Contacts of the strand formed by residues 288 - 293 (chain C) in PDB entry 5E5R
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 PHE 288 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ASN* 2.8 25.6 + - - +
225C VAL* 2.6 25.8 + - + +
226C HIS* 3.6 18.8 - + - +
227C HIS 3.5 3.1 + - - -
285C TYR 5.8 0.2 - - - -
286C SER* 3.4 23.8 - - - -
287C ILE* 1.3 79.1 - - - +
289C THR* 1.3 62.3 + - - +
299C VAL* 3.7 17.0 - - + -
300C GLU 3.4 18.2 - - - -
301C TYR* 3.7 34.5 - + - -
302C LEU* 3.9 4.2 - - - +
222D MET* 4.3 9.6 - - - -
224D GLU 4.5 4.7 - - - -
225D TYR* 3.4 41.7 - + + -
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Residues in contact with THR 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C GLY* 2.8 36.9 + - - +
226C HIS* 6.1 0.2 - - - -
227C HIS* 4.1 8.3 - - - -
288C PHE* 1.3 75.4 - - - +
290C THR* 1.3 83.9 + - - +
291C GLU* 5.9 0.2 - - + -
299C VAL* 3.4 11.4 - - - +
300C GLU* 2.8 42.0 + - + +
301C TYR 4.0 7.4 - - - +
302C LEU* 3.9 20.9 - - + -
402C FMT 3.7 2.3 - - - -
228D LYS* 5.8 0.2 - - - -
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Residues in contact with THR 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C TYR* 4.8 0.3 + - - -
227C HIS* 2.5 34.3 + - + +
289C THR* 1.3 98.6 + - - +
291C GLU* 1.3 63.5 + - - +
297C LYS* 3.7 27.6 - - - -
298C SER 3.2 12.3 - - - +
299C VAL* 4.5 5.6 - - + -
300C GLU* 4.7 0.7 - - - -
402C FMT 3.3 14.4 + - - -
228D LYS* 3.6 30.5 - - - -
230D GLU* 5.1 0.2 - - - +
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C TYR* 3.8 15.7 - - + +
289C THR* 5.9 0.4 - - + -
290C THR* 1.3 76.6 - - - +
292C GLN* 1.3 66.7 + - - +
293C GLN* 3.7 29.5 + - + +
296C VAL 3.8 1.2 - - - +
297C LYS* 3.5 2.9 - - - -
298C SER* 2.8 36.1 + - - +
300C GLU* 3.3 35.4 - - + +
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Residues in contact with GLN 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C TYR* 3.5 31.8 + - + +
66C TYR* 5.6 2.9 - - - -
291C GLU* 1.3 77.9 - - - +
293C GLN* 1.3 67.3 + - - +
294C ASP 5.1 0.9 - - - +
295C HIS 5.3 2.1 - - - +
296C VAL 3.4 13.5 - - - +
297C LYS* 3.7 24.5 - - + +
143D LEU* 3.7 29.5 - - + +
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Residues in contact with GLN 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C TYR* 6.3 4.5 - - + -
291C GLU* 3.7 25.5 + - + +
292C GLN* 1.3 77.1 - - - +
294C ASP* 1.3 75.2 + - + +
295C HIS 3.6 1.6 - - - -
296C VAL* 2.9 24.9 + - + +
298C SER* 5.4 6.5 + - - +
300C GLU* 5.7 1.0 + - - -
132D VAL* 3.6 22.0 - - + +
133D SER* 3.6 26.8 + - - +
134D VAL* 5.4 1.0 - - - +
217D ARG* 6.1 0.2 - - - +
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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