Contacts of the strand formed by residues 504 - 510 (chain F) in PDB entry 2VKX
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 SER 504 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502F SER 4.9 2.0 - - - -
503F PRO* 1.3 75.6 - - - +
505F ILE* 1.3 60.4 + - - +
506F ASP* 3.1 14.7 + - - +
519F PHE* 3.0 3.8 - - - -
520F ASP* 2.7 49.8 + - - +
588F SER* 5.0 0.4 - - - -
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Residues in contact with ILE 505 (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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654E GLY* 4.1 14.6 - - - +
503F PRO 4.2 0.2 + - - -
504F SER* 1.3 74.3 + - - +
506F ASP* 1.3 59.8 + - - +
507F GLN 3.4 25.4 - - - +
508F VAL* 3.6 11.4 - - + -
517F VAL* 3.4 15.7 - - + -
518F GLN 3.5 3.6 - - - -
519F PHE* 3.6 2.0 - - - -
574F VAL* 3.5 28.5 - - + +
575F ARG* 4.1 4.5 - - - -
576F LEU* 3.5 28.0 - - + -
588F SER* 4.0 19.2 - - - +
589F ALA 4.2 4.0 - - - +
591F SER* 3.8 19.5 + - - +
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Residues in contact with ASP 506 (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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653E SER* 3.1 40.7 + - - +
654E GLY* 4.4 5.8 - - - -
504F SER* 3.1 17.3 + - - +
505F ILE* 1.3 75.2 - - - +
507F GLN* 1.3 65.6 + - + +
518F GLN* 2.6 19.2 + - + +
519F PHE 3.7 6.1 - - - +
520F ASP* 2.3 36.4 - - - +
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Residues in contact with GLN 507 (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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623E LYS* 6.3 0.7 - - - +
626E ASP* 3.4 26.7 + - - +
630E PRO* 3.5 10.8 - - + +
631E ILE* 2.6 49.8 + - - +
653E SER* 3.7 6.7 + - - +
505F ILE* 3.4 2.6 - - - +
506F ASP* 1.3 91.0 - - + +
508F VAL* 1.3 75.2 + - - +
509F GLU* 4.2 1.3 - - + +
516F GLN 4.4 1.1 - - - +
518F GLN* 2.8 60.3 + - + +
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Residues in contact with VAL 508 (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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623E LYS* 4.3 19.8 - - + +
624E GLN 4.8 2.3 - - - +
626E ASP* 5.3 1.4 - - - +
505F ILE* 3.6 18.6 - - + -
507F GLN* 1.3 90.3 + - - +
509F GLU* 1.3 62.3 + - - +
510F PRO* 3.2 11.3 - - - +
515F ALA* 4.4 11.2 - - + -
516F GLN 3.5 4.7 - - - +
517F VAL* 4.0 16.4 - - + -
574F VAL* 4.2 8.1 - - + -
591F SER* 3.8 15.0 - - - +
593F PHE* 3.5 42.6 - - + -
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Residues in contact with GLU 509 (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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625E ASP* 2.9 28.0 - - - +
626E ASP* 2.7 51.5 + - - +
628E GLY* 4.2 6.4 + - - -
507F GLN* 5.3 1.7 - - + +
508F VAL* 1.3 72.2 - - - +
510F PRO* 1.3 64.4 - - - +
511F TYR* 3.5 38.4 - - + +
515F ALA* 3.4 2.9 - - - -
516F GLN* 2.9 43.8 + - + +
596F GLN* 4.1 0.3 + - - -
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Residues in contact with PRO 510 (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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623E LYS 4.4 2.5 - - - +
624E GLN* 3.9 14.6 - - - +
625E ASP 3.8 12.8 - - - +
508F VAL* 3.2 13.5 - - + +
509F GLU* 1.3 93.5 - - - +
511F TYR* 1.3 57.3 + - - +
515F ALA* 4.1 7.4 - - + -
593F PHE* 3.7 25.4 - - + -
594F LYS 3.4 26.9 - - - +
595F THR* 3.9 5.4 - - + -
596F GLN* 2.6 31.2 + - + -
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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