Contacts of the strand formed by residues 249 - 254 (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 TYR 249 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C TYR* 4.3 9.8 + + - +
100C GLN 4.2 6.4 + - - -
101C GLU* 5.5 0.3 - - - -
102C LEU* 4.8 13.7 + - + -
137C ALA* 3.1 33.6 - - + +
246C LEU 3.2 21.3 - - - -
247C GLY* 3.3 9.3 + - - -
248C SER* 1.3 74.7 + - - +
250C TYR* 1.3 73.2 + - - +
251C ARG* 3.7 21.1 - - + -
268C ILE* 3.7 18.8 - - + -
269C VAL 3.3 15.5 - - - +
270C PHE* 3.7 17.9 - + + -
271C ARG 4.0 1.1 - - - +
319C LYS* 3.3 7.4 - - - +
320C SER* 3.2 50.5 + - - -
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Residues in contact with TYR 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ILE* 3.7 46.7 - - + -
90C ASP* 2.4 39.1 + - - +
93C ALA* 4.4 4.3 - - + -
165C ILE* 3.7 28.2 - - + +
248C SER* 5.4 1.1 - - - -
249C TYR* 1.3 78.0 - - - +
251C ARG* 1.3 69.1 + - - +
252C TYR* 5.8 0.7 - - + -
267C TRP 3.9 0.2 - - - +
268C ILE* 3.6 1.7 - - - -
269C VAL* 2.8 43.5 + - + +
271C ARG* 3.2 27.9 + - + -
317C VAL* 3.9 12.6 - - + -
318C SER 3.2 4.7 - - - +
319C LYS* 3.7 27.9 - - + +
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Residues in contact with ARG 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C TYR* 3.7 24.6 + - + +
137C ALA 2.8 23.6 + - - +
138C GLY* 4.1 22.0 + - - -
139C LEU* 4.2 9.1 - - - +
249C TYR* 3.7 20.4 - - + -
250C TYR* 1.3 78.0 - - - +
252C TYR* 1.3 81.1 + - - +
266C GLU* 2.6 34.2 + - - +
267C TRP 2.6 40.6 + - - +
268C ILE* 3.7 18.6 - - - -
316C VAL 4.3 0.7 - - - +
317C VAL* 3.6 1.5 - - - -
318C SER* 2.5 43.8 + - - +
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Residues in contact with TYR 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C SER* 2.7 32.2 + - - -
86C ILE* 3.4 36.7 - - + +
88C ILE* 5.1 3.8 - - + -
163C HIS* 2.8 31.3 + + - -
251C ARG* 1.3 87.7 + - - +
253C THR* 1.3 82.3 + - - +
254C GLY* 4.0 1.1 - - - -
266C GLU* 4.7 0.4 - - - -
267C TRP* 3.1 48.2 + + + +
269C VAL* 4.4 10.8 - - + -
312C LEU* 4.9 2.5 - - + -
315C ARG* 3.7 17.7 - - + -
316C VAL 4.4 7.2 - - - +
317C VAL* 4.2 18.6 - - + -
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Residues in contact with THR 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C HIS* 4.5 21.5 - - + +
252C TYR* 1.3 76.7 - - - +
254C GLY* 1.3 66.6 + - - +
263C GLU* 5.9 2.9 - - + +
265C VAL 3.8 5.4 - - - +
266C GLU* 2.6 28.6 + - - +
315C ARG* 3.1 33.0 + - + +
316C VAL 5.5 0.6 + - - -
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Residues in contact with GLY 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C HIS 3.2 12.3 - - - +
84C SER* 3.2 14.8 - - - -
252C TYR* 3.9 2.1 + - - -
253C THR* 1.3 78.3 - - - +
255C SER* 1.3 63.8 + - - -
263C GLU* 3.4 16.3 - - - +
264C ILE 3.5 0.3 + - - -
265C VAL* 2.9 24.3 + - - -
267C TRP* 3.9 4.9 - - - -
315C ARG* 3.7 2.7 - - - -
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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
------------------------------------------------------------
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