Contacts of the helix formed by residues 265 - 272 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 3.6 19.3 - - - +
264A ILE* 1.4 90.6 - - + +
266A PRO* 1.4 78.6 - - + +
267A THR 3.3 0.2 - - - -
268A LEU* 2.8 36.2 + - + +
269A GLY 3.7 2.8 + - - -
291A LEU* 4.1 15.9 - - + -
393A TYR 4.7 1.1 - - - +
394A SER* 3.6 25.8 - - - +
427A GLU* 4.1 10.1 - - - +
1500A FAD 4.0 20.2 - - + +
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Residues in contact with PRO 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 4.0 5.4 - - + +
265A PRO* 1.4 81.4 - - + +
267A THR* 1.3 62.4 + - - +
269A GLY* 3.0 12.6 + - - -
282A ARG* 4.6 11.5 + - - +
285A MET* 4.3 9.0 - - + -
286A ILE* 3.4 18.3 - - - +
289A VAL* 4.0 15.9 - - + -
400A THR* 3.8 12.1 - - + +
414A LEU* 3.9 24.2 - - + -
427A GLU* 3.5 40.4 - - + +
428A THR* 5.7 3.4 - - + -
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Residues in contact with THR 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PRO* 5.0 0.2 - - + -
266A PRO* 1.3 80.9 - - - +
268A LEU* 1.3 64.0 + - + +
269A GLY 3.0 0.9 - - - -
270A MET* 3.0 30.1 + - - +
286A ILE 2.8 25.7 + - - -
287A THR* 4.8 1.6 - - - -
289A VAL* 3.4 27.4 + - - +
291A LEU* 3.7 23.1 - - + -
395A GLY* 5.8 0.2 - - - -
270B MET* 3.6 6.5 - - + +
287B THR* 4.1 35.9 + - + +
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Residues in contact with LEU 268 (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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264A ILE* 3.6 17.9 - - + +
265A PRO* 2.8 30.6 + - + +
267A THR* 1.3 77.9 - - + +
269A GLY* 1.3 60.7 + - - +
270A MET 3.0 5.6 - - - -
271A LYS* 3.0 29.2 + - + +
272A ILE* 4.4 0.9 + - - +
392A GLN 3.7 15.5 - - - +
393A TYR* 3.2 41.3 - - + +
394A SER 3.7 14.1 - - - +
395A GLY* 4.9 4.3 - - - +
1500A FAD 4.0 11.0 + - + +
270B MET* 3.4 24.9 - - + -
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Residues in contact with GLY 269 (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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262A SER* 5.7 1.3 - - - -
264A ILE* 3.7 13.8 - - - +
265A PRO 3.7 3.2 + - - -
266A PRO 3.0 13.5 + - - -
268A LEU* 1.3 78.3 - - - +
270A MET* 1.3 60.5 + - - +
271A LYS 3.1 0.4 - - - -
272A ILE* 3.2 17.1 + - - +
274A PHE* 3.4 24.0 - - - -
282A ARG* 6.1 1.3 - - - -
286A ILE* 4.0 10.9 - - - +
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Residues in contact with MET 270 (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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267A THR* 3.0 21.4 + - - +
269A GLY* 1.3 77.2 - - - +
271A LYS* 1.3 58.4 + - - +
272A ILE 3.1 0.7 - - - -
283A ASN* 4.8 4.3 - - - +
286A ILE* 3.5 35.9 - - + +
287A THR* 3.7 24.7 - - + -
267B THR* 3.6 19.7 - - - +
268B LEU* 3.4 33.0 - - + -
270B MET* 3.4 25.1 - - + -
271B LYS* 3.0 49.2 + - + +
392B GLN 5.6 0.4 - - - +
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Residues in contact with LYS 271 (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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235A VAL 3.9 2.8 - - - +
236A ILE* 4.0 4.9 - - - +
268A LEU* 3.0 33.0 + - + +
270A MET* 1.3 75.9 - - - +
272A ILE* 1.3 59.1 + - - +
273A HIS* 4.2 1.2 + - - -
392A GLN* 3.6 31.0 + - - +
393A TYR* 4.1 16.8 - - + -
1500A FAD 4.6 7.0 - - - +
269B GLY 4.7 0.2 + - - -
270B MET* 2.9 50.7 + - + +
271B LYS* 4.1 7.8 - - - +
272B ILE 3.1 17.2 + - - -
273B HIS* 2.9 50.3 + - + +
274B PHE* 5.2 1.4 - - - -
286B ILE* 5.7 2.0 - - - +
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Residues in contact with ILE 272 (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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10A VAL* 4.5 7.0 - - + -
235A VAL* 3.6 33.7 - - + +
236A ILE 3.6 3.1 - - - -
237A TYR 3.8 6.3 - - - +
238A ILE* 3.8 31.9 - - + +
262A SER* 5.4 4.0 - - - +
264A ILE* 4.0 24.9 - - + -
268A LEU 4.7 2.0 - - - +
269A GLY* 3.2 9.7 + - - +
270A MET 3.1 0.6 - - - -
271A LYS* 1.3 81.9 - - - +
273A HIS* 1.3 74.2 + - - +
274A PHE* 3.4 33.5 - - + -
1500A FAD 4.4 4.3 - - - +
271B LYS* 3.0 18.1 + - - -
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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