Contacts of the strand formed by residues 395 - 401 (chain A) in PDB entry 1K8F
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 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A CYS 2.9 8.4 + - - +
376A LYS* 3.2 30.2 - - + +
377A LYS 3.0 20.8 + - - -
393A ASN* 4.9 3.0 + - - +
394A SER* 1.3 89.9 + - - +
396A ASP* 1.3 73.3 + - + +
397A VAL* 3.5 1.7 - - - +
412A LYS 4.3 9.5 + - - -
414A ASP* 3.3 35.4 + - + +
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Residues in contact with ASP 396 (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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376A LYS* 5.6 0.2 + - - -
377A LYS* 3.2 55.2 + - + +
378A LEU 3.3 2.6 + - - +
395A LYS* 1.3 79.2 - - - +
397A VAL* 1.3 61.6 + - - +
398A LYS 4.2 0.3 + - - -
414A ASP 3.0 19.6 + - - +
415A GLY* 3.1 14.2 + - - -
417A HIS* 6.0 2.2 - - - -
436A GLU* 5.0 4.9 - - - +
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Residues in contact with VAL 397 (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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372A VAL* 4.1 16.2 - - + -
375A CYS 4.2 3.4 - - - +
378A LEU* 3.4 19.5 - - + +
380A LEU* 5.8 0.2 - - + -
391A ILE* 3.9 23.1 - - + -
394A SER* 3.4 33.7 - - - +
395A LYS 4.1 4.9 - - - +
396A ASP* 1.3 76.5 - - - +
398A LYS* 1.3 65.2 + - - +
399A VAL* 3.8 21.5 - - + -
413A THR* 4.9 0.4 - - + -
415A GLY 3.0 8.9 + - - +
416A CYS* 3.2 8.1 - - - -
417A HIS* 3.0 26.4 + - - -
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Residues in contact with LYS 398 (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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378A LEU 2.9 12.7 + - - +
379A GLY* 4.4 8.2 - - - -
380A LEU* 2.7 59.8 + - - +
381A VAL* 4.6 8.1 - - - +
396A ASP 5.5 0.4 - - - +
397A VAL* 1.3 74.7 - - - +
399A VAL* 1.3 57.9 + - - +
400A GLN* 4.2 17.7 + - - +
417A HIS* 3.6 9.6 - - + +
419A TYR* 3.5 39.3 - - + +
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Residues in contact with VAL 399 (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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380A LEU* 3.4 22.0 - - + -
382A PHE* 3.5 26.7 - - + -
389A VAL* 4.2 10.1 - - + -
391A ILE* 3.9 22.4 - - + -
397A VAL* 3.8 19.5 - - + -
398A LYS* 1.3 78.2 - - - +
400A GLN* 1.3 64.2 + - - +
401A VAL* 5.8 0.7 - - - -
408A ILE* 5.0 10.7 - - + +
416A CYS* 4.3 9.2 - - - -
417A HIS 3.0 8.1 + - - +
418A ALA* 3.6 5.3 - - - -
419A TYR* 2.8 28.7 + - - +
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Residues in contact with GLN 400 (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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380A LEU 3.0 12.6 + - - +
381A VAL* 4.2 12.7 - - + +
382A PHE* 2.9 34.3 + - - +
398A LYS* 4.2 14.5 + - - +
399A VAL* 1.3 78.0 - - - +
401A VAL* 1.3 73.9 + - - +
402A MET* 3.8 25.3 - - - +
419A TYR* 3.5 21.1 - - + +
420A LEU 4.5 1.8 + - - -
421A SER* 5.8 0.4 - - - -
448A PHE* 3.9 25.7 - - - -
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Residues in contact with VAL 401 (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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382A PHE* 3.2 36.1 - - + -
383A ASP 3.9 9.6 - - - +
400A GLN* 1.3 86.5 + - - +
402A MET* 1.3 64.2 + - - +
403A GLY 4.1 4.3 - - - +
404A LYS 4.0 8.5 - - - -
405A VAL* 3.6 29.2 - - + -
408A ILE* 4.6 4.7 - - + -
419A TYR 3.1 18.4 + - - +
420A LEU* 4.0 8.9 - - + +
421A SER* 3.4 14.7 - - - -
424A SER* 3.8 16.4 - - - +
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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