Contacts of the strand formed by residues 434 - 440 (chain A) 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 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A MSE 4.1 42.6 - - + -
346A LEU* 3.7 26.7 - - + -
347A ASP* 3.1 41.1 + - + +
365A ILE* 4.2 12.3 - - + -
366A THR 3.1 15.0 - - - +
367A HIS* 4.0 15.7 + - - -
368A ARG* 4.9 2.0 - - - -
430A ARG 5.7 0.9 - - - -
431A MSE 4.2 21.1 - - + +
432A ARG 3.2 6.8 + - - +
433A GLU* 1.4 108.9 + - + +
435A LYS* 1.3 62.4 + - - +
436A VAL* 4.0 3.7 + - + -
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Residues in contact with LYS 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A TYR 3.7 0.5 - - - +
365A ILE* 3.1 6.2 - - - +
366A THR* 2.8 49.6 + - - +
367A HIS 4.0 5.3 - - - +
368A ARG* 3.2 31.0 + - - -
370A ASN* 3.1 19.1 + - + +
371A PRO 5.0 0.4 - - - -
372A LEU 3.0 27.2 + - - +
373A SER* 4.7 4.0 - - - +
374A GLU* 4.6 21.9 - - + +
377A LEU* 4.3 16.2 - - + -
434A TYR* 1.3 73.2 - - - +
436A VAL* 1.3 61.1 + - - +
437A VAL* 4.2 1.1 - - + -
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Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ILE* 4.2 17.5 - - + -
343A MSE 4.6 3.8 - - - -
363A MSE 4.1 23.1 - - + -
364A TYR 3.3 8.7 - - - +
365A ILE* 4.2 16.4 - - + -
374A GLU* 4.4 10.6 + - - +
422A PHE* 3.4 34.9 - - + -
426A LYS* 6.2 0.2 - - + -
431A MSE 4.0 27.8 - - + +
434A TYR* 4.0 7.9 + - + -
435A LYS* 1.3 78.3 - - - +
437A VAL* 1.3 68.2 + - - +
438A VAL* 4.4 0.2 - - + -
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Residues in contact with VAL 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A MSE 3.1 6.4 - - - +
364A TYR* 2.8 39.0 + - + +
374A GLU* 3.9 39.5 - - + +
377A LEU* 4.1 20.2 - - + -
378A ALA* 3.8 36.1 - - + +
381A LEU* 4.0 6.9 - - + +
422A PHE* 4.5 0.9 - - - -
435A LYS 5.2 0.2 - - - -
436A VAL* 1.3 79.5 - - - +
438A VAL* 1.4 68.1 + - - +
439A ILE* 4.8 0.4 - - + -
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Residues in contact with VAL 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A LEU* 4.5 11.4 - - + -
361A TYR* 3.9 26.7 - - + -
362A LEU 3.3 10.3 - - - +
363A MSE 3.9 23.3 - - + -
418A VAL* 4.0 16.1 - - + +
419A LYS* 6.1 1.2 - - - +
422A PHE* 3.6 48.7 - - + -
436A VAL* 4.4 0.7 - - + -
437A VAL* 1.4 80.4 - - - +
439A ILE* 1.3 69.4 + - - +
440A PRO* 4.7 1.2 - - - +
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Residues in contact with ILE 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A TYR* 3.0 8.3 - - - +
362A LEU* 2.8 41.3 + - + +
378A ALA* 4.0 30.5 - - + +
381A LEU* 3.7 18.4 - - + +
382A GLU* 3.6 47.1 - - + +
385A THR* 4.3 5.6 - - + -
411A PHE* 4.7 2.2 - - + -
418A VAL* 4.9 0.4 - - - -
437A VAL* 4.3 2.7 - - + -
438A VAL* 1.3 80.8 - - - +
440A PRO* 1.3 82.8 - - + +
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Residues in contact with PRO 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A TYR 3.3 12.6 - - - +
361A TYR* 4.1 1.3 - - + -
385A THR* 4.3 0.2 - - - +
411A PHE* 3.3 36.0 - - + -
412A ASN* 4.2 3.4 - - - +
415A SER* 3.1 40.8 - - - +
418A VAL* 4.8 7.6 - - + -
419A LYS* 4.4 20.6 - - + +
438A VAL 4.7 0.7 - - - +
439A ILE* 1.3 100.6 - - + +
441A THR* 1.4 59.7 + - - +
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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