Contacts of the strand formed by residues 450 - 454 (chain C) in PDB entry 4QGC
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 ILE 450 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428C ILE* 3.4 14.8 - - + +
430C VAL* 4.0 20.2 - - + -
438C ALA* 4.5 13.0 - - + +
441C VAL* 3.7 14.4 - - + -
442C ALA* 3.5 41.7 - - + +
446C PRO* 3.9 22.9 - - + -
448C ALA 4.2 0.4 - - - +
449C PRO* 1.3 71.9 - - - +
451C ILE* 1.3 61.3 + - - +
452C ALA 3.3 3.2 + - - +
467C ARG 5.1 0.9 - - - +
468C GLY* 2.8 19.2 + - - +
469C ILE* 3.5 13.9 - - + +
470C PHE* 2.6 31.7 + - - -
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Residues in contact with ILE 451 (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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427C ALA* 3.8 27.1 - - + -
428C ILE 2.9 9.8 + - - +
429C ILE* 3.5 12.6 - - + +
430C VAL 2.9 24.4 + - - -
449C PRO 3.6 1.3 + - - +
450C ILE* 1.3 70.1 - - - +
452C ALA* 1.3 61.1 + - - +
453C VAL* 3.5 2.0 + - + -
470C PHE* 3.4 9.2 - - + +
472C VAL* 4.0 23.6 - - + -
493C ALA* 3.8 39.9 - - + +
496C VAL* 5.1 3.1 - - + -
497C GLY* 4.2 4.3 - - - +
502C PHE* 4.1 24.9 - - + -
503C PHE* 4.1 11.0 - - + -
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Residues in contact with ALA 452 (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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430C VAL* 3.5 7.6 - - - +
432C THR* 4.3 9.4 - - + -
438C ALA* 3.9 27.6 - - + -
450C ILE* 3.3 2.7 + - + +
451C ILE* 1.3 70.2 - - - +
453C VAL* 1.3 62.3 + - - +
454C THR* 3.8 3.8 + - + +
463C ALA* 5.2 3.4 - - + -
469C ILE* 3.9 17.5 - - + -
470C PHE 3.2 6.7 + - - -
471C PRO* 3.5 7.9 - - + +
472C VAL* 2.9 29.8 + - - +
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Residues in contact with VAL 453 (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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429C ILE* 4.0 8.7 - - + -
430C VAL 2.9 8.9 + - - -
431C LEU* 3.7 12.5 - - + +
432C THR* 3.1 25.6 + - - +
451C ILE* 4.0 8.1 - - + +
452C ALA* 1.3 72.0 - - - +
454C THR* 1.3 61.0 + - - +
472C VAL* 3.7 19.3 - - + -
474C CYS* 4.2 15.3 - - + -
489C ARG* 3.9 40.5 + - + +
492C PHE* 4.5 2.9 - - + -
493C ALA* 3.6 31.2 - - + -
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Residues in contact with THR 454 (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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432C THR* 3.3 25.1 + - + -
433C LYS* 3.8 2.3 + - - -
452C ALA* 4.6 5.2 - - + +
453C VAL* 1.3 74.7 - - - +
455C ARG* 1.3 68.6 + - - +
456C ASN* 2.9 30.4 + - - +
459C THR* 3.1 19.9 + - - +
460C ALA* 3.8 17.9 - - + +
471C PRO* 5.8 0.2 - - + -
472C VAL 3.2 12.4 + - - +
473C LEU* 3.6 3.1 - - + -
474C CYS* 2.8 27.7 + - - +
489C ARG* 6.1 1.8 - - - +
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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