Contacts of the strand formed by residues 359 - 365 (chain D) in PDB entry 3REO
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 THR 359 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190D THR* 3.8 24.6 + - + +
194D ILE* 4.4 5.1 - - + +
268D LYS* 5.0 3.5 + - - -
269D TRP* 4.0 14.9 + - + +
299D ALA* 3.7 31.4 - - + +
300D GLU* 3.9 13.7 - - - +
301D TYR* 3.8 15.4 - - - -
355D CYS* 3.2 1.7 - - - -
356D ALA* 2.8 40.2 + - - +
357D PHE 4.0 2.4 + - - -
358D ASN* 1.3 75.6 - - - +
360D TYR* 1.3 62.2 + - - +
361D VAL* 4.6 2.9 - - - +
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Residues in contact with TYR 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D VAL 3.4 2.1 - - - +
299D ALA* 3.2 5.2 - - - -
300D GLU 3.0 32.7 + - - +
302D ILE* 3.7 49.4 - - + -
352D VAL* 3.7 25.1 - - + -
354D SER 3.2 5.4 - - - -
355D CYS* 3.5 33.1 - - + -
358D ASN* 3.8 18.6 + - - -
359D THR* 1.3 75.1 - - - +
361D VAL* 1.3 62.1 + - - +
362D MET* 3.8 4.7 + - + +
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Residues in contact with VAL 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D ILE* 3.9 41.3 - - + -
198D TYR* 3.8 25.6 - - + -
266D PHE* 5.7 0.7 - - + -
297D ILE* 3.6 29.6 - - + -
298D VAL 3.4 3.1 - - - +
299D ALA* 4.4 5.8 - - + -
352D VAL* 3.7 1.9 - - - +
353D ALA* 2.7 31.8 + - + -
354D SER* 2.6 28.8 + - - +
355D CYS 5.1 0.2 - - - +
359D THR 4.6 1.6 - - - +
360D TYR* 1.3 77.2 - - - +
362D MET* 1.3 59.5 + - - +
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Residues in contact with MET 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D ILE* 3.3 5.9 - - - +
298D VAL* 2.7 64.7 + - + +
300D GLU* 4.1 14.4 - - + +
302D ILE* 4.3 17.7 - - + -
338D PHE* 3.6 55.0 - - + -
350D PHE* 3.9 12.1 - - + -
351D LYS 3.2 10.5 - - - +
352D VAL* 4.1 18.6 - - + -
360D TYR* 4.5 2.7 - - + +
361D VAL* 1.3 76.5 - - - +
363D GLU* 1.3 63.7 + - - +
364D PHE* 4.2 8.7 - - + -
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Residues in contact with GLU 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D TYR* 2.4 47.3 + - + +
200D GLY* 3.8 3.1 - - - -
295D LYS* 3.2 28.9 + - + -
296D VAL 3.3 4.3 - - - +
297D ILE* 4.5 1.8 - - + -
350D PHE* 3.3 6.8 + - - -
351D LYS* 2.8 65.8 + - + +
353D ALA* 4.5 3.4 - - + -
362D MET* 1.3 78.5 - - - +
364D PHE* 1.3 63.9 + - - +
365D LEU* 3.8 21.4 + - + +
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Residues in contact with PHE 364 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283D LEU* 3.6 42.6 - - + -
295D LYS* 3.0 6.4 - - - +
296D VAL* 2.7 39.5 + - + +
298D VAL* 3.8 24.5 - - + -
338D PHE* 3.6 30.3 - + + -
341D LEU* 4.9 1.3 - - + -
342D ALA* 3.9 19.7 - - + -
347D PHE* 3.6 23.7 - + + -
349D GLY 3.5 5.2 - - - -
350D PHE* 3.7 29.2 - + - -
362D MET* 4.3 7.4 - - + -
363D GLU* 1.3 78.6 - - - +
365D LEU* 1.3 61.4 + - - +
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Residues in contact with LEU 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D HIS 6.1 0.7 - - - +
294D GLY 4.1 0.7 - - - +
295D LYS* 3.6 28.9 - - + +
347D PHE* 3.5 3.7 - - - +
348D ARG 2.9 23.2 + - - -
349D GLY* 2.7 35.9 + - - +
350D PHE 4.6 2.2 - - - +
351D LYS* 5.2 12.3 - - + +
363D GLU* 4.0 28.7 - - + +
364D PHE* 1.3 74.6 - - - +
366D LYS* 1.3 62.2 + - - +
367D THR* 3.9 15.5 - - + +
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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