Contacts of the strand formed by residues 272 - 277 (chain A) in PDB entry 5M4G
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 MET 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A GLY 4.0 0.7 - - - +
247A SER* 3.4 3.1 - - - -
248A GLY* 2.9 28.1 + - - +
251A SER* 4.1 14.2 + - - +
270A GLY 3.8 1.0 + - - -
271A ASP* 1.3 73.8 - - - +
273A CYS* 1.3 61.5 + - - +
291A SER* 4.5 3.1 - - - -
292A PHE* 3.7 27.1 - - - +
293A PRO* 3.8 14.8 - - - -
298A PHE* 4.2 14.6 - - + -
302A GLN* 3.4 46.9 - - + +
306A TYR* 4.9 0.9 - - + -
446A PHE* 4.1 26.0 + - + +
448A GLY 4.5 6.3 - - - +
449A VAL* 4.0 23.8 - - + -
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Residues in contact with CYS 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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213A VAL* 4.7 1.6 - - - -
246A GLY 3.5 4.0 - - - -
247A SER* 4.4 6.1 - - - -
251A SER* 4.7 0.9 - - - -
267A ILE* 4.3 13.7 - - - -
272A MET* 1.3 80.2 - - - +
274A LEU* 1.3 61.2 + - - +
275A PHE* 3.7 25.4 - - + -
290A CYS 4.5 0.2 - - - -
291A SER* 3.2 6.4 - - - -
292A PHE* 2.7 59.9 + - + +
294A ALA* 3.9 29.4 - - - -
448A GLY 5.1 0.6 - - - +
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Residues in contact with LEU 274 (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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244A ILE* 3.5 9.5 - - + +
246A GLY* 2.8 31.2 + - - -
251A SER* 3.5 37.7 - - - +
273A CYS* 1.3 74.5 - - - +
275A PHE* 1.3 58.9 + - - +
276A ASP* 4.5 4.0 - - + -
289A THR* 3.5 15.3 - - + -
290A CYS 3.7 2.9 - - - -
291A SER* 3.6 10.8 - - - +
416A TYR* 3.8 9.9 - - + -
448A GLY 3.8 9.0 - - - +
450A ARG* 3.5 57.2 - - + +
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Residues in contact with PHE 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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206A HIS* 3.3 10.8 - - + +
209A VAL* 3.5 33.7 - - + -
213A VAL* 3.9 2.5 - - + -
219A GLU* 5.2 1.1 - - + -
222A LEU* 3.7 24.0 - - + -
244A ILE 3.3 3.4 - - - +
245A CYS* 3.6 29.8 - - + -
246A GLY 4.0 4.5 - - - -
247A SER* 5.3 0.9 - - - -
267A ILE* 4.3 12.6 - - + -
273A CYS* 3.7 28.3 - - + -
274A LEU* 1.3 81.8 - - - +
276A ASP* 1.3 60.4 + - - +
277A MET* 3.9 18.8 - - + -
289A THR* 3.3 3.1 - - - -
290A CYS* 2.9 39.8 + - + +
292A PHE* 3.7 21.1 - + + -
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Residues in contact with ASP 276 (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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241A TYR* 2.7 30.8 + - - -
243A CYS* 3.7 0.2 - - - -
244A ILE* 2.9 52.3 + - + +
274A LEU* 4.0 1.3 - - + -
275A PHE* 1.3 70.7 - - - +
277A MET* 1.3 60.2 + - - +
287A ASP* 3.1 0.2 - - - +
288A ILE 3.4 3.5 - - - +
289A THR* 2.9 14.7 + - + +
450A ARG* 2.8 30.3 + - - +
452A GLU* 3.4 1.0 - - - +
500A MN 2.2 36.2 + - - -
501A OH 2.9 3.8 + - - -
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Residues in contact with MET 277 (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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206A HIS* 2.9 29.8 + - + +
209A VAL* 4.1 14.6 - - + -
222A LEU 4.4 1.3 - - - +
223A GLU* 4.1 3.6 - - - -
226A PHE* 3.6 56.1 - - + -
241A TYR* 2.9 10.7 + - - -
243A CYS* 3.6 23.1 - - + -
244A ILE 4.3 2.5 - - - +
245A CYS* 3.6 19.3 - - - -
275A PHE* 4.0 26.9 - - + -
276A ASP* 1.3 84.4 - - - +
278A GLY* 1.3 57.8 + - - +
288A ILE* 2.9 16.7 + - - +
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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