Contacts of the helix formed by residues 276 - 289 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274D GLY 3.8 0.8 + - - -
275D GLN* 1.3 76.6 - - - +
277D GLU* 1.3 66.9 + - - +
278D GLU* 3.0 6.2 + - - +
279D GLU* 3.0 32.4 + - - +
280D ALA* 2.9 20.8 + - - +
305D ALA* 4.9 1.1 - - - -
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Residues in contact with GLU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D SER* 1.3 74.0 - - - +
278D GLU* 1.3 61.5 + - + +
280D ALA* 3.8 3.1 + - - +
281D SER* 2.9 14.2 + - - -
305D ALA* 3.5 24.8 - - - +
306D LEU 4.0 2.8 - - - -
308D ALA* 3.3 25.2 + - + +
309D SER* 2.8 51.2 + - - -
331D ARG* 2.8 51.6 + - - +
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Residues in contact with GLU 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D SER* 3.1 5.4 + - - +
277D GLU* 1.3 78.0 - - + +
279D GLU* 1.3 57.2 + - - +
280D ALA 3.1 1.6 - - - -
281D SER* 2.9 4.1 + - - -
282D PHE* 2.7 73.6 + - + -
331D ARG* 2.5 35.0 + - - -
343D TYR* 3.1 14.2 + - - -
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Residues in contact with GLU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ILE* 5.9 2.1 - - - +
274D GLY 4.7 1.0 - - - +
275D GLN* 3.5 27.4 - - + +
276D SER* 3.0 36.1 + - - +
278D GLU* 1.3 75.8 - - - +
280D ALA* 1.3 56.5 + - - +
282D PHE* 3.9 4.6 - - - +
283D ASN* 3.0 44.9 + - - +
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Residues in contact with ALA 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D SER* 4.4 2.9 - - - -
275D GLN* 3.6 20.4 + - + +
276D SER 2.9 16.7 + - - +
277D GLU 3.9 1.8 - - - +
279D GLU* 1.3 76.9 - - - +
281D SER* 1.3 57.6 + - - +
283D ASN* 3.9 1.0 - - - +
284D LEU* 2.8 26.2 + - - +
302D TYR* 3.1 41.8 + - + -
305D ALA* 3.8 14.4 - - + -
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Residues in contact with SER 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D GLU 2.9 15.0 + - - -
278D GLU* 2.9 8.2 + - - -
280D ALA* 1.3 77.5 - - - +
282D PHE* 1.3 58.7 + - - +
284D LEU* 4.5 0.2 - - - -
285D ASN* 2.9 31.1 + - - +
331D ARG* 3.0 17.1 + - - -
334D VAL* 3.7 19.2 - - - +
335D ASN* 2.7 25.3 + - - -
338D ALA* 3.3 8.1 - - - +
343D TYR* 4.4 8.7 - - - -
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Residues in contact with PHE 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D PRO* 4.5 15.4 - - + +
278D GLU* 2.7 54.9 + - + +
279D GLU* 3.9 5.6 - - - +
281D SER* 1.3 72.3 - - - +
283D ASN* 1.3 62.6 + - - +
285D ASN* 3.2 7.4 + - - +
286D ALA* 2.8 30.1 + - - +
343D TYR* 3.8 20.9 - + - -
344D GLU 6.0 3.4 - - - -
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Residues in contact with ASN 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D MET* 3.7 19.6 - - - +
235D THR* 5.2 1.2 - - - +
246D PRO* 3.1 33.9 - - - +
249D ILE* 3.8 29.2 - - + +
250D ALA* 4.6 0.2 - - - +
275D GLN* 2.7 20.9 - - - +
279D GLU* 3.0 27.5 + - - +
280D ALA 3.9 0.4 - - - +
282D PHE* 1.3 77.7 - - - +
284D LEU* 1.3 64.3 + - - +
286D ALA* 3.2 6.8 + - - +
287D ILE* 2.9 29.7 + - - +
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Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D MET* 4.1 4.8 - - + +
270D PHE* 4.2 13.2 - - + -
280D ALA 2.8 22.9 + - - +
281D SER* 3.8 3.4 - - - +
283D ASN* 1.3 72.4 - - - +
285D ASN* 1.3 64.7 + - - +
287D ILE* 3.1 9.1 + - + +
288D ASN* 3.0 20.9 + - - +
298D LEU 3.3 26.2 - - - +
299D THR 3.8 12.1 - - - +
300D PHE* 3.7 41.5 - - + -
302D TYR* 3.5 9.4 - - + +
335D ASN* 4.0 14.1 - - - +
338D ALA* 3.7 13.5 - - + +
339D ALA* 4.1 3.8 - - - +
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Residues in contact with ASN 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D SER 2.9 18.1 + - - +
282D PHE* 3.4 7.2 - - - +
284D LEU* 1.3 76.4 - - - +
286D ALA* 1.3 63.5 + - - +
288D ASN* 2.9 14.7 + - - +
289D ARG* 3.0 45.2 + - - +
338D ALA* 3.2 15.1 - - + +
341D GLY* 3.0 14.9 + - - -
343D TYR* 2.9 51.8 + - + +
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Residues in contact with ALA 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D PRO* 3.2 39.5 - - + +
247D GLU* 4.1 15.0 - - - +
250D ALA* 3.5 7.5 - - + +
282D PHE 2.8 16.3 + - - +
283D ASN 3.5 7.0 - - - +
285D ASN* 1.3 73.8 - - - +
287D ILE* 1.3 58.5 + - - +
289D ARG* 2.9 25.3 + - - +
290D CYS* 3.0 10.7 + - - -
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Residues in contact with ILE 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D MET* 4.0 24.5 - - + -
249D ILE* 5.5 1.1 - - + -
250D ALA* 3.4 25.5 - - - +
253D THR* 3.8 13.5 - - + +
254D VAL* 3.8 9.7 - - + +
270D PHE* 3.8 34.8 - - + -
283D ASN* 2.9 19.0 + - - +
284D LEU* 3.2 9.9 - - + +
286D ALA* 1.3 76.3 - - - +
288D ASN* 1.3 57.8 + - - +
290D CYS* 3.0 25.2 + - - +
294D ARG* 3.6 6.8 - - - -
298D LEU* 3.4 29.4 - - + -
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Residues in contact with ASN 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D LEU* 3.0 14.5 + - - +
285D ASN 2.9 4.5 + - - +
287D ILE* 1.3 74.1 - - - +
289D ARG* 1.3 60.2 + - - +
294D ARG* 2.8 33.4 + - - +
298D LEU* 2.8 39.9 + - - +
338D ALA 2.9 20.5 + - - +
339D ALA* 3.2 21.8 - - - +
340D GLN* 3.9 4.9 - - - +
341D GLY* 3.4 23.1 + - - +
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Residues in contact with ARG 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D GLU* 5.0 9.3 + - - -
285D ASN* 3.0 26.6 + - - +
286D ALA* 2.9 14.6 + - - +
288D ASN* 1.3 79.7 - - - +
290D CYS* 1.3 66.6 + - - +
291D PRO* 3.5 5.5 - - - +
341D GLY* 2.8 32.2 + - - +
344D GLU* 5.2 8.1 + - - -
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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