Contacts of the helix formed by residues 266 - 271 (chain A) in PDB entry 2FBW
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 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 3.5 28.3 - - + -
131A GLY* 2.7 40.4 + - - +
253A HIS* 4.0 6.5 + - - +
255A THR* 5.0 0.2 - - - -
264A ILE 3.4 2.8 + - - -
265A THR* 1.3 70.7 + - - +
267A GLY* 1.3 58.7 + - - +
268A CYS 3.0 0.9 - - - -
269A ARG* 2.9 49.1 + - - +
270A GLY* 2.9 21.3 + - - -
294A LEU* 4.7 3.6 - - + -
295A ALA 5.3 0.4 - - - -
297A ARG* 2.9 45.8 + - - +
410A GLY* 4.4 2.1 + - - -
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Residues in contact with GLY 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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128A ARG* 3.9 17.0 - - - -
130A PHE* 3.5 16.0 - - - -
265A THR* 2.6 25.0 + - - -
266A GLU* 1.3 71.2 - - - +
268A CYS* 1.3 50.5 - - - -
270A GLY* 3.5 2.4 - - - -
271A GLU* 2.7 39.9 + - - +
337A LEU* 4.0 7.0 - - - -
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Residues in contact with CYS 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* 3.7 16.2 - - - -
265A THR* 3.0 22.8 + - - +
267A GLY* 1.3 78.0 - - - +
269A ARG* 1.3 55.1 + - + +
271A GLU* 3.4 3.1 + - - +
272A GLY 3.3 5.0 + - - -
273A GLY* 2.7 29.6 + - - -
323A LEU* 4.0 12.6 - - + -
325A LEU* 3.7 20.1 - - + +
328A LEU* 4.8 0.2 - - - +
337A LEU* 3.9 15.5 - - - -
340A ILE* 3.7 35.4 - - - -
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Residues in contact with ARG 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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253A HIS* 4.0 8.1 - - - -
254A PRO* 3.8 24.5 - - - +
255A THR* 4.2 11.7 + - - +
265A THR 5.3 0.4 + - - -
266A GLU* 2.9 58.3 + - - +
268A CYS* 1.3 74.5 - - + +
270A GLY* 1.3 67.6 + - - +
272A GLY* 3.1 13.0 + - - -
273A GLY 3.6 20.3 + - - +
275A LEU* 4.2 16.4 - - + -
293A ASP* 2.8 46.4 + - + +
294A LEU* 3.9 24.9 - - + +
295A ALA 4.8 2.4 + - - -
300A VAL* 4.1 19.0 - - - +
323A LEU* 4.2 15.0 - - + +
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Residues in contact with GLY 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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128A ARG* 5.2 1.2 - - - +
129A ALA* 3.4 45.9 + - - +
266A GLU 2.9 13.4 + - - -
267A GLY* 3.2 4.4 + - - -
269A ARG* 1.3 78.0 - - - +
271A GLU* 1.3 62.0 + - - +
272A GLY* 3.4 0.5 + - - -
294A LEU* 3.8 8.8 - - - +
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Residues in contact with GLU 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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126A TYR* 2.7 29.1 + - - -
128A ARG* 2.9 37.3 + - - +
267A GLY 2.7 25.0 + - - +
268A CYS 3.4 4.0 + - - +
269A ARG 3.2 0.4 - - - -
270A GLY* 1.3 73.4 - - - +
272A GLY* 1.3 56.7 + - - +
273A GLY 3.8 0.7 - - - -
328A LEU* 3.8 12.4 - - + +
332A GLN* 3.0 39.0 + - + +
336A ARG* 3.7 21.1 + - + +
337A LEU* 4.2 13.5 - - + -
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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