Contacts of the strand formed by residues 450 - 460 (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 GLU 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A LEU* 3.6 2.2 - - - -
445A ASN* 4.3 3.4 - - - -
449A TYR* 1.3 74.1 - - - +
451A ARG* 1.3 72.3 + - - +
452A VAL* 3.4 16.9 + - + +
486A GLY* 3.2 0.3 - - - -
487A VAL* 2.9 39.3 + - + +
278B LYS* 3.8 25.2 + - - +
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Residues in contact with ARG 451 (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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441A ARG* 3.5 22.0 - - + +
444A LEU* 3.3 26.3 - - + +
445A ASN* 4.6 2.4 + - - +
450A GLU* 1.3 81.8 - - - +
452A VAL* 1.3 63.2 + - - +
453A ASP* 3.1 38.9 + - - +
454A GLU* 3.9 9.1 - - - +
484A LEU* 4.1 16.4 - - + -
485A VAL 3.4 15.0 - - - +
237B SER 5.2 2.0 + - - -
238B GLY* 2.8 31.5 + - - -
239B GLU* 4.4 0.4 - - - +
241B LEU* 3.5 19.4 - - - +
242B ASP* 2.9 43.7 + - - +
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Residues in contact with VAL 452 (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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450A GLU* 3.7 15.5 - - + +
451A ARG* 1.3 81.3 - - - +
453A ASP* 1.3 65.3 + - - +
485A VAL* 2.8 17.8 + - + +
486A GLY 4.4 0.2 - - - -
487A VAL* 3.6 37.2 - - + +
278B LYS* 3.4 31.0 - - + +
279B ALA* 4.0 1.4 - - - -
280B VAL* 3.6 27.1 - - + -
283B ARG* 2.7 30.7 + - - +
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Residues in contact with ASP 453 (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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451A ARG* 3.1 18.0 + - - +
452A VAL* 1.3 78.8 - - + +
454A GLU* 1.3 63.0 + - - +
484A LEU 4.0 0.2 - - - -
485A VAL* 3.0 44.5 + - + +
501A ASP* 4.7 4.5 - - + +
237B SER 5.0 2.1 - - - +
279B ALA* 3.7 0.2 - - - -
280B VAL* 2.7 31.4 + - - +
281B PHE* 2.8 26.4 + - + +
283B ARG* 2.8 38.0 + - - +
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Residues in contact with GLU 454 (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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437A MET* 5.3 1.7 - - - +
441A ARG* 2.8 32.6 + - - -
451A ARG* 3.9 6.5 + - - +
453A ASP* 1.3 80.5 + - - +
455A ILE* 1.3 65.2 + - - +
482A HIS* 2.6 36.5 + - + +
483A CYS 3.5 11.0 - - - +
484A LEU* 3.6 16.9 - - + +
501A ASP* 3.9 5.6 + - - +
237B SER 5.8 1.2 + - - -
241B LEU* 3.5 16.6 - - + +
245B ARG* 5.5 2.5 + - - -
258B ASP* 4.3 2.6 - - - +
285B LYS* 2.8 33.8 + - - +
287B HIS* 4.0 14.2 - - + -
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Residues in contact with ILE 455 (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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429A PHE* 3.8 19.1 - - + -
431A TRP* 5.2 3.1 - - + -
454A GLU* 1.3 75.4 - - - +
456A ILE* 1.3 71.8 + - - +
457A TRP 4.6 0.2 - - - +
481A GLU 3.9 0.2 - - - +
482A HIS* 3.5 3.1 - - - -
483A CYS* 2.8 44.4 + - + +
485A VAL* 3.9 9.2 - - + -
501A ASP* 3.3 20.9 - - + +
503A ILE* 3.8 28.9 - - + -
517A ILE* 3.9 10.3 - - + -
520A MET* 3.9 15.0 - - + -
281B PHE* 3.7 32.5 - - + -
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Residues in contact with ILE 456 (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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454A GLU* 3.8 1.1 + - + +
455A ILE* 1.3 83.8 - - - +
457A TRP* 1.3 59.6 + - - +
458A VAL* 3.8 4.8 + - + -
480A LYS* 4.0 16.4 - - + -
481A GLU 3.3 3.8 - - - +
482A HIS* 3.8 34.3 - - + +
501A ASP 3.0 4.4 + - - -
502A VAL* 3.4 10.7 - - + +
503A ILE 2.9 25.5 + - - +
260B CYS* 3.9 15.3 - - + -
262B ILE* 3.6 31.9 - - + -
285B LYS* 3.5 33.7 - - + -
287B HIS* 4.6 2.5 - - + -
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Residues in contact with TRP 457 (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* 4.3 15.0 - + + -
455A ILE* 4.2 1.0 - - - +
456A ILE* 1.3 70.7 - - - +
458A VAL* 1.3 69.6 + - - +
459A LYS* 3.6 23.9 + - + +
480A LYS* 3.0 6.8 - - - -
481A GLU* 2.8 63.7 + - + +
503A ILE* 3.4 16.4 - - + -
505A ALA* 2.9 30.2 + - - +
506A GLU 3.8 18.6 - - - -
507A VAL* 4.0 15.0 - - + -
511A SER 5.8 0.9 - - - -
512A HIS 3.8 16.8 - - - -
513A LYS* 4.1 16.6 - - + -
514A PRO* 3.5 36.8 - - + -
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Residues in contact with VAL 458 (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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456A ILE* 4.4 7.4 - - + -
457A TRP* 1.3 74.5 - - - +
459A LYS* 1.3 64.6 + - - +
460A THR* 3.6 4.2 + - + -
466A ILE* 4.0 14.6 - - + -
479A GLY 3.5 4.3 - - - +
480A LYS* 4.4 1.1 - - + +
502A VAL* 4.0 15.3 - - + -
503A ILE 2.7 12.5 + - - +
504A VAL* 3.6 8.1 - - + +
505A ALA 3.2 24.6 + - - -
134B ILE* 3.9 21.8 - - + -
262B ILE* 3.5 31.4 - - + -
313B LEU* 3.9 23.1 - - + -
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Residues in contact with LYS 459 (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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457A TRP* 3.7 36.8 - - + +
458A VAL* 1.3 71.0 - - - +
460A THR* 1.3 63.5 + - - +
466A ILE* 4.0 21.5 - - - +
467A ILE 4.6 1.9 + - - -
478A HIS* 4.9 9.3 + - - +
479A GLY* 3.0 14.3 + - - +
480A LYS 4.3 16.5 + - - +
481A GLU* 3.4 31.1 + - + +
505A ALA 3.6 5.4 - - - -
507A VAL* 3.7 27.4 - - + -
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Residues in contact with THR 460 (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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458A VAL* 4.4 6.1 - - + +
459A LYS* 1.3 78.9 - - - +
461A ASN* 1.3 68.2 + - - +
464A GLN* 4.0 27.1 - - - +
465A ARG 3.3 10.8 - - - +
466A ILE 4.7 0.4 - - - +
467A ILE* 5.5 2.5 - - - -
504A VAL* 3.7 26.9 - - + +
505A ALA* 3.3 21.8 + - - -
506A GLU* 3.4 23.4 + - - +
507A VAL* 3.9 7.4 + - - +
134B ILE* 4.5 9.9 - - + -
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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