Contacts of the strand formed by residues 361 - 367 (chain B) in PDB entry 1U2X
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 361 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B GLU* 5.0 3.1 + - - +
335B LEU* 3.4 38.1 - - + +
338B SER* 3.6 23.9 + - - -
356B VAL* 5.1 3.5 - - + +
358B THR* 2.5 70.5 + - + +
360B TYR* 1.3 85.7 - - + +
362B LEU* 1.3 72.3 + - - +
363B MSE 4.3 18.5 - - + +
414B ARG* 5.8 3.6 - - - -
418B VAL* 4.0 23.1 - - + -
438B VAL* 3.9 11.4 - - + -
439B ILE 3.1 17.7 - - - +
441B THR* 3.6 4.4 - - - +
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLN* 5.5 1.1 - - - +
356B VAL 3.4 6.1 - - - +
357B HIS* 3.6 29.4 - - + -
358B THR 4.2 0.4 - - - +
361B TYR* 1.3 78.5 - - - +
363B MSE 1.3 62.5 + - - +
381B LEU* 3.4 44.2 - - + +
385B THR* 3.8 14.4 - - - -
437B VAL 4.0 0.2 - - - +
438B VAL* 3.3 3.8 - - - -
439B ILE* 2.9 41.2 + - + +
441B THR* 3.6 22.9 - - + -
457B ILE* 3.6 28.5 - - + -
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Residues in contact with MSE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 5.3 0.7 - - - -
338B SER* 3.8 26.2 - - - +
339B ILE* 3.6 27.8 - - - -
342B GLY* 5.1 0.4 - - - -
354B LEU 3.8 0.2 - - - +
355B GLN* 3.2 8.1 - - - +
356B VAL* 2.9 69.7 + - + +
361B TYR* 4.3 12.6 - - + -
362B LEU* 1.3 77.0 - - - +
364B TYR* 1.3 72.8 + - - +
365B ILE* 3.8 19.5 - - + -
381B LEU* 3.9 5.4 - - - -
436B VAL* 4.2 5.4 - - + -
437B VAL 3.1 12.8 - - - +
438B VAL* 3.9 12.1 - - + -
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Residues in contact with TYR 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B SER* 5.2 4.4 + - - -
353B ILE* 3.3 38.4 - - + -
354B LEU 3.2 7.9 - - - -
355B GLN* 3.7 20.9 - - + -
363B MSE 1.3 73.5 - - - +
365B ILE* 1.3 66.5 + - - +
366B THR* 5.0 1.3 - - + -
377B LEU* 3.6 40.2 - - + -
380B SER* 2.7 27.7 + - - -
381B LEU* 3.4 31.1 - - + +
435B LYS 3.7 1.0 - - - +
436B VAL* 3.4 4.9 - - - -
437B VAL* 2.9 38.6 + - + +
461B ALA* 3.3 18.0 + - + +
462B PHE* 4.7 0.7 - - - -
465B TYR* 3.7 10.5 - + - +
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Residues in contact with ILE 365 (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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339B ILE* 3.8 9.9 - - - +
342B GLY* 3.6 32.5 - - - +
343B MSE 3.6 26.0 - - + +
346B LEU* 3.8 18.3 - - + +
353B ILE* 3.6 2.9 - - - +
354B LEU* 2.8 44.0 + - + +
356B VAL* 5.6 0.2 - - + -
363B MSE 3.8 27.6 - - + -
364B TYR* 1.3 78.7 - - - +
366B THR* 1.3 63.5 + - - +
434B TYR* 4.1 10.1 - - + -
435B LYS 3.3 9.0 - - - +
436B VAL* 4.2 8.7 - - + -
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Residues in contact with THR 366 (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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346B LEU* 4.0 7.4 - - - -
352B GLU 3.9 8.5 - - - -
353B ILE* 3.3 33.4 - - + -
364B TYR* 5.0 1.3 - - + -
365B ILE* 1.3 74.1 - - - +
367B HIS* 1.3 65.2 + - - +
370B ASN* 3.8 20.9 - - - +
377B LEU* 4.0 18.8 - - + -
434B TYR* 3.2 8.3 - - - +
435B LYS* 2.8 51.9 + - - +
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Residues in contact with HIS 367 (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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346B LEU* 3.9 23.9 - - + +
350B ASN* 3.7 20.4 + - - -
351B PHE 2.8 23.5 + - - -
352B GLU* 3.5 21.1 + - + -
366B THR* 1.3 85.5 + - - +
368B ARG* 1.3 68.3 + - + +
369B ASP* 3.5 18.4 - - - +
370B ASN* 3.0 16.7 + - + +
433B GLU 3.7 5.9 + - - +
434B TYR* 3.8 17.0 - + - -
435B LYS* 3.8 1.5 - - - -
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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
------------------------------------------------------------
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