Contacts of the helix formed by residues 241 - 253 (chain B) in PDB entry 1XAI
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 GLY 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ASN 3.1 1.8 + - - -
240B LEU* 1.3 77.3 - - - +
242B HIS* 1.3 59.0 + - - +
243B THR* 3.5 3.7 + - - +
244B PHE 4.6 0.9 - - - -
245B GLY* 3.2 18.6 + - - -
260B VAL* 3.8 7.9 - - - +
263B GLY* 3.3 37.6 - - - -
264B ILE* 3.9 6.3 - - - -
267B GLN* 4.5 5.6 - - - +
323B MET* 6.1 2.4 - - - +
324B VAL 4.5 5.3 + - - +
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Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B GLU* 4.1 0.9 - - - -
181B LYS* 3.7 12.3 - - + -
238B LEU 3.4 18.2 - - - -
239B ASN* 3.0 29.2 + - - +
240B LEU 3.0 16.2 + - - -
241B GLY* 1.3 77.6 - - - +
243B THR* 1.3 62.0 + - - +
244B PHE 3.3 0.7 - - - -
245B GLY* 3.3 4.7 - - - +
246B HIS* 2.5 48.2 + + - +
256B HIS* 3.6 13.0 + + - -
260B VAL* 3.8 13.4 - - + +
313B ASP* 5.0 0.2 - - - -
501B CRB 3.2 19.8 + - + -
601B ZN 2.1 36.5 - - - -
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Residues in contact with THR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASN 4.2 2.5 + - - -
241B GLY* 3.5 1.5 + - - -
242B HIS* 1.3 80.7 - - - +
244B PHE* 1.3 60.2 + - - +
246B HIS* 4.4 2.3 - - - +
247B ALA* 3.7 15.6 + - - +
309B TYR* 5.5 1.0 - - - -
310B MET* 3.6 24.6 - - + +
313B ASP* 3.5 23.1 + - + +
315B LYS* 2.8 27.1 + - - +
321B VAL* 4.5 6.3 - - + -
322B GLN 3.6 8.4 + - - +
323B MET* 3.6 36.3 - - + +
324B VAL 4.5 1.9 + - - -
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Residues in contact with PHE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B GLY* 4.3 2.0 + - - -
243B THR* 1.3 78.4 - - - +
245B GLY* 1.3 66.7 + - - +
247B ALA* 3.2 5.9 + - + +
248B VAL* 3.1 38.1 + - + +
262B VAL* 4.2 9.6 - - + -
263B GLY* 4.2 8.5 - - - +
266B TYR* 3.4 62.1 - + + -
301B LEU* 3.9 11.2 - - + -
303B PHE* 5.8 2.5 - + - -
306B LEU* 3.5 35.0 - - + -
310B MET* 4.0 22.2 - - + -
323B MET* 5.5 0.8 - - + +
346B CYS* 3.8 22.4 - - + -
349B LEU* 3.7 15.3 - - + -
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Residues in contact with GLY 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B GLY 3.2 21.5 + - - -
242B HIS* 3.1 4.2 + - - -
244B PHE* 1.3 79.1 - - - +
246B HIS* 1.3 56.7 + - - +
248B VAL* 3.2 2.6 + - - -
249B GLU* 2.9 30.4 + - - +
256B HIS* 6.0 0.9 - - - -
259B ALA* 3.3 28.3 - - - +
260B VAL* 4.5 3.4 - - - -
263B GLY* 4.1 0.6 - - - -
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Residues in contact with HIS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LYS* 3.5 23.4 + - + +
146B ASN* 4.6 0.4 - - - -
239B ASN* 4.7 1.4 + - - -
242B HIS* 2.5 36.7 + + + +
243B THR* 4.4 2.2 - - - +
245B GLY* 1.3 71.7 - - - -
247B ALA* 1.3 61.4 + - - +
249B GLU* 3.3 22.9 - - - +
250B TYR* 3.2 20.4 + - - +
256B HIS* 3.7 21.9 - + - -
309B TYR* 3.5 25.9 + - + +
313B ASP* 5.4 5.6 + - - +
314B LYS* 5.2 2.9 + - - -
501B CRB 3.0 43.1 + - + -
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B THR 3.7 11.7 + - - +
244B PHE* 3.2 12.0 + - + +
245B GLY 3.1 0.8 - - - -
246B HIS* 1.3 80.1 - - - +
248B VAL* 1.3 49.8 + - - +
250B TYR* 4.7 0.3 - - - +
251B TYR* 2.7 38.1 + - - +
306B LEU* 3.1 25.7 - - + +
309B TYR* 3.8 17.7 - - + -
310B MET* 3.9 21.5 - - + -
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B PHE* 3.1 35.1 + - + +
245B GLY* 3.2 4.4 + - - +
247B ALA* 1.3 75.9 - - - +
249B GLU* 1.3 59.5 + - - +
252B HIS* 2.7 55.7 + - - +
253B LYS 3.6 0.3 + - - -
254B ILE* 3.9 24.6 - - + +
259B ALA* 4.4 7.0 - - + +
262B VAL* 5.0 8.3 - - + -
297B MET* 4.8 3.1 - - + -
301B LEU* 3.9 23.1 - - + -
306B LEU* 4.0 12.1 - - + -
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Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B GLU* 4.7 6.9 - - + +
145B LYS* 2.8 39.9 + - - +
245B GLY 2.9 14.8 + - - +
246B HIS* 3.3 17.6 - - - +
248B VAL* 1.3 75.4 - - - +
250B TYR* 1.3 62.0 + - - +
253B LYS* 2.6 35.3 + - - -
254B ILE* 3.8 19.7 - - - +
256B HIS* 3.1 33.6 + - - +
259B ALA* 3.9 11.9 - - + +
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Residues in contact with TYR 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ASN* 5.0 8.7 - - + -
141B SER 3.1 21.3 + - - -
142B LYS* 3.0 29.3 + - - -
143B GLN 4.4 0.9 - - - -
144B GLY* 4.2 14.1 - - - -
145B LYS* 4.3 7.6 - - + +
246B HIS 3.2 7.7 + - - +
249B GLU* 1.3 85.4 - - - +
251B TYR* 1.3 63.3 - - + +
253B LYS* 3.3 22.8 - - - +
309B TYR* 3.2 42.8 - + + +
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Residues in contact with TYR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ALA 2.7 19.0 + - - +
248B VAL* 4.7 0.2 - - - -
249B GLU 3.2 0.4 - - - -
250B TYR* 1.3 86.7 - - + +
252B HIS* 1.3 97.3 + + - +
253B LYS* 3.3 5.4 - - - +
300B ASP 4.7 1.4 + - - -
302B ASP* 3.1 28.8 + - + +
305B THR* 3.3 31.1 + - + -
306B LEU* 3.1 32.8 - - + -
309B TYR* 5.4 4.0 - - + -
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Residues in contact with HIS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B VAL* 2.7 26.0 + - + +
251B TYR* 1.3 111.5 - + - +
253B LYS* 1.3 74.2 + - - +
254B ILE* 3.3 18.2 + - + +
297B MET* 3.9 17.5 - - + +
300B ASP* 3.4 16.5 + - + +
301B LEU* 3.4 47.2 - - + +
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Residues in contact with LYS 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B GLU* 2.6 16.0 + - - -
250B TYR* 3.3 20.2 - - - +
251B TYR 4.3 4.9 - - - +
252B HIS* 1.3 83.6 - - - +
254B ILE* 1.3 58.0 + - - +
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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
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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