Contacts of the helix formed by residues 263 - 271 (chain A) in PDB entry 1FO4
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 GLU 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A THR* 1.3 82.1 + - - +
264A ILE* 1.3 66.1 + - - +
265A GLY 3.2 0.9 - - - -
266A ILE* 2.9 12.3 + - - +
267A GLU* 2.4 54.2 + - - +
354A THR* 3.2 38.1 - - + +
394A ARG* 3.4 14.2 + - - -
3006A FAD 2.8 41.6 + - - +
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Residues in contact with ILE 264 (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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256A LYS* 3.8 20.6 - - + -
258A VAL* 3.9 26.2 - - + -
261A ASN* 3.5 10.8 - - - +
263A GLU* 1.3 72.3 - - - +
265A GLY* 1.3 63.5 + - - +
267A GLU* 3.1 19.1 + - - +
268A MET* 2.9 50.9 + - + +
275A PHE* 4.0 11.2 - - + -
278A ILE* 4.9 2.0 - - + -
3006A FAD 2.8 53.2 + - - +
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Residues in contact with GLY 265 (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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74A LEU* 4.3 11.8 - - - +
261A ASN* 2.9 37.4 + - - -
264A ILE* 1.3 77.0 - - - +
266A ILE* 1.3 57.2 - - - +
268A MET* 3.7 9.7 + - - +
269A LYS* 3.1 30.8 + - - +
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Residues in contact with ILE 266 (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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45A GLU* 3.9 28.0 - - + +
74A LEU* 4.0 15.7 - - + -
261A ASN 4.4 0.2 + - - -
262A THR 3.5 22.2 - - - +
263A GLU* 2.9 13.7 + - - +
265A GLY* 1.3 75.4 - - - +
267A GLU* 1.3 58.5 + - + +
270A PHE* 2.7 65.9 + - + +
271A LYS* 3.6 5.2 + - + +
3006A FAD 4.2 5.6 - - + -
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Residues in contact with GLU 267 (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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256A LYS* 4.8 2.9 - - - -
263A GLU* 2.4 44.5 + - - +
264A ILE* 3.6 18.6 - - - +
266A ILE* 1.3 79.1 - - + +
268A MET* 1.3 57.2 + - - +
271A LYS* 2.9 36.7 + - + +
273A GLN* 3.1 31.6 + - + +
275A PHE* 3.5 24.8 - - + -
354A THR* 5.2 0.3 - - - +
394A ARG* 4.5 5.4 + - - +
3006A FAD 5.2 1.9 + - - -
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Residues in contact with MET 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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22A PRO 6.0 2.0 - - - +
23A GLU* 5.5 18.2 - - - +
76A PRO* 6.1 0.9 - - + -
234A VAL* 5.9 3.6 - - - -
261A ASN* 3.8 9.9 - - - +
264A ILE* 2.9 42.2 + - + +
265A GLY* 3.7 14.4 - - - +
267A GLU* 1.3 78.1 - - - +
269A LYS* 1.3 61.5 + - - +
272A ASN* 4.0 9.5 + - - -
273A GLN 3.3 25.3 + - - +
274A LEU* 5.3 2.5 - - - -
275A PHE* 4.2 19.7 - - + +
278A ILE* 4.6 14.1 - - + -
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Residues in contact with LYS 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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44A GLY* 4.7 7.4 - - - +
74A LEU* 6.3 0.2 - - + -
265A GLY 3.1 18.2 + - - +
268A MET* 1.3 81.1 - - - +
270A PHE* 1.3 91.6 + - + +
272A ASN* 4.9 1.3 + - - +
679A GLU* 2.7 44.5 + - - +
828A ASP* 3.2 23.7 + - - -
830A ASN* 5.8 1.0 + - - +
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Residues in contact with PHE 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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43A CYS 4.0 13.2 - - - -
44A GLY 3.4 26.7 - - - -
45A GLU* 4.2 19.7 - - + -
266A ILE* 2.7 50.0 + - + +
269A LYS* 1.3 100.6 - - + +
271A LYS* 1.3 66.6 + - + +
272A ASN* 3.4 9.7 + - - -
828A ASP* 6.1 1.6 - - + -
829A ARG* 6.4 0.7 - - + -
830A ASN* 3.7 35.7 - - + -
1222A ARG 5.9 0.2 - - - -
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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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266A ILE* 3.6 6.2 + - + +
267A GLU* 2.9 31.4 + - + +
270A PHE* 1.3 83.1 - - + +
272A ASN* 1.3 74.5 + - - +
273A GLN* 3.1 23.1 + - + +
393A TYR* 6.0 1.8 + - - -
394A ARG* 6.0 4.3 - - - +
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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