Contacts of the helix formed by residues 268 - 273 (chain A) in PDB entry 5FHH
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 LEU 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A THR* 3.2 27.2 - - + +
254A ALA 3.2 17.5 - - - +
255A SER* 4.9 2.9 - - - -
266A THR 3.7 0.2 - - - -
267A THR* 1.3 70.2 - - - +
269A HIS* 1.3 69.9 + - - +
270A ALA 3.0 0.8 - - - +
271A PHE* 3.8 14.2 - - + +
272A ALA* 2.9 31.0 + - + +
303A LEU* 5.6 4.5 - - + -
305A ILE* 4.1 21.5 - - + -
311A VAL* 4.8 14.1 - - + -
315A LEU* 4.2 24.5 - - + -
319A LEU* 3.5 34.5 - - + -
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Residues in contact with HIS 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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267A THR* 2.3 23.6 + - - +
268A LEU* 1.3 77.8 - - - +
270A ALA* 1.3 64.7 + - + +
272A ALA* 5.3 0.2 - - - -
273A GLY* 4.2 0.9 - - - -
274A ILE 2.7 29.4 + - - +
275A GLY* 3.2 35.7 - - - -
315A LEU* 6.0 1.5 - - - +
461A SER* 6.2 2.7 - - - -
465A ALA* 4.0 27.4 - - + +
466A GLN* 5.9 0.7 - - + -
534A THR* 5.1 15.2 - - + +
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A THR* 5.0 3.8 - - - -
267A THR* 3.2 17.7 + - - +
268A LEU 3.0 0.8 - - - -
269A HIS* 1.3 79.6 - - + +
271A PHE* 1.3 68.6 + - - +
273A GLY* 2.8 16.5 + - - -
466A GLN* 4.0 24.0 - - + -
531A VAL* 4.5 4.7 - - + -
532A GLN* 3.7 34.0 - - + +
533A ALA 6.0 0.2 - - - -
534A THR* 6.5 1.1 - - - -
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Residues in contact with PHE 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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251A VAL* 3.4 38.1 - - + -
253A THR* 4.6 8.1 - - + -
266A THR* 4.0 23.3 - - - -
267A THR 4.4 0.6 - - - +
268A LEU* 3.4 19.2 + - + +
270A ALA* 1.3 79.0 - - - +
272A ALA* 1.3 67.7 + - + +
273A GLY* 3.0 2.1 + - - -
293A VAL* 4.7 10.9 - - - +
296A GLY* 4.1 22.0 - - - -
297A TRP* 3.4 41.6 + + - +
300A CYS* 4.4 4.9 - - - -
303A LEU* 3.7 20.2 - - + -
319A LEU* 6.2 0.2 - - + -
532A GLN* 5.4 4.7 - - - +
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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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268A LEU* 2.9 24.5 + - + +
269A HIS 4.5 0.4 - - - +
271A PHE* 1.3 83.7 - - + +
273A GLY* 1.3 58.5 + - - +
274A ILE* 3.0 28.9 - - + +
288A ALA* 4.7 0.7 - - - +
293A VAL* 3.0 18.7 - - - +
297A TRP* 5.0 6.7 - - - -
315A LEU* 6.2 0.9 - - + -
319A LEU* 3.7 33.9 - - + -
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Residues in contact with GLY 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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269A HIS 3.6 2.1 + - - -
270A ALA 2.8 18.8 + - - -
271A PHE 3.0 0.4 - - - -
272A ALA* 1.3 79.4 - - - +
274A ILE* 1.3 60.1 + - - +
287A LEU* 3.0 30.7 - - - +
293A VAL* 3.8 18.6 - - - -
533A ALA 4.8 1.6 - - - -
534A THR* 4.2 14.0 - - - -
535A GLY 4.0 2.6 + - - -
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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