Contacts of the strand formed by residues 425 - 430 (chain A) in PDB entry 1X11
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 ILE 425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A LEU* 5.3 8.3 - - + -
361A VAL* 3.7 37.7 - - + -
365A LYS* 4.0 14.4 - - - +
421A ASP* 3.1 6.2 - - - -
422A ILE* 2.9 44.2 + - + +
423A GLY 3.0 0.2 - - - -
424A ASN* 1.3 86.2 - - + +
426A VAL* 1.3 69.9 + - - +
427A VAL* 4.2 2.5 - - + -
462A VAL* 3.7 27.1 - - + -
463A PHE 3.5 4.7 - - - +
464A GLU* 5.1 5.6 - - + -
468A ALA* 3.6 5.6 - - - +
470B LEU* 4.9 5.4 - - + -
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Residues in contact with VAL 426 (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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390A LEU* 4.9 1.8 - - + -
419A ILE* 3.8 23.8 - - + -
420A ALA 3.4 5.6 - - - +
425A ILE* 1.3 78.3 - - - +
427A VAL* 1.3 67.0 + - - +
428A LEU* 4.1 0.7 - - + -
461A HIS 3.6 1.0 - - - +
462A VAL* 3.4 5.7 - - - +
463A PHE* 2.9 54.2 + - + +
465A SER* 4.3 9.4 - - - -
468A ALA* 3.7 30.1 - - + +
471A ILE* 4.0 30.7 - - + -
472A ALA* 5.3 1.1 - - + +
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Residues in contact with VAL 427 (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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357A ALA* 4.1 34.1 - - + +
360A ALA* 4.3 10.8 - - + -
361A VAL* 4.0 26.2 - - + -
418A TYR* 4.4 1.1 - - + -
419A ILE* 3.1 10.7 - - - -
420A ALA 2.8 40.0 + - - +
422A ILE* 5.0 4.0 - - + -
425A ILE* 4.2 4.7 - - + -
426A VAL* 1.3 79.2 - - - +
428A LEU* 1.3 62.9 + - - +
429A MSE 3.9 7.4 + - + -
460A CYS* 4.3 14.1 - - + -
461A HIS 3.4 6.5 - - - +
462A VAL* 4.2 10.8 - - + -
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Residues in contact with LEU 428 (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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390A LEU* 5.2 4.5 - - + -
397A ILE* 3.5 31.0 - - + -
399A VAL* 5.9 0.7 - - + -
409A MSE 5.1 2.0 - - + -
411A HIS* 3.8 18.4 - - + +
416A ILE* 4.0 23.1 - - + -
418A TYR 4.0 0.9 - - - -
419A ILE* 3.9 21.1 - - + -
426A VAL 4.1 0.8 - - - -
427A VAL* 1.3 71.8 - - - +
429A MSE 1.3 61.0 + - - +
430A ALA* 5.3 0.4 - - + -
459A ILE 3.6 2.3 - - - +
460A CYS* 3.4 1.9 - - - -
461A HIS* 2.7 72.4 + - + +
463A PHE* 4.1 15.7 - - + -
475A ILE* 4.2 7.9 - - + -
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Residues in contact with MSE 429 (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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342A LEU* 5.3 0.4 - - - -
353A ARG* 4.0 20.4 - - - +
356A GLN* 3.4 42.2 - - + +
357A ALA* 4.0 15.5 - - + +
416A ILE* 3.2 6.5 - - - +
417A SER* 2.8 35.9 + - - +
418A TYR* 2.9 44.7 + - + +
427A VAL* 3.9 4.2 + - + -
428A LEU* 1.3 72.5 - - - +
430A ALA* 1.3 54.4 + - - +
458A MSE 4.1 15.9 - - + -
459A ILE 3.7 1.8 - - - -
460A CYS* 3.7 26.2 - - - +
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Residues in contact with ALA 430 (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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411A HIS* 4.6 10.8 - - + -
415A THR* 3.6 8.7 - - - +
416A ILE* 3.9 19.7 - - + +
417A SER* 4.7 0.2 - - - -
428A LEU 3.9 1.0 + - - -
429A MSE 1.3 73.0 - - - +
431A ARG* 1.3 63.7 + - - +
458A MSE 3.4 8.7 - - - +
459A ILE* 2.8 50.1 + - + +
461A HIS* 4.5 12.6 - - + +
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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