Contacts of the strand formed by residues 296 - 301 (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 VAL 296 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C GLU 3.8 0.9 - - - +
292C GLN* 3.4 5.4 - - - +
293C GLN* 2.9 37.4 + - + +
294C ASP 3.7 1.1 - - - +
295C HIS* 1.3 85.3 - - + +
297C LYS* 1.3 71.0 + - - +
298C SER* 4.1 3.1 + - - +
132D VAL* 3.6 43.1 - - + -
134D VAL* 4.3 4.5 - - + -
140D VAL* 4.3 16.6 - - + -
141D VAL 3.2 7.0 - - - +
142D LEU* 3.5 23.6 - - + -
143D LEU* 4.5 1.4 - - - +
212D THR* 5.1 5.6 - - - -
214D LEU* 4.6 1.8 - - + -
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Residues in contact with LYS 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C HIS* 5.4 0.6 + - - -
228C GLU* 4.5 13.9 + - - -
290C THR* 3.7 34.5 + - + +
291C GLU 3.5 8.1 - - - +
292C GLN* 3.7 26.5 - - + +
295C HIS 4.3 0.2 - - - -
296C VAL* 1.3 74.1 - - - +
298C SER* 1.3 63.0 + - - +
140D VAL* 3.2 4.9 - - - +
141D VAL* 2.5 57.6 + - + +
143D LEU* 4.8 6.7 - - + +
228D LYS* 4.6 2.6 - - - +
230D GLU* 2.5 34.3 + - - +
252D LEU* 5.2 1.0 - - - +
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Residues in contact with SER 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C THR* 3.2 7.0 - - - -
291C GLU* 2.8 49.3 + - - +
293C GLN* 5.4 5.7 + - - +
296C VAL* 5.0 4.7 - - - -
297C LYS* 1.3 76.5 - - - +
299C VAL* 1.3 61.8 + - - +
300C GLU* 2.7 25.2 + - - +
134D VAL* 5.3 1.8 - - - -
138D GLN* 3.6 21.8 - - - -
139D GLY 3.4 6.1 - - - -
140D VAL* 4.0 7.2 - - - -
252D LEU* 5.6 0.2 - - - -
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Residues in contact with VAL 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C HIS* 4.1 20.4 - - + +
288C PHE* 3.7 22.0 - - + -
289C THR 3.4 13.2 - - - +
290C THR* 4.4 2.7 - - + +
298C SER* 1.3 71.4 - - - +
300C GLU* 1.3 62.7 + - - +
138D GLN* 2.9 23.4 + - - +
139D GLY 3.1 8.8 + - - +
222D MET* 3.7 11.4 - - - +
225D TYR* 4.3 15.3 - - + +
228D LYS* 4.5 16.4 - - + -
252D LEU* 3.5 37.5 - - + -
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Residues in contact with GLU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C PHE* 3.4 10.3 - - - -
289C THR* 2.8 43.5 + - + +
291C GLU* 3.3 35.8 - - + +
293C GLN* 5.7 1.0 + - - -
298C SER* 2.7 25.8 + - - +
299C VAL* 1.3 74.7 - - - +
301C TYR* 1.3 65.8 + - - +
135D ARG* 5.1 6.2 + - - +
138D GLN* 2.9 23.4 + - - +
222D MET* 4.3 9.6 - - - +
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Residues in contact with TYR 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C TYR 5.6 0.7 - - - -
287C ILE 4.1 4.9 - - - +
288C PHE* 3.7 33.1 - + - -
289C THR* 4.0 3.4 - - - +
300C GLU* 1.3 80.0 + - - +
302C LEU* 1.3 59.3 + - - +
303C ARG* 3.6 56.6 + - + +
135D ARG* 5.7 3.1 - - - -
221D VAL 4.3 3.4 + - - -
222D MET* 3.4 28.6 - - + +
223D GLY* 2.7 35.3 + - - -
224D GLU 5.7 0.7 - - - -
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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