Contacts of the strand formed by residues 434 - 440 (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 434 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343B MSE 4.2 42.0 - - + -
346B LEU* 3.7 34.7 + - + -
347B ASP* 2.9 44.4 + - + +
365B ILE* 4.1 13.5 - - + -
366B THR 3.2 7.2 - - - +
367B HIS* 3.8 18.0 - + - -
368B ARG* 4.6 2.0 - - - -
431B MSE 3.8 25.2 - - - +
432B ARG 3.3 4.4 - - - +
433B GLU* 1.4 103.7 - - + +
435B LYS* 1.3 58.8 + - - +
436B VAL* 4.7 1.8 - - + -
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Residues in contact with LYS 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B TYR 3.7 1.0 - - - +
365B ILE* 3.3 5.0 - - - +
366B THR* 2.8 50.1 + - - +
367B HIS 3.8 7.2 - - - +
368B ARG* 3.1 30.5 + - - +
370B ASN* 3.0 18.4 + - + +
371B PRO 4.8 0.4 + - - -
372B LEU 2.8 24.4 + - - +
373B SER* 4.7 3.6 - - - +
374B GLU* 4.9 19.2 - - + +
377B LEU* 4.1 19.7 - - + +
431B MSE 5.4 0.7 - - - -
434B TYR* 1.3 72.2 - - - +
436B VAL* 1.4 61.0 + - - +
437B VAL* 5.3 0.8 - - + +
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Residues in contact with VAL 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ILE* 4.1 23.6 - - + -
343B MSE 4.5 8.1 - - - -
363B MSE 4.2 17.0 - - + -
364B TYR 3.4 8.5 - - - +
365B ILE* 4.2 18.8 - - + -
374B GLU* 4.4 10.0 + - - +
422B PHE* 3.4 33.4 - - + -
426B LYS* 5.9 0.3 - - - -
431B MSE 3.6 30.8 - - - +
434B TYR* 4.1 2.9 + - + +
435B LYS* 1.4 77.5 - - - +
437B VAL* 1.3 66.7 + - - +
438B VAL* 4.4 0.2 - - + -
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Residues in contact with VAL 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B MSE 3.1 7.1 - - - +
364B TYR* 2.9 38.8 + - + +
374B GLU* 4.0 26.9 - - + +
377B LEU* 3.8 31.2 - - + -
378B ALA* 3.8 33.4 - - + +
381B LEU* 3.9 8.7 - - + +
422B PHE* 4.5 2.0 - - - -
435B LYS* 5.3 1.3 - - + -
436B VAL* 1.3 79.9 - - - +
438B VAL* 1.3 69.6 + - - +
439B ILE* 4.7 0.2 - - + -
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Residues in contact with VAL 438 (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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335B LEU* 4.8 9.4 - - + -
339B ILE* 5.0 0.2 - - + -
361B TYR* 3.9 14.8 - - + -
362B LEU 3.3 9.4 - - - +
363B MSE 3.9 24.0 - - + -
418B VAL* 3.7 26.7 - - + +
419B LYS* 6.0 1.7 - - - +
422B PHE* 3.7 49.6 - - + -
436B VAL* 4.4 0.7 - - + -
437B VAL* 1.3 80.9 - - - +
439B ILE* 1.3 66.8 + - - +
440B PRO* 4.8 0.7 - - - +
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Residues in contact with ILE 439 (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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361B TYR* 3.1 8.5 - - - +
362B LEU* 2.9 40.9 + - + -
378B ALA* 4.0 31.2 - - + +
381B LEU* 3.6 22.0 - - + +
382B GLU* 3.4 48.9 - - + +
385B THR* 4.2 6.3 - - + -
411B PHE* 4.7 1.6 - - + -
418B VAL* 4.6 1.1 - - - -
437B VAL* 4.7 1.3 - - + -
438B VAL* 1.3 78.2 - - - +
440B PRO* 1.3 82.7 - - + +
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Residues in contact with PRO 440 (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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360B TYR 3.3 12.1 - - - +
361B TYR* 4.1 1.3 - - + -
385B THR* 4.3 0.2 - - - +
411B PHE* 3.3 34.9 - - + -
412B ASN* 4.0 3.4 - - - +
415B SER* 3.2 43.1 - - - +
418B VAL* 4.5 8.9 - - + -
419B LYS* 4.4 18.8 - - + -
438B VAL 4.8 0.4 - - - +
439B ILE* 1.3 102.3 - - + +
441B THR* 1.3 61.2 + - - +
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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