Contacts of the strand formed by residues 267 - 273 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A MET* 3.8 15.5 - - + +
242A ILE* 3.8 28.9 - - + -
260A TRP 4.2 0.4 - - - +
261A ASP 3.7 17.5 - - - +
262A PHE* 3.4 12.8 - - + -
264A LEU* 3.1 29.2 + - + +
266A ARG* 1.3 76.1 - - - +
268A LYS* 1.3 57.0 + - - +
269A SER 3.6 20.9 - - - +
270A ILE* 3.6 21.1 - - + -
290A ARG* 3.3 22.7 + - - -
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Residues in contact with LYS 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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140A ARG* 3.6 33.8 - - - +
144A ARG* 4.7 4.8 - - - +
239A ASP* 3.0 33.2 + - + +
240A MET 3.0 6.1 + - - +
262A PHE* 3.8 2.7 - - - -
265A PRO 3.5 20.0 - - - +
266A ARG* 3.0 22.2 + - - +
267A VAL* 1.3 74.0 - - - +
269A SER* 1.3 62.4 + - - +
289A TRP* 3.4 2.8 - - - -
290A ARG* 3.0 35.4 + - + +
294A ALA* 3.4 21.7 - - + +
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Residues in contact with SER 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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133A GLY* 4.3 7.3 + - - -
137A MET* 5.3 0.2 - - - +
140A ARG* 4.6 6.6 + - - -
240A MET 3.8 2.3 + - - -
241A HIS* 2.8 34.3 + - - +
242A ILE 3.2 19.6 + - - -
262A PHE* 3.8 1.8 - - - -
267A VAL* 3.6 3.5 - - - +
268A LYS* 1.3 78.8 - - - +
270A ILE* 1.3 70.1 + - - +
287A VAL* 4.6 1.3 - - - -
288A ILE 3.1 13.9 - - - -
289A TRP* 3.5 26.4 + - - -
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Residues in contact with ILE 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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108A TRP* 3.4 36.4 - - + -
241A HIS* 3.6 3.8 + - - -
242A ILE* 3.4 17.0 - - + +
244A ALA* 4.2 0.9 - - + -
260A TRP* 3.9 19.5 - - + -
261A ASP* 3.8 34.5 - - + -
262A PHE* 3.7 28.5 - - + +
267A VAL* 3.6 11.2 - - + -
269A SER* 1.3 80.9 - - - +
271A SER* 1.3 69.2 + - - +
287A VAL* 3.2 4.0 - - - +
288A ILE 2.8 30.8 + - - -
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Residues in contact with SER 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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108A TRP* 4.1 2.7 - - - -
126A SER* 4.9 2.8 + - - -
129A ALA* 3.7 22.7 - - - -
130A CYS* 4.0 12.1 - - - -
241A HIS* 2.7 29.0 + - - -
242A ILE 3.1 5.9 + - - -
243A ASP* 4.0 7.3 + - - -
244A ALA* 2.8 32.9 + - - +
245A ALA 4.5 0.9 - - - -
270A ILE* 1.3 76.3 - - - +
272A ALA* 1.3 59.9 + - - +
286A TRP 3.1 11.4 - - - -
287A VAL* 4.1 1.8 - - - -
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Residues in contact with ALA 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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108A TRP* 3.5 28.0 - - + -
126A SER* 3.2 12.0 + - - -
244A ALA 3.5 19.1 - - - +
245A ALA* 3.8 5.6 - - - +
248A GLY* 4.6 0.2 - - - -
249A PHE* 3.8 17.5 - - + -
271A SER* 1.3 77.2 - - - +
273A SER* 1.3 59.4 + - - +
285A GLY* 3.5 1.9 - - - -
286A TRP* 2.8 31.0 + - + +
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Residues in contact with SER 273 (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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126A SER* 2.6 21.0 + - - +
245A ALA* 3.1 18.8 + - - +
249A PHE* 3.7 16.3 - - - -
272A ALA* 1.3 70.3 - - - +
274A GLY* 1.3 64.2 + - - +
275A HIS* 4.0 9.2 - - - -
276A LYS* 2.8 48.2 + - - +
277A PHE 4.3 0.2 + - - -
278A GLY 3.8 2.9 + - - -
284A CYS 3.9 3.6 - - - -
285A GLY* 4.3 1.3 - - - -
467A PO4 3.2 4.8 + - - -
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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