Contacts of the strand formed by residues 401 - 405 (chain F) in PDB entry 5KRA
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 401 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395F SER* 3.7 12.8 - - - +
398F HIS* 3.0 23.7 + - + +
399F PRO 3.1 7.9 + - - +
400F GLY* 1.3 85.6 + - - +
402F LEU* 1.3 61.1 + - - +
403F LEU 4.1 0.4 - - - -
409F LEU* 3.7 41.7 - - + -
410F LEU 3.3 11.2 - - - +
411F ASP* 3.9 24.7 + - + +
414F GLN* 5.3 2.9 - - - +
429F LEU* 3.4 13.2 - - - +
432F SER* 5.2 0.9 + - - -
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Residues in contact with LEU 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391F LEU* 4.3 10.8 - - + -
392F VAL* 5.2 1.8 - - - -
395F SER* 3.6 15.5 - - - +
401F LYS* 1.3 79.0 - - - +
403F LEU* 1.3 59.4 + - - +
404F PHE* 3.2 30.5 + - + -
409F LEU* 3.7 3.0 - - - -
410F LEU 2.7 29.9 + - - -
425F PHE* 3.5 38.8 - - + +
428F LEU* 3.7 46.9 - - + +
429F LEU* 3.8 17.5 - - + -
432F SER* 5.1 1.6 - - - -
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Residues in contact with LEU 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326F ILE* 6.1 1.1 - - + -
391F LEU* 3.4 6.6 - - - +
394F ARG* 2.8 65.2 + - + +
395F SER* 2.8 18.8 + - - +
398F HIS* 3.9 19.3 - - + +
402F LEU* 1.3 69.2 - - - +
404F PHE* 1.3 53.7 + - - +
405F ALA 3.3 26.0 - - - +
406F PRO* 4.0 16.8 - - + +
408F LEU 3.9 0.4 - - - -
409F LEU* 3.7 29.3 - - + +
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Residues in contact with PHE 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327F LEU 4.7 2.1 - - - +
346F LEU* 3.7 22.7 - - + -
349F LEU* 3.2 18.7 - - + +
353F GLU* 4.3 0.3 - - - +
391F LEU* 3.6 33.2 - - + -
394F ARG* 2.8 23.4 + - - +
402F LEU* 3.2 21.5 + - + -
403F LEU* 1.3 73.3 - - - +
405F ALA* 1.3 59.6 + - - +
408F LEU* 3.2 21.9 + - + +
410F LEU* 4.0 20.6 - - + -
425F PHE* 3.8 28.5 - + - -
601F 6WT 3.6 50.7 - + - -
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Residues in contact with ALA 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326F ILE* 5.3 0.2 - - - -
327F LEU 3.7 6.5 - - - +
328F TYR 4.2 0.2 - - - -
329F SER* 3.6 26.5 - - - +
349F LEU* 4.3 4.0 - - + -
394F ARG* 5.1 1.3 - - - +
403F LEU* 3.2 12.3 - - - +
404F PHE* 1.3 78.9 - - - +
406F PRO* 1.3 67.5 - - + +
407F ASN* 3.3 18.2 - - - +
408F LEU* 2.7 31.9 + - + +
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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