Contacts of the strand formed by residues 267 - 273 (chain D) in PDB entry 3FZ7
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 VAL 267 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240D MET* 3.8 12.6 - - - +
242D ILE* 3.7 29.8 - - + -
260D TRP 4.0 3.6 - - - +
261D ASP 3.4 27.1 - - - +
262D PHE* 3.2 23.5 - - + -
264D LEU* 3.1 20.7 + - + +
266D ARG* 1.3 73.4 - - - +
268D LYS* 1.3 57.0 + - - +
269D SER 3.6 10.3 - - - +
270D ILE* 3.6 31.4 - - + -
290D ARG* 3.2 14.7 + - - -
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Residues in contact with LYS 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D ARG* 3.6 34.7 - - - +
239D ASP* 2.9 37.3 + - + +
240D MET 3.1 5.6 + - - +
262D PHE* 3.8 2.5 - - - -
265D PRO 3.4 20.6 - - - +
266D ARG 3.1 15.1 + - - +
267D VAL* 1.3 75.8 - - - +
269D SER* 1.3 63.5 + - - +
289D TRP* 3.4 3.5 - - - -
290D ARG* 3.0 35.5 + - - +
294D ALA* 3.5 17.5 - - + +
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Residues in contact with SER 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D GLY* 4.4 6.3 + - - -
140D ARG* 4.7 6.1 + - - -
240D MET 3.8 2.1 + - - -
241D HIS* 2.7 36.4 + - - +
242D ILE 3.1 21.5 + - - -
262D PHE* 3.7 2.7 - - - -
267D VAL* 3.5 3.5 - - - +
268D LYS* 1.3 82.0 - - - +
270D ILE* 1.3 67.5 + - - +
287D VAL* 4.7 0.7 - - - -
288D ILE 3.2 14.4 - - - -
289D TRP* 3.4 26.1 + - - -
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Residues in contact with ILE 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D TRP* 3.3 35.1 - - + -
241D HIS* 3.8 3.6 - - - -
242D ILE* 3.6 12.3 - - + +
244D ALA* 4.0 3.8 - - + -
260D TRP* 3.7 20.4 - - + -
261D ASP* 3.8 31.9 - - + -
262D PHE* 3.5 32.1 - - + +
267D VAL* 3.6 12.6 - - + -
269D SER* 1.3 81.4 - - - +
271D SER* 1.3 70.8 + - - +
287D VAL* 3.2 3.5 - - - +
288D ILE 2.9 30.8 + - - -
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Residues in contact with SER 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D TRP* 4.0 2.0 - - - -
126D SER* 4.9 2.4 + - - -
129D ALA* 3.7 21.8 - - - -
130D CYS* 3.8 16.7 - - - -
241D HIS* 2.7 28.6 + - - -
242D ILE 3.2 6.0 + - - -
243D ASP* 4.1 4.2 + - - -
244D ALA* 2.8 32.5 + - - +
245D ALA* 4.2 0.9 - - - -
270D ILE* 1.3 76.2 - - - +
272D ALA* 1.3 62.6 + - - +
286D TRP 3.1 11.4 - - - -
287D VAL* 4.2 2.0 - - - -
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Residues in contact with ALA 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D TRP* 3.5 27.3 - - + -
126D SER* 3.4 9.2 + - - -
244D ALA 3.4 13.5 - - - +
245D ALA* 3.7 9.2 - - - +
248D GLY* 4.3 0.9 - - - -
249D PHE* 3.7 19.7 - - + -
271D SER* 1.3 78.1 - - - +
273D SER* 1.3 59.8 + - - +
274D GLY 3.9 0.2 - - - -
285D GLY* 3.5 1.9 - - - -
286D TRP* 2.8 31.7 + - + +
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Residues in contact with SER 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D SER* 2.7 22.4 + - - +
245D ALA* 2.9 20.1 + - - +
249D PHE* 3.8 7.0 - - - -
272D ALA* 1.3 71.8 - - - +
274D GLY* 1.3 62.6 + - - +
275D HIS* 3.8 16.6 - - - -
276D LYS* 3.0 43.9 + - - -
277D PHE 4.0 0.9 + - - -
278D GLY 3.7 10.4 + - - -
284D CYS 3.9 4.3 - - - -
285D GLY* 4.2 2.0 - - - -
467D PO4 3.6 1.4 + - - -
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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