Contacts of the strand formed by residues 426 - 432 (chain A) in PDB entry 5K7W
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 426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A ALA* 3.3 11.9 - - - -
423A GLN* 3.6 11.6 + - - +
425A ASP* 1.3 75.3 - - - +
427A PHE* 1.3 66.7 + - - -
487A VAL* 3.5 4.6 - - - +
488A LYS* 2.9 34.4 + - - +
491A PRO* 3.9 15.2 - - - +
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Residues in contact with PHE 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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390A ALA 3.0 13.3 + - - +
391A VAL* 3.3 8.4 - - + -
392A VAL 2.9 26.0 + - - +
423A GLN* 3.2 9.5 + - - +
426A GLY* 1.3 75.0 - - - -
428A LEU* 1.3 60.6 + - - +
429A PHE* 4.0 20.0 - - + -
485A VAL* 4.8 3.1 - - + -
486A GLY 3.2 15.7 - - - +
487A VAL* 3.8 21.1 - - + -
491A PRO* 3.9 21.5 - - + -
494A PHE* 3.8 44.9 - + + -
524A LEU* 4.1 16.8 - - + -
525A SER* 5.6 2.9 - - - -
280B VAL* 3.7 34.8 - - + -
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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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392A VAL* 3.3 30.1 - - + +
393A MET* 5.0 0.2 - - - -
394A ALA* 5.1 4.0 - - + +
419A ILE* 4.8 7.6 - - + -
427A PHE* 1.3 74.5 - - - +
429A PHE* 1.3 79.8 + - - +
430A LEU* 4.3 11.7 - - + -
444A LEU* 4.3 20.0 - - + -
447A TRP* 4.0 23.8 - - + -
449A TYR* 3.5 44.2 - - + +
484A LEU 3.5 0.9 - - - +
485A VAL* 3.3 6.9 - - - +
486A GLY 2.8 30.5 + - - +
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Residues in contact with PHE 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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391A VAL* 3.6 31.4 - - + -
392A VAL 2.8 8.9 + - - +
393A MET* 3.3 18.4 - - + +
394A ALA 2.9 28.1 + - - +
427A PHE* 4.0 15.9 - - + -
428A LEU* 1.3 78.6 - - - +
430A LEU* 1.3 59.0 - - - +
431A TRP 4.1 0.2 - - - -
455A ILE* 3.8 13.7 - - + -
483A CYS* 3.8 14.6 - - - -
484A LEU 3.3 4.0 - - - -
485A VAL* 4.0 19.1 - - + -
517A ILE* 4.5 4.5 - - + -
521A ILE* 3.7 26.2 - - + -
524A LEU* 3.9 12.8 - - + -
281B PHE* 3.7 37.2 - + - -
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Residues in contact with LEU 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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394A ALA* 3.6 17.9 - - + +
396A PRO* 3.9 16.4 - - + -
398A TRP* 3.8 34.8 - - + -
428A LEU* 4.3 16.2 - - + -
429A PHE* 1.3 72.8 - - - +
431A TRP* 1.3 65.2 + - - +
432A VAL* 3.6 3.9 + - + -
440A GLY* 3.7 27.4 - - - +
444A LEU* 4.9 3.1 - - + +
447A TRP* 4.1 27.1 - - + -
483A CYS* 3.6 2.2 - - - -
484A LEU* 2.8 49.3 + - + +
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Residues in contact with TRP 431 (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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393A MET* 4.1 19.5 - - + -
394A ALA 3.1 21.8 + - - +
395A ASP* 3.7 30.9 - - + +
396A PRO* 3.9 5.2 - - - +
398A TRP* 2.8 22.3 + - - -
430A LEU* 1.3 72.2 - - - +
432A VAL* 1.3 61.4 + - - +
455A ILE* 5.2 2.5 - - + -
457A TRP* 4.3 17.0 - - + -
481A GLU* 4.2 21.8 - - + -
482A HIS 3.4 24.5 - - - -
483A CYS* 3.6 30.3 - - + +
503A ILE* 4.9 7.6 - - + -
513A LYS* 3.5 45.8 - - + +
514A PRO* 4.3 9.2 - - + -
517A ILE* 4.7 19.5 - - + +
601A SAH 5.7 0.4 + - - -
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Residues in contact with VAL 432 (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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398A TRP* 3.8 13.0 - - + +
430A LEU* 3.8 8.3 - - + +
431A TRP* 1.3 81.2 - - - +
433A THR* 1.3 63.2 + - - +
436A ALA 3.3 26.0 - - - +
437A MET* 3.5 25.2 - - - +
440A GLY* 4.0 9.2 - - - -
481A GLU* 4.6 3.1 - - - +
482A HIS* 3.0 28.1 + - + +
484A LEU* 3.8 38.8 - - + -
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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