Contacts of the strand formed by residues 405 - 410 (chain A) in PDB entry 5XOU
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 ALA 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A ALA 4.1 2.2 + - - -
346A LEU* 3.7 10.3 - - + +
347A ALA 3.0 23.0 + - - -
403A VAL* 3.4 4.1 - - - +
404A GLN* 1.3 80.2 - - - +
406A VAL* 1.3 64.9 + - - +
430A LEU* 4.8 1.6 - - - -
431A PRO* 3.3 13.7 - - - +
454A LEU* 3.9 19.7 - - + +
457A LYS* 4.1 6.7 - - + +
458A ALA* 3.8 25.1 - - + +
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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
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347A ALA* 3.2 23.8 - - + +
349A LEU* 3.9 14.8 - - + +
381A LEU* 4.2 12.3 - - + -
403A VAL* 4.4 6.1 - - + -
405A ALA* 1.3 79.4 - - - +
407A LEU* 1.3 67.0 + - - +
408A VAL* 3.7 21.8 - - + -
425A LEU* 3.8 26.0 - - + -
430A LEU* 4.5 16.2 - - + -
431A PRO 2.9 10.7 + - - +
432A SER* 3.2 2.4 - - - -
433A GLN 2.8 26.9 + - - -
454A LEU* 3.5 5.8 - - - +
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Residues in contact with LEU 407 (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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347A ALA 2.8 12.1 + - - +
348A LEU* 3.3 20.2 - - + +
349A LEU 2.9 25.3 + - - -
357A TRP* 3.4 30.7 - - + -
361A LEU* 4.0 20.0 - - + -
406A VAL* 1.3 71.9 - - - +
408A VAL* 1.3 60.8 + - - +
409A LEU* 4.8 5.8 - - + -
433A GLN* 3.6 30.3 - - + +
435A LEU* 4.3 20.9 - - + -
450A ALA* 4.9 0.9 - - + -
451A LEU* 4.6 11.9 - - + -
454A LEU* 3.7 22.8 - - + +
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Residues in contact with VAL 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 LEU* 3.3 18.6 - - + +
351A LEU* 3.9 29.2 - - + -
406A VAL* 3.7 19.3 - - + -
407A LEU* 1.3 73.9 - - - +
409A LEU* 1.3 61.2 + - - +
410A THR* 3.6 10.2 + - + -
421A LEU* 4.0 15.7 - - + -
425A LEU* 4.6 3.4 - - + -
432A SER* 4.2 15.3 - - - -
433A GLN 2.8 17.8 + - - +
434A ILE* 3.6 12.3 - - + +
435A LEU 2.9 29.2 + - - +
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Residues in contact with LEU 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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348A LEU* 3.8 16.8 - - + -
349A LEU 3.0 7.5 + - - +
350A ARG* 3.6 43.7 - - - +
351A LEU* 2.8 29.5 + - - +
352A ASP* 3.9 3.7 + - - +
358A PRO* 3.7 26.2 - - + -
361A LEU* 4.7 4.7 - - + -
407A LEU* 3.9 3.8 + - + -
408A VAL* 1.3 69.4 - - - +
410A THR* 1.3 59.9 + - - +
435A LEU* 3.5 39.3 - - + +
437A VAL* 4.4 20.6 - - + -
439A LEU* 4.7 6.1 - - + -
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Residues in contact with THR 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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351A LEU* 3.8 22.8 - - - +
408A VAL* 4.1 6.7 - - + +
409A LEU* 1.3 75.8 - - - +
411A PRO* 1.3 95.4 + - - +
413A MET* 3.5 23.6 - - + +
434A ILE* 3.7 30.1 - - + -
435A LEU 3.4 3.6 + - - -
436A ASN* 3.1 11.3 - - - +
437A VAL* 2.9 23.6 + - - +
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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