Contacts of the helix formed by residues 270 - 275 (chain A) in PDB entry 5AM1
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 SER 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A HIS* 3.2 32.5 - - - +
269A GLU* 1.3 79.4 - - - +
271A TRP* 1.4 78.8 + - - +
272A TYR* 2.9 21.0 + - - +
273A SER* 3.2 10.8 + - - -
274A TRP* 4.3 0.5 - - - -
292A ASP* 3.9 6.9 + - - -
296A TYR* 5.3 0.2 - - - -
449A PHE* 3.7 12.4 - - - -
450A TYR* 3.8 21.3 - - - -
453A GLN* 4.8 7.0 - - - +
454A PHE* 5.5 0.9 - - - -
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Residues in contact with TRP 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A CYS* 4.1 12.3 - - + -
234A PRO* 3.9 27.6 - - + -
237A MET* 4.0 14.1 - - + -
239A HIS* 4.5 5.7 - + - -
251A HIS* 3.9 15.5 - + - -
253A VAL* 3.6 31.6 - - + -
265A HIS* 4.3 0.2 - - - -
270A SER* 1.4 79.4 + - - +
272A TYR* 1.4 79.4 + + - +
273A SER 3.1 0.2 - - - -
274A TRP* 3.0 33.2 + - - +
275A ARG* 5.2 0.7 - - - -
278A ILE* 3.8 25.4 - - + +
290A ALA* 3.4 17.8 - - - +
291A MET 3.2 24.0 + - - +
292A ASP* 3.2 33.0 + - - +
298A GLU* 5.2 1.2 + - - -
449A PHE* 3.7 21.4 - + - -
453A GLN* 4.9 2.9 + - - -
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Residues in contact with TYR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A SER* 4.8 1.2 + - - -
232A CYS 3.4 26.4 + - - -
234A PRO* 3.9 16.8 - - + +
270A SER* 2.9 17.0 + - - +
271A TRP* 1.4 99.1 - + + +
273A SER* 1.3 54.3 + - - +
274A TRP 3.0 5.4 - - - -
275A ARG* 2.9 68.5 + - + +
445A GLU 5.7 0.2 - - - -
446A GLU* 3.5 34.4 + - + +
449A PHE* 3.5 37.2 - + + +
450A TYR* 3.8 9.9 - + - +
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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
----------------------------------------------------------
265A HIS* 4.5 2.7 - - - -
269A GLU* 2.7 42.7 + - - +
270A SER 3.2 12.3 + - - -
271A TRP 3.1 1.2 - - - -
272A TYR* 1.3 76.2 - - - +
274A TRP* 1.4 57.4 + - - +
275A ARG* 3.4 8.2 + - - +
276A TYR* 5.2 1.6 + - - -
277A GLN* 3.9 0.3 - - - +
450A TYR* 2.8 23.0 + - - -
527A GLN* 3.2 34.7 - - - +
528A MET* 4.7 6.4 + - - +
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Residues in contact with TRP 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 3.7 46.1 - - + +
264A CYS 3.6 20.0 - - - +
265A HIS* 3.4 22.6 - - + +
270A SER 4.3 8.5 - - - -
271A TRP* 3.0 20.9 + - - +
273A SER* 1.4 77.0 - - - +
275A ARG* 1.4 56.6 + - - +
276A TYR 3.2 3.8 - - - -
277A GLN* 2.9 49.9 + - + -
278A ILE* 3.0 18.8 + - + +
290A ALA* 4.7 2.9 - - + -
291A MET 5.2 0.4 - - - -
332A ILE* 3.9 35.0 - - + -
333A GLY 4.3 1.8 - - - -
334A HIS* 4.0 7.9 - - + -
358A LEU* 3.9 16.8 - - + -
527A GLN* 3.6 30.1 - - + -
538A LEU* 4.7 3.4 - - + -
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Residues in contact with ARG 275 (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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231A SER* 3.3 27.8 - - - +
232A CYS* 3.3 18.6 - - + +
272A TYR* 2.9 72.0 + - + +
273A SER* 3.4 7.0 + - - +
274A TRP* 1.4 76.7 - - - +
276A TYR* 1.4 75.7 + - + +
278A ILE* 4.2 2.2 - - - +
279A PRO* 3.2 23.7 - - - +
441A MET 4.4 1.0 + - - -
442A VAL* 3.6 23.8 - - - +
446A GLU* 3.3 25.5 + - - +
450A TYR* 3.2 21.6 + - - -
528A MET* 3.6 28.5 - - - +
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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