Contacts of the strand formed by residues 286 - 291 (chain B) in PDB entry 4X7C
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 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B CYS 4.3 4.7 - - - -
285B THR* 1.3 82.9 - - - +
287B ARG* 1.3 67.2 + - - +
301B MET* 3.8 18.5 - - - +
303B LEU* 4.1 26.0 - - + -
320B PRO* 6.2 0.9 - - + -
323B THR* 4.5 13.5 - - + -
324B PRO* 3.4 37.7 - - + -
351B VAL* 4.3 17.9 - - + -
358B PHE* 3.8 17.9 - + - -
360B PRO* 4.5 0.9 - - + -
365B VAL* 4.0 16.6 - - + -
367B PHE* 3.8 21.1 - + + -
381B THR 4.0 0.2 - - - +
382B LYS* 3.4 3.8 - - - +
383B PHE* 2.8 40.9 + + + +
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PRO* 3.6 22.4 - - - +
282B ASN* 3.3 23.3 + - - -
285B THR* 3.1 28.9 + - - -
286B PHE* 1.3 79.8 - - - +
288B GLY* 1.3 53.8 + - - +
301B MET* 3.6 6.5 - - - +
303B LEU* 3.3 8.9 - - - +
304B ALA* 2.7 32.1 + - + +
305B SER 3.8 15.5 - - - +
306B LEU* 3.3 31.4 + - - +
308B TRP* 3.7 42.5 - - + +
381B THR 3.3 4.5 - - - -
382B LYS* 3.9 28.2 - - + +
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Residues in contact with GLY 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B ARG* 1.3 76.1 - - - +
289B ASP* 1.3 60.5 + - - -
301B MET* 3.8 5.9 - - - -
302B ASN 3.2 13.5 - - - -
304B ALA* 3.8 10.3 - - - -
308B TRP* 3.5 10.8 - - - -
379B GLN 3.5 1.2 - - - +
380B ASN* 3.7 1.1 - - - -
381B THR* 2.7 40.3 + - - +
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Residues in contact with ASP 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B GLY* 1.3 75.7 - - - +
290B VAL* 1.3 66.5 + - - +
291B THR* 4.6 4.2 - - - +
300B THR 3.7 0.2 - - - +
301B MET* 3.2 2.9 - - - -
302B ASN* 2.7 57.0 + - - +
378B HIS* 4.2 31.6 + - - +
379B GLN 3.7 15.5 - - - +
381B THR* 4.2 0.2 - - - -
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ASP* 1.3 80.5 - - - +
291B THR* 1.3 69.2 + - - +
299B TYR* 4.2 19.5 - - + -
300B THR 3.2 5.4 - - - +
301B MET* 3.7 36.8 - - + +
334B LEU* 5.2 5.6 - - + -
336B GLN* 3.9 5.2 - - - +
367B PHE* 5.3 0.7 - - + -
375B PHE* 3.7 32.5 - - + +
376B GLU 3.9 2.9 + - - +
377B THR* 3.6 21.1 - - - +
378B HIS 4.4 0.9 + - - -
379B GLN 4.7 0.6 + - - -
381B THR* 3.8 22.0 + - + +
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Residues in contact with THR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B ASP* 4.6 3.8 - - - +
290B VAL* 1.3 80.6 - - - +
292B HIS* 1.3 65.0 + - - +
299B TYR* 3.5 4.6 - - - -
300B THR* 2.9 44.1 + - - +
302B ASN* 4.4 16.9 + - - +
377B THR* 4.4 18.4 - - + -
378B HIS* 5.9 3.8 - - + +
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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