Contacts of the helix formed by residues 265 - 272 (chain B) in PDB entry 2XFN
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 PRO 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ARG* 3.6 19.1 - - - +
264B ILE* 1.4 94.1 - - + +
266B PRO* 1.3 77.1 - - + +
267B THR 3.3 0.2 - - - -
268B LEU* 2.9 34.8 + - + +
291B LEU* 4.0 22.4 - - + -
393B TYR 4.7 0.7 - - - +
394B SER* 3.6 19.1 - - - +
427B GLU* 4.1 10.1 - - - +
1500B FAD 3.8 23.1 - - - +
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Residues in contact with PRO 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 4.0 5.4 - - + +
265B PRO* 1.3 81.1 - - + +
267B THR* 1.3 63.2 + - - +
269B GLY* 3.0 13.2 + - - -
282B ARG* 4.6 11.3 + - - +
285B MET* 4.3 7.4 - - + -
286B ILE* 3.4 17.9 - - - +
289B VAL* 4.0 16.8 - - + -
400B THR* 3.7 11.2 - - + +
414B LEU* 3.9 25.4 - - + -
427B GLU* 3.5 40.6 - - + +
428B THR* 5.6 3.4 - - + -
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Residues in contact with THR 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A MET* 3.6 6.9 - - - +
287A THR* 4.2 33.9 + - + -
265B PRO 5.0 0.2 - - - +
266B PRO* 1.3 80.5 - - - +
268B LEU* 1.3 66.0 + - + +
269B GLY 3.1 0.4 - - - -
270B MET* 2.9 30.0 + - - +
286B ILE 2.8 25.5 + - - -
287B THR* 4.7 1.7 - - - -
289B VAL* 3.4 27.9 + - - +
291B LEU* 3.7 23.1 - - + -
395B GLY* 5.8 0.2 - - - -
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A MET* 3.4 26.5 - - + -
287A THR* 5.4 0.4 - - + -
264B ILE* 3.5 19.4 - - + +
265B PRO* 2.9 26.4 + - + +
267B THR* 1.3 80.1 - - + +
269B GLY* 1.3 64.0 + - - +
270B MET 3.0 1.3 - - - -
271B LYS* 3.1 25.5 + - + +
272B ILE* 4.4 1.9 + - - +
392B GLN 3.7 15.0 - - - +
393B TYR* 3.1 41.5 - - + +
394B SER 3.7 19.1 - - - +
395B GLY* 4.7 4.3 - - - +
1500B FAD 4.1 10.0 + - + +
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Residues in contact with GLY 269 (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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262B SER* 5.7 1.1 - - - -
264B ILE* 3.7 14.1 - - - +
265B PRO 3.7 3.2 + - - -
266B PRO 3.0 14.1 + - - -
268B LEU* 1.3 77.6 - - - +
270B MET* 1.4 60.3 + - - +
271B LYS 3.2 0.7 + - - -
272B ILE* 3.2 22.8 + - - +
274B PHE* 3.5 16.7 - - - -
282B ARG* 6.0 1.3 - - - -
286B ILE* 3.9 11.9 - - - +
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Residues in contact with MET 270 (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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267A THR* 3.6 18.8 - - - +
268A LEU* 3.4 33.7 - - + -
270A MET* 3.4 21.1 - - + -
271A LYS* 2.9 49.5 + - + +
267B THR* 2.9 20.2 + - - +
269B GLY* 1.4 76.7 - - - +
271B LYS* 1.3 57.5 + - - +
272B ILE 3.1 1.7 + - - -
283B ASN* 4.8 4.9 - - - +
286B ILE* 3.5 41.8 - - + +
287B THR* 3.7 21.1 - - + -
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Residues in contact with LYS 271 (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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269A GLY 4.7 0.2 + - - -
270A MET* 3.0 52.2 + - + +
271A LYS* 4.1 8.2 - - - +
272A ILE 3.0 17.8 + - - -
273A HIS* 2.9 49.0 + - + +
274A PHE* 5.1 1.4 - - - -
286A ILE* 5.7 1.8 - - - +
235B VAL 3.9 2.6 - - - +
236B ILE* 4.0 4.5 - - - +
268B LEU* 3.5 22.2 - - + +
269B GLY 3.1 1.8 - - - -
270B MET* 1.3 76.0 - - - +
272B ILE* 1.3 59.0 + - - +
273B HIS* 4.2 1.6 + - - -
392B GLN* 3.6 39.1 + - - +
393B TYR* 4.0 17.5 - - + -
1500B FAD 4.6 5.8 - - - +
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Residues in contact with ILE 272 (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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271A LYS* 3.1 17.1 + - - -
10B VAL* 4.4 10.1 - - + -
235B VAL* 3.6 32.3 - - + +
236B ILE 3.6 3.1 - - - -
237B TYR 3.9 6.1 - - - +
238B ILE* 3.8 31.6 - - + +
262B SER* 5.5 3.6 - - - +
264B ILE* 4.1 22.9 - - + -
268B LEU 4.6 2.9 - - - +
269B GLY* 3.2 11.0 + - - +
270B MET 3.1 0.6 - - - -
271B LYS* 1.3 79.8 - - - +
273B HIS* 1.3 71.3 + - - +
274B PHE* 3.3 37.9 - - + -
1500B FAD 4.3 4.7 - - - +
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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