Contacts of the helix formed by residues 245 - 258 (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 THR 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A TYR* 1.3 74.2 - - - +
246A PRO* 1.3 67.7 - - + +
247A GLU* 2.7 40.4 - - + +
248A GLU* 2.6 51.7 + - - +
249A ILE* 2.9 12.4 + - - +
96I ARG* 4.3 2.1 + - - +
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Residues in contact with PRO 246 (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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244A TYR 3.8 3.8 - - - +
245A THR* 1.3 90.5 - - + +
247A GLU* 1.3 69.2 + - - +
249A ILE* 3.8 5.0 - - + +
250A ALA* 2.9 22.0 + - - +
282A PHE* 4.5 18.2 - - + +
283A ASN* 3.1 33.8 + - - +
286A ALA* 3.2 24.6 - - + +
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Residues in contact with GLU 247 (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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245A THR* 2.7 34.9 - - + +
246A PRO* 1.3 89.5 - - - +
248A GLU* 1.3 53.6 + - + +
250A ALA* 3.1 7.4 + - - +
251A MET* 2.8 37.3 + - - +
286A ALA* 4.1 15.1 - - - +
289A ARG* 5.0 10.2 + - - -
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Residues in contact with GLU 248 (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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199A LEU* 3.7 12.8 - - + +
244A TYR* 3.0 19.6 - - + +
245A THR* 2.6 40.8 + - - +
247A GLU* 1.3 78.1 - - + +
249A ILE* 1.3 60.8 + - - +
251A MET* 3.3 8.0 + - - +
252A ALA* 3.1 18.2 + - - +
96I ARG* 2.4 35.7 + - - -
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Residues in contact with ILE 249 (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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199A LEU* 4.4 9.9 - - + -
233A MET* 4.7 5.6 - - + -
234A VAL 3.5 20.8 - - - +
235A THR* 3.9 21.8 - - + -
236A PRO* 4.8 3.8 - - + -
244A TYR* 4.3 20.6 - - + +
245A THR 2.9 14.5 + - - +
246A PRO* 3.8 8.3 - - + +
248A GLU* 1.3 72.1 - - - +
250A ALA* 1.3 63.3 + - - +
252A ALA* 3.3 2.6 + - - +
253A THR* 2.9 39.4 + - - +
279A GLU* 5.9 2.2 - - - +
283A ASN* 3.8 36.6 - - + +
287A ILE* 5.5 1.3 - - + -
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Residues in contact with ALA 250 (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 2.9 19.2 + - - +
247A GLU* 3.4 5.6 - - - +
249A ILE* 1.3 76.8 - - - +
251A MET* 1.3 57.7 + - - +
254A VAL* 2.9 37.2 + - - +
286A ALA* 3.5 8.3 - - + +
287A ILE* 3.4 46.9 - - + +
290A CYS* 4.5 5.8 - - + -
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Residues in contact with MET 251 (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 2.8 16.8 + - - +
248A GLU* 3.5 10.1 - - - +
249A ILE 3.2 0.2 - - - -
250A ALA* 1.3 78.3 - - - +
252A ALA* 1.3 54.5 - - - +
254A VAL* 4.2 1.0 - - - +
255A THR* 2.7 40.5 + - - +
290A CYS* 3.9 5.1 - - - -
291A PRO* 3.8 33.7 - - + -
292A LEU* 3.6 28.9 - - + +
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Residues in contact with ALA 252 (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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199A LEU* 3.9 13.9 - - + -
203A GLN* 3.4 24.5 - - - +
234A VAL* 3.3 25.8 - - + -
248A GLU 3.1 15.8 + - - +
249A ILE 3.8 1.8 - - - +
251A MET* 1.3 73.4 - - - +
253A THR* 1.3 59.7 + - - +
255A THR* 3.3 2.0 + - - -
256A ALA* 2.9 31.5 + - - +
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Residues in contact with THR 253 (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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232A ASN 5.2 0.7 - - - +
233A MET* 3.7 11.5 - - - +
234A VAL* 2.9 34.0 + - + +
249A ILE* 2.9 22.1 + - - +
250A ALA 3.8 2.5 - - - -
252A ALA* 1.3 77.0 - - - +
254A VAL* 1.3 63.2 + - + +
256A ALA* 3.4 2.3 + - - +
257A LEU* 3.0 26.4 + - + +
270A PHE* 3.3 40.2 - - + -
287A ILE* 3.8 14.1 - - + +
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Residues in contact with VAL 254 (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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250A ALA 2.9 20.6 + - - +
251A MET 4.2 0.4 - - - +
253A THR* 1.3 74.0 - - + +
255A THR* 1.3 67.0 + - - +
257A LEU* 3.3 6.6 + - + +
258A ARG* 2.9 43.2 + - + +
287A ILE* 3.8 30.1 - - + +
290A CYS* 4.0 19.5 - - + -
292A LEU* 3.8 14.6 - - + -
294A ARG* 3.8 23.1 - - + -
296A TRP* 6.0 0.9 - - + +
298A LEU* 4.3 7.6 - - + -
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Residues in contact with THR 255 (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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203A GLN* 3.7 8.1 - - - +
251A MET* 2.7 27.9 + - - +
252A ALA* 3.6 4.4 - - - -
254A VAL* 1.3 79.8 - - - +
256A ALA* 1.3 66.6 + - - +
258A ARG* 3.2 12.0 + - + +
259A ARG* 3.2 61.0 + - + +
292A LEU* 3.6 12.3 - - - +
225D GLU* 4.6 3.1 - - - +
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Residues in contact with ALA 256 (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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203A GLN* 3.9 10.0 - - + +
206A THR* 4.1 13.5 - - + -
207A GLU* 3.7 28.5 - - + -
210A LEU* 5.2 1.3 - - - -
234A VAL* 4.0 11.7 - - + -
252A ALA 2.9 17.3 + - - +
253A THR 3.6 4.0 - - - +
255A THR* 1.3 76.6 - - - +
257A LEU* 1.3 63.4 + - + +
259A ARG* 3.1 14.0 + - - +
260A THR* 3.2 17.8 + - - +
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Residues in contact with LEU 257 (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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206A THR* 5.9 0.9 - - + -
210A LEU* 3.8 17.3 - - + -
229A LEU* 4.0 10.8 - - + -
231A PRO* 4.3 6.3 - - + -
253A THR* 3.0 19.8 + - + +
254A VAL* 3.8 6.5 - - + +
256A ALA* 1.3 79.7 - - + +
258A ARG* 1.3 59.2 + - - +
259A ARG 3.2 0.5 + - - -
260A THR* 4.0 2.5 - - - -
261A VAL* 2.8 49.6 + - + +
268A VAL* 3.8 16.6 - - + -
270A PHE* 3.5 34.5 - - + -
296A TRP* 3.4 17.2 - - + +
298A LEU* 3.9 13.9 - - + -
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Residues in contact with ARG 258 (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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254A VAL* 2.9 42.6 + - + +
255A THR* 3.4 13.0 - - + +
257A LEU* 1.3 75.8 - - - +
259A ARG* 1.3 56.4 + - + +
260A THR 3.4 0.4 - - - -
292A LEU* 4.0 19.6 - - - +
293A PRO* 3.0 48.9 + - - +
294A ARG* 6.3 0.4 - - + -
295A PRO* 5.9 0.2 - - - +
296A TRP* 3.8 14.1 - - + -
225D GLU* 5.5 4.0 + - - +
262D PRO* 3.7 0.2 - - - +
263D PRO* 3.3 38.6 + - + +
264D ALA* 2.8 50.0 + - + +
295D PRO* 5.1 5.7 + - - +
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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