Contacts of the strand formed by residues 465 - 470 (chain C) in PDB entry 2VK8
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 465 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377C PHE* 3.9 17.0 - + - -
437C ARG* 3.8 25.6 - - + -
438C VAL 2.9 18.2 + - - +
439C ILE* 4.0 13.9 - - + -
440C LEU* 2.9 32.4 + - - +
463C LYS 4.3 3.1 - - - -
464C PRO* 1.3 73.4 - - - +
466C LEU* 1.3 61.9 + - - +
467C PHE* 3.7 17.7 - + + -
527C PHE* 2.7 55.6 + + - -
528C ASN 3.4 8.8 + - - -
529C ASP 3.2 19.9 + - - -
530C ASN* 3.6 9.5 + - + -
534C ARG* 3.4 24.5 - - - -
536C ILE* 4.4 2.7 - - + -
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Residues in contact with LEU 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C THR* 6.3 0.2 - - + -
422C THR* 4.0 8.1 - - + -
440C LEU* 3.9 27.4 - - + -
442C ILE* 5.9 0.2 - - + -
454C ILE* 4.2 27.1 - - + -
457C MET* 4.1 13.7 - - + -
464C PRO* 3.8 26.0 - - + +
465C TYR* 1.3 73.2 - - - +
467C PHE* 1.3 64.1 + - - +
468C VAL* 3.6 4.9 + - + -
499C LEU* 4.7 3.4 - - + -
533C ILE* 4.3 13.0 - - + -
534C ARG 2.9 20.8 + - - +
535C MET* 3.3 27.4 - - + +
536C ILE* 2.8 25.5 + - - +
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Residues in contact with PHE 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C PHE* 4.1 17.5 - + - -
439C ILE* 4.0 15.3 - - + -
440C LEU* 2.8 22.0 + - - +
441C PHE* 3.5 37.2 - + + -
442C ILE* 3.0 29.5 + - - +
465C TYR* 3.7 24.7 - - + -
466C LEU* 1.3 70.3 - - - +
468C VAL* 1.3 60.4 + - - +
469C LEU* 4.0 1.2 + - - +
518C TRP* 4.1 17.5 - + - -
522C THR* 4.7 7.2 - - + -
527C PHE* 4.1 15.9 - + - -
536C ILE* 3.4 42.4 - - + +
538C VAL* 4.1 10.8 - - + -
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Residues in contact with VAL 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C ILE* 3.3 16.2 - - + +
443C GLY 4.6 0.2 - - - -
444C ASP* 4.2 10.5 - - - -
447C LEU* 4.0 32.3 - - + -
466C LEU* 4.1 11.7 - - + +
467C PHE* 1.3 74.3 - - - +
469C LEU* 1.3 65.3 + - - +
470C ASN 3.3 3.7 + - - +
495C HIS* 4.1 26.7 - - + +
535C MET* 4.1 23.3 - - + -
536C ILE 2.9 10.8 + - - +
537C GLU* 3.7 7.2 - - + +
538C VAL* 2.9 28.1 + - - -
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Residues in contact with LEU 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C GLN* 4.1 0.7 - - - +
370C MET* 4.1 11.0 - - + -
371C TRP* 3.9 17.9 - - + -
390C THR* 3.8 17.0 - - - +
391C SER* 3.3 26.7 - - - +
441C PHE* 4.1 13.0 - - + -
442C ILE 2.8 15.8 + - - +
443C GLY* 4.0 5.2 - - - -
444C ASP* 3.1 22.8 + - - +
467C PHE 4.9 2.0 - - - +
468C VAL* 1.3 69.6 - - - +
470C ASN* 1.3 61.7 + - - +
471C ASN* 3.3 11.4 + - - +
538C VAL* 3.7 29.6 - - + -
540C LEU* 4.0 23.8 - - + -
1564C TPP 4.9 4.3 - - - +
1565C MG 4.1 0.2 - - - -
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Residues in contact with ASN 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444C ASP* 3.6 10.7 - - - +
468C VAL 3.3 2.0 + - - +
469C LEU* 1.3 71.0 - - - +
471C ASN* 1.3 55.9 - - - +
472C ASP* 3.1 19.4 + - - +
493C TRP 5.4 2.2 + - - -
495C HIS* 4.0 13.8 + - + -
537C GLU* 2.8 33.4 + - + +
538C VAL 2.8 14.6 + - - +
539C MET* 3.7 25.0 - - - +
540C LEU* 3.0 26.0 + - - +
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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