Contacts of the strand formed by residues 461 - 469 (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 GLU 461 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411F VAL* 5.5 0.3 - - - +
412F LYS 4.6 0.9 - - - +
413F LEU* 3.6 13.5 - - + +
414F ARG* 2.6 68.6 + - + +
415F SER 4.1 2.5 + - - +
444F ARG* 3.0 44.3 + - - +
456F THR 3.8 0.9 - - - +
457F GLU* 3.4 0.9 - - - -
458F TYR 3.0 32.8 + - - +
459F ASP 3.2 5.2 + - - +
460F GLY* 1.3 78.1 - - - +
462F ILE* 1.3 63.5 + - - +
463F PHE* 3.9 4.8 - - + +
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Residues in contact with ILE 462 (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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444F ARG* 3.6 14.9 + - - -
455F THR* 3.9 27.4 - - + +
456F THR 3.4 12.8 - - - +
457F GLU* 4.1 24.9 - - + +
460F GLY 3.9 3.3 + - - +
461F GLU* 1.3 76.2 - - - +
463F PHE* 1.3 62.8 + - - +
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Residues in contact with PHE 463 (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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413F LEU* 4.3 8.7 - - + -
420F HIS* 4.2 2.0 - + - -
439F PHE* 4.1 4.9 - + - -
441F HIS* 3.4 33.9 - + - -
444F ARG* 3.6 39.0 - - + +
455F THR* 3.4 7.3 - - - -
456F THR* 3.0 65.8 + - + -
458F TYR* 4.2 18.4 - - + -
461F GLU* 3.9 10.1 - - - +
462F ILE* 1.3 75.4 - - - +
464F PRO* 1.3 79.4 - - + +
465F SER* 3.2 18.6 + - - -
476F GLN* 4.2 8.1 - - + -
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Residues in contact with PRO 464 (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* 3.4 16.1 - - - +
444F ARG* 3.5 8.5 - - - +
445F ALA* 3.2 40.0 + - + +
446F VAL* 5.0 0.7 - - - -
447F CYS* 4.4 9.6 - - - +
452F VAL* 4.0 26.2 - - + -
454F GLY 3.4 8.1 - - - +
455F THR* 4.5 0.7 - - + -
463F PHE* 1.3 91.6 - - + +
465F SER* 1.3 62.8 + - - +
466F ALA 3.2 1.3 - - - -
467F VAL* 4.0 15.3 - - + -
476F GLN* 4.5 0.2 - - - +
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Residues in contact with SER 465 (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* 4.3 0.9 - - - -
426F VAL* 3.4 15.1 - - - +
439F PHE* 3.6 18.2 - - - -
454F GLY 3.1 2.4 + - - -
455F THR* 3.2 13.7 + - - -
456F THR* 2.7 35.3 + - - -
463F PHE* 3.2 8.2 + - - -
464F PRO* 1.3 71.7 - - - +
466F ALA* 1.3 57.2 + - - +
475F PHE* 3.5 1.9 - - - -
476F GLN* 2.7 38.7 + - - -
477F PHE* 4.0 4.7 - - - -
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Residues in contact with ALA 466 (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* 4.5 0.4 - - - -
428F PHE* 3.7 25.8 - - + -
452F VAL* 3.8 2.1 - - - +
453F LEU* 2.8 24.9 + - + -
454F GLY* 3.0 26.0 + - - +
464F PRO* 3.2 1.1 - - - +
465F SER* 1.3 81.6 - - - +
467F VAL* 1.3 67.5 + - - +
474F GLY 3.1 11.4 - - - +
475F PHE* 3.8 9.9 - - + -
477F PHE* 4.8 1.1 - - + -
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Residues in contact with VAL 467 (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 20.4 - - + -
390F LEU* 4.4 0.7 - - + -
391F PHE* 4.1 16.2 - - + -
406F ILE* 4.2 18.4 - - + -
447F CYS* 3.9 21.8 - - - -
451F HIS* 3.2 13.9 - - + +
453F LEU* 3.7 8.7 - - - +
464F PRO* 4.0 12.1 - - + -
466F ALA* 1.3 80.4 - - - +
468F ARG* 1.3 64.9 + - - +
472F ILE 4.5 0.2 - - - -
473F LEU* 3.5 3.6 - - - -
474F GLY* 2.9 43.8 + - - +
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Residues in contact with ARG 468 (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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406F ILE* 4.8 2.0 - - - +
429F LYS* 4.4 14.5 - - - +
430F ASP* 2.6 44.4 + - - -
431F THR* 3.7 10.7 + - - +
432F PHE* 5.0 2.8 - - - -
450F GLU 4.0 7.8 + - - +
451F HIS* 2.8 40.1 + - - +
452F VAL 5.3 1.0 + - - -
453F LEU* 3.9 36.2 - - + +
467F VAL* 1.3 77.6 - - - +
469F LYS* 1.3 64.8 + - - +
470F GLY 4.0 18.3 + - - +
472F ILE 3.3 7.9 - - - +
473F LEU* 4.1 10.7 - - + +
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Residues in contact with LYS 469 (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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405F LEU 3.5 25.3 + - - +
406F ILE* 4.1 18.4 - - + +
407F GLU* 2.6 38.8 + - - +
451F HIS* 3.6 20.0 - - + +
468F ARG* 1.3 76.0 - - - +
470F GLY* 1.3 64.1 + - - +
471F ARG 3.3 0.5 + - - -
472F ILE* 3.0 33.4 + - + +
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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