Contacts of the helix formed by residues 276 - 289 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A GLY 3.8 0.6 + - - -
275A GLN* 1.3 76.3 - - - +
277A GLU* 1.3 66.0 + - - +
278A GLU* 3.0 6.1 + - - +
279A GLU* 3.0 32.2 + - - +
280A ALA* 2.9 21.7 + - - +
305A ALA* 4.9 1.3 - - - -
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A SER* 1.3 72.5 - - - +
278A GLU* 1.3 61.0 + - + +
280A ALA* 3.9 2.6 - - - +
281A SER* 2.9 14.2 + - - -
305A ALA* 3.5 25.5 - - - +
306A LEU 4.0 2.8 - - - +
308A ALA* 3.3 23.7 + - + +
309A SER* 2.8 51.2 + - - -
331A ARG* 2.8 53.1 + - - +
335A ASN* 4.8 0.2 - - - +
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 3.1 5.0 + - - +
277A GLU* 1.3 78.1 - - + +
279A GLU* 1.3 56.4 + - - +
280A ALA 3.1 1.8 - - - -
281A SER* 2.9 3.6 + - - -
282A PHE* 2.7 74.0 + - + -
331A ARG* 2.5 35.6 + - - -
343A TYR* 3.1 13.3 + - - -
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ILE* 5.9 2.3 - - - +
274A GLY 4.7 1.0 - - - +
275A GLN* 3.5 26.3 - - + +
276A SER* 3.0 36.5 + - - +
278A GLU* 1.3 76.6 - - - +
280A ALA* 1.3 57.3 + - - +
282A PHE* 3.9 4.8 - - - +
283A ASN* 3.0 44.9 + - - +
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A SER* 4.4 2.7 - - - -
275A GLN* 3.6 20.8 + - + +
276A SER 2.9 16.1 + - - +
277A GLU 3.9 1.8 - - - +
279A GLU* 1.3 75.9 - - - +
281A SER* 1.3 58.3 + - - +
283A ASN* 3.8 0.9 - - - +
284A LEU* 2.8 26.2 + - - +
302A TYR* 3.1 42.3 + - + -
305A ALA* 3.8 14.6 - - + -
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Residues in contact with SER 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLU 2.9 14.8 + - - -
278A GLU* 2.9 8.2 + - - -
280A ALA* 1.3 77.7 - - - +
282A PHE* 1.3 58.1 + - - +
285A ASN* 2.9 31.6 + - - +
331A ARG* 3.0 17.5 + - - -
334A VAL* 3.7 19.0 - - - +
335A ASN* 2.7 26.7 + - - -
338A ALA* 3.3 8.7 - - - +
343A TYR* 4.4 8.5 - - - -
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PRO* 4.5 15.4 - - + +
278A GLU* 2.7 55.1 + - + +
279A GLU* 3.9 5.8 - - - +
281A SER* 1.3 71.9 - - - +
283A ASN* 1.3 63.8 + - - +
285A ASN* 3.2 7.1 + - - +
286A ALA* 2.8 30.2 + - - +
343A TYR* 3.8 20.6 - + - -
344A GLU 6.0 3.6 - - - -
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Residues in contact with ASN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A MET* 3.7 19.6 - - - +
235A THR* 5.2 1.2 - - - +
246A PRO* 3.1 33.1 - - - +
249A ILE* 3.8 28.5 - - + +
250A ALA* 4.6 0.2 - - - +
275A GLN* 2.7 21.3 - - - +
279A GLU* 3.0 27.0 + - - +
280A ALA 3.9 0.7 - - - +
282A PHE* 1.3 76.5 - - - +
284A LEU* 1.3 65.8 + - - +
286A ALA* 3.2 6.0 + - - +
287A ILE* 2.9 29.5 + - - +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A MET* 4.1 4.8 - - + +
270A PHE* 4.2 13.7 - - + -
280A ALA 2.8 22.1 + - - +
281A SER* 3.8 3.4 - - - +
283A ASN* 1.3 72.6 - - - +
285A ASN* 1.3 63.7 + - - +
287A ILE* 3.1 10.3 + - + +
288A ASN* 3.0 20.7 + - - +
298A LEU 3.3 26.5 - - - +
299A THR 3.8 11.9 - - - +
300A PHE* 3.7 41.7 - - + -
302A TYR* 3.5 9.6 - - + +
335A ASN* 4.0 14.4 - - - +
338A ALA* 3.7 12.6 - - + +
339A ALA* 4.1 3.4 - - - +
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A SER 2.9 18.6 + - - +
282A PHE* 3.4 6.7 - - - +
284A LEU* 1.3 76.2 - - - +
286A ALA* 1.3 64.2 - - - +
288A ASN* 2.9 15.4 + - - +
289A ARG* 3.0 45.0 + - - +
338A ALA* 3.2 15.3 - - + +
341A GLY* 3.0 14.4 + - - -
343A TYR* 2.9 51.8 + - + +
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PRO* 3.2 38.6 - - + +
247A GLU* 4.1 14.4 - - - +
250A ALA* 3.5 7.3 - - + +
282A PHE 2.8 17.4 + - - +
283A ASN 3.5 7.0 - - - +
285A ASN* 1.3 73.4 - - - +
287A ILE* 1.3 58.5 + - - +
289A ARG* 2.9 24.8 + - - +
290A CYS* 3.0 10.7 + - - -
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Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A MET* 4.0 24.5 - - + -
249A ILE* 5.3 1.1 - - + -
250A ALA* 3.4 25.1 - - - -
253A THR* 3.8 13.7 - - + +
254A VAL* 3.8 10.1 - - + +
270A PHE* 3.8 35.4 - - + -
283A ASN* 2.9 17.9 + - + +
284A LEU* 3.2 10.1 - - + +
286A ALA* 1.3 75.8 - - - +
288A ASN* 1.3 58.6 + - - +
290A CYS* 3.0 25.4 + - - +
294A ARG* 3.6 6.6 - - - -
298A LEU* 3.4 29.4 - - + -
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Residues in contact with ASN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LEU* 3.0 15.4 + - - +
285A ASN 2.9 4.5 + - - +
287A ILE* 1.3 72.9 - - - +
289A ARG* 1.3 59.8 + - - +
294A ARG* 2.8 34.7 + - - +
298A LEU* 2.8 39.6 + - - +
338A ALA 2.9 20.5 + - - +
339A ALA* 3.2 21.5 - - - +
340A GLN* 3.9 4.7 - - - +
341A GLY* 3.4 23.2 + - - +
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLU* 5.0 9.3 + - - -
285A ASN* 3.0 27.1 + - - +
286A ALA* 2.9 14.2 + - - +
288A ASN* 1.3 80.0 - - - +
290A CYS* 1.3 66.2 + - - +
291A PRO* 3.5 5.5 - - - +
294A ARG* 4.3 0.2 - - - -
341A GLY* 2.8 30.9 + - - +
344A GLU* 5.2 7.5 + - - -
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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