Contacts of the strand formed by residues 288 - 293 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASN* 3.1 25.1 + - - +
225A VAL* 2.7 27.4 + - + +
226A HIS* 3.7 17.0 - + - +
227A HIS 3.9 2.9 + - - +
285A TYR 5.6 0.2 - - - -
286A SER* 3.3 23.6 - - - -
287A ILE* 1.3 78.8 - - - +
289A THR* 1.3 65.9 + - - +
299A VAL* 3.5 16.2 - - + -
300A GLU 3.3 18.8 - - - -
301A TYR* 3.8 33.4 - + - -
302A LEU* 3.9 2.7 - - - +
222B MET* 4.2 11.2 - - + -
223B GLY 5.4 0.7 - - - -
224B GLU 4.6 4.5 - - - -
225B TYR* 3.4 43.3 - + + -
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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
----------------------------------------------------------
121A GLY* 2.6 35.9 + - - +
227A HIS* 4.1 10.7 + - - +
288A PHE* 1.3 76.1 - - - +
290A THR* 1.3 87.7 + - - +
291A GLU* 5.1 4.3 - - + +
299A VAL* 3.5 5.2 - - - +
300A GLU* 2.7 40.5 + - + +
301A TYR 3.9 10.3 - - - +
302A LEU* 3.9 19.7 - - + -
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Residues in contact with THR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A HIS* 2.6 30.1 + - - +
289A THR* 1.3 95.6 + - - +
291A GLU* 1.3 69.8 + - - +
292A GLN 4.3 0.2 - - - -
297A LYS* 3.7 26.4 - - - -
298A SER 3.1 13.0 - - - +
299A VAL* 4.5 11.0 - - + -
300A GLU* 4.6 0.4 - - - +
228B LYS* 3.2 31.9 - - + +
230B GLU* 5.2 0.4 - - - +
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 4.4 14.6 - - - +
63A SER* 4.7 9.7 + - - -
289A THR* 5.1 4.9 - - + +
290A THR* 1.3 80.3 - - - +
292A GLN* 1.3 58.9 + - - +
293A GLN* 3.4 21.6 + - + +
296A VAL 3.5 1.6 - - - +
297A LYS* 3.4 6.6 - - - -
298A SER* 2.9 37.4 + - - +
300A GLU* 3.4 34.5 - - + +
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Residues in contact with GLN 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 3.8 36.2 + - + -
290A THR 4.3 0.4 - - - -
291A GLU* 1.3 69.3 - - - +
293A GLN* 1.3 59.5 + - - +
294A ASP 3.9 12.0 + - - +
296A VAL 4.2 2.6 - - - +
297A LYS* 4.1 30.0 - - + +
143B LEU* 3.2 32.3 - - - +
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Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 5.3 2.7 - - - +
291A GLU* 4.3 21.0 + - + +
292A GLN* 1.3 73.3 + - - +
294A ASP* 1.3 71.9 + - + +
296A VAL* 2.8 34.7 + - - +
298A SER* 4.2 14.1 + - - -
300A GLU* 5.1 2.4 + - - -
132B VAL* 3.5 30.1 - - + +
133B SER 4.5 9.1 + - - +
134B VAL* 5.5 1.2 - - - +
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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