Contacts of the strand formed by residues 431 - 436 (chain A) in PDB entry 1UD8
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 GLY 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A VAL* 4.0 10.9 - - - +
430A GLY* 1.3 74.4 - - - -
432A SER* 1.3 58.2 + - - -
468A PHE* 3.4 5.2 - - - +
469A THR* 2.8 46.1 + - - +
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Residues in contact with SER 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A VAL* 4.3 9.7 - - - +
424A ILE* 4.8 0.2 - - - -
431A GLY* 1.3 71.0 - - - -
433A LYS* 1.3 62.9 + - - +
466A GLU* 2.7 25.2 + - - -
467A PHE 2.9 18.6 - - - -
468A PHE* 3.3 32.9 - - - -
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Residues in contact with LYS 433 (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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399A TYR* 3.5 28.7 - - + -
401A ASP* 2.8 29.8 + - - +
402A HIS* 4.3 3.4 - - - +
405A VAL* 3.3 21.2 + - + +
406A VAL* 3.8 23.1 - - - +
407A GLY 3.8 4.9 - - - +
424A ILE* 3.9 15.3 - - + -
432A SER* 1.3 77.6 + - - +
434A TRP* 1.3 68.4 + - - +
435A MET* 3.4 22.6 + - + +
466A GLU* 4.4 3.6 - - - -
467A PHE* 2.9 30.0 + - - +
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Residues in contact with TRP 434 (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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399A TYR* 4.1 6.4 - - - -
433A LYS* 1.3 75.5 - - - +
435A MET* 1.3 62.4 + - - +
458A THR 6.0 0.4 - - - -
460A ASN* 4.2 11.7 - - + -
464A TRP* 3.4 39.1 - + + -
465A GLY* 3.5 39.7 - - - -
466A GLU* 3.5 40.7 + - + -
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Residues in contact with MET 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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399A TYR* 3.4 34.5 - - + -
407A GLY* 3.9 4.9 - - - -
408A TRP 3.7 13.0 - - - +
409A THR* 3.4 24.2 - - + -
422A ALA* 3.9 5.6 - - + -
423A THR 3.6 20.0 - - - +
424A ILE* 4.8 3.4 - - + -
433A LYS* 3.4 33.6 + - + +
434A TRP* 1.3 76.5 - - - +
436A TYR* 1.3 62.9 + - - +
437A VAL* 3.9 5.4 + - - +
464A TRP* 3.5 6.8 - - - -
465A GLY 3.2 29.1 + - - +
467A PHE* 3.9 25.5 - - + -
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Residues in contact with TYR 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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397A HIS* 3.7 25.6 - + + +
399A TYR* 2.7 18.5 + - - +
409A THR* 2.7 28.6 + - - -
411A GLU* 3.4 17.5 + - - -
435A MET* 1.3 72.3 - - - +
437A VAL* 1.3 56.8 + - - +
438A GLY* 3.2 20.8 - - - -
439A ARG* 2.8 24.8 + - + +
440A GLN* 4.3 0.9 + - - -
462A ASP 3.2 21.3 - - - -
463A GLY 3.5 8.7 - - - -
464A TRP* 3.0 40.3 - + + -
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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