Contacts of the strand formed by residues 288 - 293 (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 ILE 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ASN* 3.6 23.8 - - - +
202A SER* 3.7 27.1 - - - -
203A SER* 3.6 24.5 - - - +
206A HIS* 3.3 24.5 + - + +
241A TYR* 3.5 4.6 + - - -
276A ASP* 3.4 1.7 - - - +
277A MET 2.9 30.3 + - - +
286A SER* 5.0 1.1 - - - -
287A ASP* 1.3 81.8 - - - +
289A THR* 1.3 71.8 + - - +
290A CYS* 4.2 9.2 - - - -
452A GLU* 3.6 10.5 - - - +
466A THR* 3.7 22.0 - - + +
468A VAL* 4.4 2.2 - - + -
470A ARG* 4.3 1.1 - - - +
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Residues in contact with THR 289 (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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274A LEU* 3.5 31.2 - - + -
275A PHE 3.3 11.2 - - - +
276A ASP* 2.9 17.4 + - + -
288A ILE* 1.3 73.1 - - - +
290A CYS* 1.3 59.6 + - - +
450A ARG* 3.4 27.3 + - - +
451A ILE* 3.9 1.7 - - - -
452A GLU* 2.9 48.8 + - - +
470A ARG* 2.8 26.5 + - - -
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Residues in contact with CYS 290 (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* 3.6 31.6 - - - +
210A MET* 3.8 26.0 - - + -
273A CYS 3.9 0.7 - - - +
274A LEU* 3.7 1.2 - - - -
275A PHE* 2.9 33.5 + - + +
288A ILE* 4.2 2.2 - - - -
289A THR* 1.3 75.8 - - - +
291A SER* 1.3 62.5 + - - +
292A PHE* 4.1 12.9 - - + -
468A VAL* 3.8 29.4 - - - -
469A PRO 5.2 1.1 - - - +
470A ARG* 3.8 6.1 - - - +
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Residues in contact with SER 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A MET* 5.6 0.2 - - - +
272A MET* 4.8 1.1 - - - -
273A CYS 3.2 7.9 - - - -
274A LEU* 3.6 13.0 - - - +
290A CYS* 1.3 72.0 - - - +
292A PHE* 1.3 66.3 + - - +
306A TYR* 3.3 27.0 + - - -
448A GLY 5.1 0.4 - - - -
449A VAL* 3.7 26.7 - - - -
450A ARG 2.8 36.6 + - - -
451A ILE* 5.4 0.4 - - - +
470A ARG* 4.9 1.6 - - - +
475A ILE* 3.8 9.2 - - - +
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Residues in contact with PHE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A HIS* 6.2 0.2 - - - -
209A VAL* 4.8 1.1 - - + -
210A MET* 3.4 34.3 - - + -
213A VAL* 4.0 14.8 - - + -
272A MET* 3.7 10.5 - - - +
273A CYS* 2.7 50.6 + - + -
275A PHE* 3.7 34.3 - + - -
290A CYS* 4.1 16.6 - - + -
291A SER* 1.3 83.1 - - - +
293A PRO* 1.3 75.6 - - + +
298A PHE* 4.4 1.6 - - - -
475A ILE* 3.7 19.5 - - + -
479A MET* 3.6 28.0 - - + -
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Residues in contact with PRO 293 (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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270A GLY 6.2 0.4 - - - -
271A ASP 3.6 8.3 - - - +
272A MET* 3.8 4.9 - - - -
292A PHE* 1.3 86.9 - - + +
294A ALA* 1.3 66.3 + - - +
295A ASN* 3.9 6.3 - - - +
296A GLY* 3.0 15.7 + - - -
297A LYS 3.5 42.6 - - - +
298A PHE* 3.5 32.8 - - + +
302A GLN* 3.8 15.0 - - - +
475A ILE* 4.5 2.7 - - + -
479A MET* 3.2 13.4 - - - +
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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
------------------------------------------------------------
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