Contacts of the strand formed by residues 405 - 410 (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 VAL 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A HIS* 3.0 35.7 + - + +
404A ASP* 1.3 77.1 - - + +
406A VAL* 1.3 61.3 + - - +
424A ILE* 3.3 32.1 - - + -
425A MET 3.2 7.6 - - - +
426A SER* 3.6 17.9 - - - +
429A PRO 4.2 3.4 - - - +
430A GLY 4.2 2.7 - - - +
431A GLY* 4.0 21.1 - - - +
432A SER 4.3 14.4 - - - +
433A LYS* 3.3 14.7 + - - +
469A THR* 4.1 6.3 - - + -
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A MET* 3.6 39.7 - - + +
399A TYR 3.7 12.6 - - - +
400A PHE* 4.1 29.8 - - + -
402A HIS 3.0 28.0 - - - +
404A ASP 4.7 0.2 - - - +
405A VAL* 1.3 73.9 - - - +
407A GLY* 1.3 61.0 + - - +
408A TRP* 4.9 2.2 - - + -
424A ILE* 3.8 2.3 - - - +
425A MET* 3.0 46.0 + - + +
433A LYS* 3.8 7.2 - - - +
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Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A TYR* 2.8 30.1 + - - -
400A PHE* 4.3 1.7 + - - -
406A VAL* 1.3 79.2 - - - +
408A TRP* 1.3 78.0 + - - +
423A THR* 3.0 15.0 - - - -
424A ILE* 4.3 0.9 - - - -
433A LYS* 3.8 2.8 - - - +
435A MET* 3.9 12.3 - - - -
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Residues in contact with TRP 408 (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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349A ALA 3.7 0.4 - - - -
350A THR* 3.5 34.5 - - + -
353A THR* 3.1 35.3 + - - -
354A ARG* 3.2 44.9 - - + +
396A GLN* 4.8 4.9 - - + -
397A HIS 3.1 14.8 - - - +
398A ASP* 3.7 5.6 - - - +
399A TYR* 4.2 3.1 - - - -
400A PHE* 3.6 34.1 - + - -
406A VAL* 4.9 2.0 - - + -
407A GLY* 1.3 89.2 - - - +
409A THR* 1.3 73.0 + - - +
410A ARG* 5.1 0.7 - - - -
421A LEU* 4.8 3.6 - - + -
423A THR* 2.8 50.7 + - + +
425A MET* 3.5 22.9 - - + -
435A MET* 3.7 1.8 - - - -
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Residues in contact with THR 409 (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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395A THR 4.3 0.4 - - - -
396A GLN* 3.0 6.9 - - - +
397A HIS* 2.7 51.8 + - - +
399A TYR* 4.2 0.4 - - + -
408A TRP* 1.3 82.7 - - - +
410A ARG* 1.3 69.4 + - - +
421A LEU* 3.3 8.1 - - - -
422A ALA* 3.6 13.2 - - + -
435A MET* 3.4 27.8 - - + -
436A TYR 2.7 28.1 + - - +
437A VAL* 3.8 11.9 - - + -
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Residues in contact with ARG 410 (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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4A ASN* 5.1 1.0 + - - +
353A THR 3.1 20.3 + - - +
354A ARG 4.0 2.0 + - - -
355A GLU* 3.7 27.7 + - - +
392A ALA* 3.1 34.9 + - - +
393A TYR* 3.0 28.8 - - - +
394A GLY 3.1 21.7 + - - +
395A THR 3.2 5.4 - - - -
396A GLN* 3.5 28.2 + - - +
408A TRP* 5.1 2.5 - - + -
409A THR* 1.3 84.0 - - - +
411A GLU* 1.3 57.1 + - - +
412A GLY 3.1 2.9 - - - -
420A GLY* 2.9 6.9 - - - -
421A LEU* 2.8 60.5 + - + +
437A VAL* 4.9 1.1 - - - -
446A TRP* 4.4 3.5 - - - -
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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
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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