Contacts of the strand formed by residues 443 - 447 (chain F) in PDB entry 1K9V
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 TYR 443 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388F GLN* 3.1 23.6 + - - +
394F SER* 3.9 11.7 - - - -
395F GLU* 4.0 8.2 - - + +
396F GLU* 3.3 64.5 + - + +
410F VAL* 3.5 14.6 - - + -
411F VAL* 3.3 7.2 - - - -
412F LYS* 3.2 47.4 - - + -
413F LEU* 4.6 0.9 - - - -
441F HIS* 2.7 28.7 + - - +
442F THR* 1.3 98.3 - - + +
444F ARG* 1.3 58.4 + - - +
476F GLN* 3.4 0.7 - - - +
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Residues in contact with ARG 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388F GLN* 5.1 0.2 - - - -
410F VAL* 3.2 7.9 - - - +
411F VAL* 2.8 54.8 + - + +
412F LYS 4.5 2.0 - - - +
413F LEU* 4.0 14.6 - - + -
414F ARG* 4.8 4.8 - - - +
441F HIS* 4.8 0.2 - - - -
443F TYR* 1.3 74.3 - - - +
445F ALA* 1.3 83.0 + - - +
446F VAL* 3.6 22.8 - - - +
461F GLU* 3.0 33.5 + - - +
462F ILE 3.6 18.2 + - - -
463F PHE* 3.6 29.8 - - + +
464F PRO* 3.5 13.3 - - - +
476F GLN* 4.1 6.7 - - - -
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Residues in contact with ALA 445 (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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387F MET* 4.0 18.7 - - + +
388F GLN* 5.2 2.4 - - + +
391F PHE* 3.6 38.6 - - + -
409F ASN 3.5 5.2 - - - -
410F VAL* 4.4 5.2 - - + -
444F ARG* 1.3 95.1 + - - +
446F VAL* 1.3 61.3 + - - +
464F PRO* 3.2 22.2 + - + +
467F VAL* 5.0 0.2 - - + -
476F GLN* 4.6 3.8 + - - -
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Residues in contact with VAL 446 (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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408F GLY* 3.2 4.9 - - - -
409F ASN* 2.8 45.8 + - - +
411F VAL* 3.7 26.9 - - + -
444F ARG* 3.6 25.8 - - - +
445F ALA* 1.3 79.3 - - - +
447F CYS* 1.3 64.3 + - - +
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Residues in contact with CYS 447 (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 PHE* 3.6 22.7 - - + -
407F GLU 3.7 11.9 - - - +
408F GLY* 4.4 0.4 - - - -
446F VAL* 1.3 78.1 - - - +
448F GLU* 1.3 72.4 + - - +
449F GLU 4.0 0.5 + - - -
451F HIS* 4.2 10.5 - - + -
452F VAL* 3.9 19.4 - - - +
464F PRO* 4.4 10.2 - - - +
467F VAL* 3.9 24.7 - - - -
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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