Contacts of the helix formed by residues 263 - 272 (chain X) in PDB entry 3FEW
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 263 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261X HIS 5.0 3.4 - - - +
262X LYS* 1.3 75.9 - - - +
264X PRO* 1.3 76.0 - - + +
265X GLU* 3.7 13.5 + - - +
266X GLU* 2.9 41.2 + - - +
267X ILE* 3.0 20.1 + - - +
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Residues in contact with PRO 264 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245X TYR* 5.2 1.3 - - - +
262X LYS 4.5 1.3 - - - +
263X THR* 1.3 85.8 - - - +
265X GLU* 1.3 65.2 + - - +
267X ILE* 3.0 14.2 + - + +
268X TYR* 2.9 60.0 + - + +
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Residues in contact with GLU 265 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239X ARG* 6.2 1.1 - - - +
263X THR* 3.2 17.1 - - - +
264X PRO* 1.3 85.6 - - - +
266X GLU* 1.3 63.2 + - + +
268X TYR* 3.4 18.4 + - + +
269X GLU* 3.1 22.3 + - - +
274X ASN* 4.8 2.9 + - - -
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Residues in contact with GLU 266 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256X MET* 4.0 2.8 - - - +
261X HIS 4.5 1.4 - - - +
262X LYS* 3.4 27.9 + - + +
263X THR* 2.9 51.3 + - - +
265X GLU* 1.3 78.6 - - + +
267X ILE* 1.3 62.9 - - - +
269X GLU* 3.5 7.5 + - - +
270X ALA* 3.1 23.6 + - - +
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Residues in contact with ILE 267 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245X TYR* 3.6 24.5 - - + +
253X ALA* 3.9 29.6 - - + +
256X MET* 3.7 16.8 - - + -
257X ASP* 4.0 13.5 - - + +
262X LYS* 3.8 24.5 - - + +
263X THR 3.0 20.9 + - - +
264X PRO* 3.0 12.0 + - + +
266X GLU* 1.3 74.9 - - - +
268X TYR* 1.3 65.1 + - - +
270X ALA* 3.2 2.3 + - - +
271X LEU* 3.1 42.5 + - + +
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Residues in contact with TYR 268 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239X ARG* 4.2 14.4 - - - +
242X VAL* 3.4 40.5 - - + +
245X TYR* 3.3 28.9 + + - -
264X PRO* 2.9 40.7 + - + +
265X GLU* 3.4 17.7 + - + +
267X ILE* 1.3 75.6 - - - +
269X GLU* 1.3 62.1 + - - +
271X LEU* 3.3 1.9 + - - -
272X GLY 3.3 4.0 + - - -
273X PHE* 2.9 60.6 + + + +
274X ASN* 4.5 1.6 - - - +
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Residues in contact with GLU 269 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265X GLU 3.1 13.8 + - - +
266X GLU* 3.7 10.8 - - - +
267X ILE 3.3 0.2 - - - -
268X TYR* 1.3 74.6 - - - +
270X ALA* 1.3 65.0 + - + +
272X GLY* 3.1 14.9 + - - -
273X PHE 4.9 0.2 - - - +
274X ASN* 2.8 42.4 + - - +
275X ASN* 5.4 3.1 - - - +
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Residues in contact with ALA 270 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256X MET* 3.5 35.7 - - + -
266X GLU 3.1 10.5 + - - +
267X ILE 3.2 0.9 + - - +
269X GLU* 1.3 78.6 - - - +
271X LEU* 1.3 62.5 - - - +
272X GLY 3.7 0.3 + - - -
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Residues in contact with LEU 271 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243X ARG* 4.7 1.7 + - - -
245X TYR* 3.6 36.3 - - + -
249X GLU* 4.2 33.5 - - + +
252X LYS* 4.1 34.5 - - + +
253X ALA* 4.5 1.1 - - + -
256X MET* 4.7 8.3 - - - -
267X ILE* 3.1 26.7 + - + +
269X GLU 3.2 0.2 - - - -
270X ALA* 1.3 79.7 - - - +
272X GLY* 1.3 59.9 + - - +
273X PHE* 3.4 21.6 + - + -
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Residues in contact with GLY 272 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243X ARG* 6.0 0.4 - - - -
269X GLU 3.1 13.5 + - - -
270X ALA 3.3 1.8 + - - -
271X LEU* 1.3 78.7 - - - +
273X PHE* 1.3 63.5 + - - +
274X ASN 2.9 8.0 + - - -
275X ASN* 2.9 40.1 + - - +
276X GLU 4.6 0.5 + - - -
280X ARG* 5.5 0.5 + - - -
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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