2.9 4.7 - - - -
340J GLN* 2.7 32.9 + - - +
342J LYS* 3.1 52.5 + - + +
343J TYR* 3.8 22.4 - - + -
344J GLU 5.5 0.4 - - - +
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Residues in contact with ALA 338 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281J SER* 3.3 29.2 - - - +
284J LEU* 3.6 9.7 - - + +
285J ASN* 3.2 30.6 - - + +
288J ASN* 2.9 16.5 + - - -
334J VAL 2.8 12.1 + - - +
335J ASN* 3.7 11.9 - - - +
337J LEU* 1.3 76.2 - - - +
339J ALA* 1.3 56.7 + - - +
340J GLN 2.9 2.8 + - - -
341J GLY 3.1 6.5 + - - -
343J TYR* 3.7 5.5 - - + +
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Residues in contact with ALA 339 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J GLY* 4.3 10.7 + - - -
284J LEU* 4.2 4.0 - - - -
288J ASN* 3.2 22.0 + - - +
298J LEU 4.2 3.0 + - - +
299J THR* 3.8 32.7 - - + +
300J PHE* 4.4 4.9 - - + -
335J ASN 2.8 16.7 + - - +
336J GLY* 3.6 13.0 - - - +
337J LEU 2.9 0.6 - - - -
338J ALA* 1.3 76.1 - - - +
340J GLN* 1.3 61.0 + - - +
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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