Contacts of the strand formed by residues 480 - 488 (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 LYS 480 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A ILE* 4.0 19.7 - - + -
457A TRP 3.0 15.9 - - - +
458A VAL* 4.4 1.8 - - + -
459A LYS* 4.3 7.5 + - - +
478A HIS* 3.6 11.4 + - - +
479A GLY* 1.3 80.7 - - - +
481A GLU* 1.3 69.6 - - - +
482A HIS* 2.8 34.2 + - - +
258B ASP* 2.7 31.5 + - - +
260B CYS* 3.7 13.7 - - - -
312B ASP* 2.9 41.3 + - - +
313B LEU* 3.6 16.2 - - + -
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Residues in contact with GLU 481 (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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431A TRP* 4.2 12.5 - - + -
432A VAL 4.6 1.9 - - - +
433A THR* 4.4 19.6 + - - -
456A ILE* 3.3 4.9 - - - -
457A TRP* 2.8 66.1 + - + +
459A LYS* 3.4 25.3 + - - +
480A LYS* 1.3 77.6 - - - +
482A HIS* 1.3 67.6 + - - +
513A LYS* 4.8 13.2 + - - -
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Residues in contact with HIS 482 (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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431A TRP* 3.4 9.6 - - - -
432A VAL* 3.0 48.5 + - + +
437A MET* 3.6 23.9 - - + +
454A GLU* 2.6 27.4 + - - +
455A ILE 3.5 4.3 - - - +
456A ILE* 3.8 17.5 - - + +
480A LYS* 2.8 39.6 + - + +
481A GLU* 1.3 83.0 - - - +
483A CYS* 1.3 59.4 + - - +
258B ASP* 3.3 30.0 - - + +
287B HIS* 4.2 3.6 - + - -
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Residues in contact with CYS 483 (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* 5.7 0.2 - - - -
429A PHE* 3.8 26.5 - - - -
430A LEU 3.5 28.3 - - - -
431A TRP* 3.6 39.0 - - + -
454A GLU* 3.5 2.2 - - - -
455A ILE* 2.8 50.3 + - + +
482A HIS* 1.3 73.9 - - - +
484A LEU* 1.3 68.1 + - - +
485A VAL* 3.7 0.9 + - - +
517A ILE* 5.3 1.6 - - - -
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Residues in contact with LEU 484 (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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428A LEU 3.5 0.9 - - - +
429A PHE* 3.3 6.1 - - - -
430A LEU* 2.8 41.1 + - + +
432A VAL* 3.8 30.7 - - + -
437A MET 4.7 0.9 - - - +
440A GLY 3.9 9.2 - - - +
441A ARG* 3.9 48.0 - - + +
444A LEU* 4.0 19.7 - - + -
451A ARG* 4.1 9.9 - - + -
453A ASP 4.1 3.1 - - - -
454A GLU* 3.6 30.7 - - - +
483A CYS* 1.3 73.3 - - - +
485A VAL* 1.3 59.7 + - - +
486A GLY 4.1 0.4 - - - -
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Residues in contact with VAL 485 (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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427A PHE* 4.8 3.8 - - + -
428A LEU 3.3 7.6 - - - +
429A PHE* 4.0 22.9 - - + -
444A LEU* 4.3 2.5 - - - -
451A ARG* 3.4 3.8 - - - -
452A VAL* 2.8 34.3 + - + +
453A ASP* 3.0 36.5 + - + +
455A ILE* 3.9 28.5 - - + -
483A CYS 4.0 5.2 - - - +
484A LEU* 1.3 77.6 - - - +
486A GLY* 1.3 65.4 + - - +
280B VAL* 4.5 8.5 - - + -
281B PHE* 4.2 9.4 - - + -
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Residues in contact with GLY 486 (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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427A PHE* 3.2 10.4 - - - +
428A LEU* 2.8 33.0 + - - -
444A LEU* 3.9 17.6 - - - +
449A TYR* 3.7 11.2 - - - -
450A GLU 3.2 11.0 - - - -
452A VAL* 4.4 2.5 - - - -
485A VAL* 1.3 74.4 - - - +
487A VAL* 1.3 60.5 + - - -
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Residues in contact with VAL 487 (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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426A GLY 3.5 9.6 - - - +
427A PHE* 3.8 24.0 - - + -
448A GLY 4.2 0.5 - - - +
449A TYR* 3.2 5.8 - - - -
450A GLU* 2.9 41.6 + - + +
452A VAL* 3.6 28.7 - - + -
486A GLY* 1.3 74.0 - - - +
488A LYS* 1.3 64.8 + - - +
489A GLY 4.7 2.9 - - - +
491A PRO* 3.8 22.0 - - + -
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Residues in contact with LYS 488 (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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420A PRO* 3.0 23.5 + - - +
423A GLN* 2.5 35.5 + - + +
424A ASP* 4.0 12.9 + - - +
425A ASP* 3.2 1.4 - - - -
426A GLY 2.9 31.1 + - - +
447A TRP 3.6 21.5 - - - -
448A GLY* 3.4 21.1 - - - +
449A TYR* 3.5 30.5 - - + +
487A VAL* 1.3 75.4 - - - +
489A GLY* 1.3 70.5 + - - +
491A PRO* 3.6 3.8 - - - +
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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