Contacts of the helix formed by residues 245 - 258 (chain I) 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 THR 245 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244I TYR* 1.3 74.2 - - - +
246I PRO* 1.3 66.5 - - + +
247I GLU* 2.7 40.6 - - + +
248I GLU* 2.6 52.7 + - - +
249I ILE* 2.9 12.6 + - - +
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Residues in contact with PRO 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I TYR 3.8 4.0 - - - +
245I THR* 1.3 89.4 - - + +
247I GLU* 1.3 69.4 + - - +
249I ILE* 3.8 5.1 - - + +
250I ALA* 2.9 21.5 + - - +
282I PHE* 4.5 18.6 - - + +
283I ASN* 3.1 33.6 + - - +
286I ALA* 3.2 24.6 - - + +
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Residues in contact with GLU 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245I THR* 2.7 35.5 - - + +
246I PRO* 1.3 90.7 - - - +
248I GLU* 1.3 52.9 + - + +
250I ALA* 3.1 7.2 + - - +
251I MET* 2.8 38.2 + - - +
286I ALA* 4.1 14.6 - - - +
289I ARG* 5.0 10.2 + - - -
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Residues in contact with GLU 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199I LEU* 3.7 12.3 - - + +
243I LYS 4.0 2.4 - - - +
244I TYR* 3.0 30.3 - - + +
245I THR* 2.6 46.1 + - - +
247I GLU* 1.3 78.6 - - + +
249I ILE* 1.3 61.4 + - - +
251I MET* 3.3 7.7 + - - +
252I ALA* 3.1 18.2 + - - +
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Residues in contact with ILE 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199I LEU* 4.4 10.1 - - + -
233I MET* 4.7 6.1 - - + -
234I VAL 3.5 20.8 - - - +
235I THR* 3.9 21.1 - - + -
236I PRO* 4.8 4.0 - - + -
244I TYR* 4.3 20.0 - - + +
245I THR 2.9 13.7 + - - +
246I PRO* 3.8 8.7 - - + +
248I GLU* 1.3 73.8 - - - +
250I ALA* 1.3 63.3 + - - +
252I ALA* 3.3 2.4 + - - +
253I THR* 2.9 39.4 + - - +
279I GLU* 5.9 1.8 - - - +
283I ASN* 3.8 37.0 - - + +
287I ILE* 5.5 1.6 - - + -
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Residues in contact with ALA 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246I PRO 2.9 19.0 + - - +
247I GLU* 3.4 4.9 - - - +
249I ILE* 1.3 76.8 - - - +
251I MET* 1.3 59.0 + - - +
254I VAL* 2.9 36.7 + - - +
286I ALA* 3.5 9.2 - - + +
287I ILE* 3.4 46.4 - - + +
290I CYS* 4.5 6.3 - - + -
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Residues in contact with MET 251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247I GLU 2.8 17.7 + - - +
248I GLU* 3.5 10.5 - - - +
250I ALA* 1.3 77.3 - - - +
252I ALA* 1.3 54.0 + - - +
254I VAL* 4.2 0.7 - - - +
255I THR* 2.7 41.1 + - - +
290I CYS* 3.9 5.6 - - - -
291I PRO* 3.8 32.8 - - + -
292I LEU* 3.6 28.9 - - + +
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Residues in contact with ALA 252 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199I LEU* 3.9 14.8 - - + -
203I GLN* 3.4 24.3 - - - +
234I VAL* 3.3 25.4 - - + -
248I GLU 3.1 15.9 + - - +
249I ILE 3.8 1.3 - - - +
251I MET* 1.3 74.4 - - - +
253I THR* 1.3 61.4 + - - +
255I THR* 3.3 1.6 + - - -
256I ALA* 2.9 31.9 + - - +
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Residues in contact with THR 253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I ASN 5.2 0.4 - - - +
233I MET* 3.7 11.2 - - - +
234I VAL* 2.9 33.6 + - + +
249I ILE* 2.9 21.7 + - - +
250I ALA 3.8 2.7 - - - -
252I ALA* 1.3 78.0 - - - +
254I VAL* 1.3 64.0 + - + +
256I ALA* 3.4 1.6 + - - +
257I LEU* 3.0 25.8 + - + +
270I PHE* 3.3 40.6 - - + -
287I ILE* 3.8 13.2 - - + -
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Residues in contact with VAL 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250I ALA 2.9 21.0 + - - +
251I MET 4.2 0.7 - - - +
253I THR* 1.3 74.0 - - + +
255I THR* 1.3 67.8 + - - +
257I LEU* 3.3 6.6 + - + +
258I ARG* 2.9 43.5 + - + +
287I ILE* 3.8 28.7 - - + +
290I CYS* 4.0 20.4 - - + -
292I LEU* 3.8 14.6 - - + -
294I ARG* 3.8 24.0 - - + -
296I TRP* 6.0 0.9 - - + +
298I LEU* 4.3 7.9 - - + -
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Residues in contact with THR 255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203I GLN* 3.7 7.4 - - - +
251I MET* 2.7 27.3 + - - +
252I ALA* 3.6 4.9 - - - -
254I VAL* 1.3 79.2 - - - +
256I ALA* 1.3 65.9 + - - +
258I ARG* 3.2 11.2 + - + +
259I ARG* 3.2 62.2 + - + +
292I LEU* 3.6 14.2 - - + +
225L GLU* 4.4 3.4 - - - +
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Residues in contact with ALA 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203I GLN* 3.9 10.3 - - + +
206I THR* 4.1 14.4 - - + -
207I GLU* 3.7 28.3 - - + -
210I LEU* 5.2 1.3 - - - -
234I VAL* 4.0 10.8 - - + -
252I ALA 2.9 17.9 + - - +
253I THR 3.6 4.3 - - - +
255I THR* 1.3 77.2 - - - +
257I LEU* 1.3 64.2 + - + +
259I ARG* 3.1 14.7 + - - +
260I THR* 3.2 17.3 + - - +
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Residues in contact with LEU 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206I THR* 5.9 0.7 - - + -
210I LEU* 3.8 17.7 - - + -
229I LEU* 4.0 10.8 - - + -
231I PRO* 4.3 5.8 - - + -
253I THR* 3.0 19.3 + - + +
254I VAL* 3.8 7.2 - - - +
256I ALA* 1.3 80.0 - - + +
258I ARG* 1.3 58.2 + - - +
259I ARG 3.2 0.9 + - - -
260I THR* 4.0 2.2 - - - -
261I VAL* 2.8 49.5 + - + +
268I VAL* 3.8 16.6 - - + -
270I PHE* 3.5 34.5 - - + -
296I TRP* 3.4 17.5 - - + +
298I LEU* 3.9 14.1 - - + -
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Residues in contact with ARG 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254I VAL* 2.9 43.4 + - + +
255I THR* 3.4 13.0 - - + +
257I LEU* 1.3 76.6 - - - +
259I ARG* 1.3 55.9 + - + +
260I THR 3.4 0.7 - - - -
292I LEU* 4.0 19.8 - - - +
293I PRO* 3.0 48.0 + - - +
294I ARG* 6.3 0.2 - - + -
295I PRO* 5.7 0.2 - - - +
296I TRP* 3.8 14.4 - - + -
225L GLU* 5.6 3.8 + - - +
263L PRO* 3.3 37.2 + - + +
264L ALA* 2.6 50.8 + - + +
295L PRO* 5.1 6.1 + - - +
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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