Contacts of the helix formed by residues 276 - 289 (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 SER 276 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274J GLY 3.8 0.8 + - - -
275J GLN* 1.3 76.1 - - - +
277J GLU* 1.3 66.9 + - - +
278J GLU* 3.0 6.2 + - - +
279J GLU* 3.0 33.4 + - - +
280J ALA* 2.9 21.4 + - - +
305J ALA* 4.9 0.9 - - - -
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Residues in contact with GLU 277 (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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276J SER* 1.3 73.2 - - - +
278J GLU* 1.3 60.9 + - + +
280J ALA* 3.8 2.9 + - - +
281J SER* 2.9 14.2 + - - -
305J ALA* 3.5 24.5 - - - +
306J LEU 4.0 2.9 - - - +
308J ALA* 3.3 25.0 + - + +
309J SER* 2.8 50.1 + - - -
331J ARG* 2.8 52.2 + - - +
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Residues in contact with GLU 278 (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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276J SER* 3.1 5.6 + - - +
277J GLU* 1.3 77.8 - - + +
279J GLU* 1.3 56.6 + - - +
280J ALA 3.1 1.8 - - - -
281J SER* 2.9 3.7 + - - -
282J PHE* 2.7 73.8 + - + -
331J ARG* 2.5 35.0 + - - -
343J TYR* 3.1 14.7 + - - -
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Residues in contact with GLU 279 (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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241F PRO* 5.4 14.9 - - + +
274J GLY 4.7 1.4 - - - +
275J GLN* 3.5 26.4 - - - +
276J SER* 3.0 36.2 + - - +
278J GLU* 1.3 76.4 - - - +
280J ALA* 1.3 57.1 + - - +
282J PHE* 3.9 5.1 - - - +
283J ASN* 3.0 44.3 + - - +
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Residues in contact with ALA 280 (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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272J SER* 4.4 2.9 - - - -
275J GLN* 3.6 19.8 + - + +
276J SER 2.9 15.3 + - - +
277J GLU 3.9 2.2 - - - +
279J GLU* 1.3 77.4 - - - +
281J SER* 1.3 57.5 + - - +
283J ASN* 3.9 1.0 - - - +
284J LEU* 2.8 26.0 + - - +
302J TYR* 3.1 41.4 + - + -
305J ALA* 3.8 14.8 - - + -
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Residues in contact with SER 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J GLU 2.9 15.3 + - - -
278J GLU* 2.9 8.6 + - - -
280J ALA* 1.3 78.3 - - - +
282J PHE* 1.3 58.0 + - - +
284J LEU* 4.5 0.2 - - - -
285J ASN* 2.9 31.6 + - - +
331J ARG* 3.0 17.5 + - - -
334J VAL* 3.7 18.8 - - - +
335J ASN* 2.7 27.0 + - - -
338J ALA* 3.3 7.2 - - - +
343J TYR* 4.4 9.2 - - - -
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Residues in contact with PHE 282 (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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246J PRO* 4.5 15.8 - - + +
278J GLU* 2.7 56.9 + - + +
279J GLU* 3.9 5.8 - - - +
281J SER* 1.3 73.0 - - - +
283J ASN* 1.3 62.2 + - - +
285J ASN* 3.2 7.2 + - - +
286J ALA* 2.8 30.5 + - - +
343J TYR* 3.8 20.6 - + - -
344J GLU 6.0 3.4 - - - -
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Residues in contact with ASN 283 (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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233J MET* 3.7 20.0 - - - +
235J THR* 5.2 0.9 - - - +
246J PRO* 3.1 32.9 - - - +
249J ILE* 3.8 29.6 - - + +
250J ALA* 4.6 0.3 + - - +
275J GLN* 2.7 20.5 - - - +
279J GLU* 3.0 26.5 + - - +
280J ALA 3.9 0.9 - - - +
282J PHE* 1.3 77.3 - - - +
284J LEU* 1.3 64.5 + - - +
286J ALA* 3.2 5.5 + - - +
287J ILE* 2.9 28.5 + - - +
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Residues in contact with LEU 284 (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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233J MET* 4.1 5.3 - - + +
270J PHE* 4.2 13.5 - - + -
280J ALA 2.8 23.3 + - - +
281J SER* 3.8 3.4 - - - +
283J ASN* 1.3 72.4 - - - +
285J ASN* 1.3 63.1 + - - +
287J ILE* 3.1 9.1 + - + +
288J ASN* 3.0 22.3 + - - +
298J LEU 3.3 25.8 - - - +
299J THR 3.8 12.1 - - - +
300J PHE* 3.7 41.5 - - + -
302J TYR* 3.5 11.0 - - + +
335J ASN* 4.0 15.0 - - - +
338J ALA* 3.7 11.7 - - + +
339J ALA* 4.1 3.1 - - - +
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Residues in contact with ASN 285 (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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281J SER 2.9 19.1 + - - +
282J PHE* 3.4 7.0 - - - +
284J LEU* 1.3 75.8 - - - +
286J ALA* 1.3 65.4 + - - +
288J ASN* 2.9 13.9 + - - +
289J ARG* 3.0 45.0 + - - +
338J ALA* 3.2 15.7 - - + +
341J GLY* 3.0 13.8 + - - -
343J TYR* 2.9 52.2 + - + +
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Residues in contact with ALA 286 (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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246J PRO* 3.2 38.8 - - + +
247J GLU* 4.1 14.1 - - - +
250J ALA* 3.5 7.1 - - + +
282J PHE 2.8 16.9 + - - +
283J ASN 3.5 7.4 - - - +
285J ASN* 1.3 73.4 - - - +
287J ILE* 1.3 58.4 + - - +
289J ARG* 2.9 24.7 + - - +
290J CYS* 3.0 10.9 + - - -
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Residues in contact with ILE 287 (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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233J MET* 4.0 24.0 - - + -
249J ILE* 5.3 1.1 - - + -
250J ALA* 3.4 26.0 - - - -
253J THR* 3.8 13.7 - - + +
254J VAL* 3.8 9.9 - - + +
270J PHE* 3.8 36.3 - - + -
283J ASN* 2.9 18.8 + - + +
284J LEU* 3.1 10.1 + - + +
286J ALA* 1.3 76.1 - - - +
288J ASN* 1.3 59.4 - - - +
290J CYS* 3.0 25.2 + - - +
294J ARG* 3.6 6.6 - - - -
298J LEU* 3.4 28.9 - - + -
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Residues in contact with ASN 288 (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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284J LEU* 3.0 14.5 + - - +
285J ASN 2.9 4.7 + - - +
287J ILE* 1.3 73.1 - - - +
289J ARG* 1.3 59.2 + - - +
294J ARG* 2.8 33.6 + - - +
298J LEU* 2.8 40.4 + - - +
338J ALA 2.9 20.5 + - - +
339J ALA* 3.2 21.1 - - - +
340J GLN* 3.9 4.6 - - - +
341J GLY* 3.4 23.4 - - - +
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Residues in contact with ARG 289 (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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247J GLU* 5.0 9.5 + - - -
285J ASN* 3.0 27.2 + - - +
286J ALA* 2.9 14.6 + - - +
288J ASN* 1.3 79.8 - - - +
290J CYS* 1.3 66.7 + - - +
291J PRO* 3.5 6.1 - - - +
294J ARG* 4.3 0.2 - - - -
341J GLY* 2.8 31.4 + - - +
344J GLU* 5.2 8.5 + - - -
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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
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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