Contacts of the strand formed by residues 467 - 477 (chain C) in PDB entry 3CB4
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 467 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109C GLU* 4.1 15.0 - - - +
110C ALA* 3.2 33.5 + - - +
111C GLN* 5.1 6.7 - - - -
408C MET* 3.3 10.4 - - - +
409C LEU* 3.1 38.9 + - - +
455C PHE* 5.9 1.1 - - - -
458C LEU* 5.2 0.8 - - - +
465C TYR 4.0 2.0 + - - -
466C ALA* 1.3 73.2 - - - +
468C LEU* 1.3 60.0 + - - +
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Residues in contact with LEU 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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81C HIS* 5.8 4.3 - - - -
110C ALA* 4.4 2.2 - - - -
111C GLN* 4.4 19.1 + - - +
406C CYS* 4.4 9.2 - - + -
407C HIS 3.6 3.1 - - - -
408C MET* 4.6 11.4 - - + -
450C VAL* 5.5 1.8 - - + -
454C PHE* 3.6 33.9 - - + -
455C PHE* 3.7 40.3 - - + -
458C LEU* 4.3 16.4 - - + -
466C ALA 4.1 0.4 + - - -
467C SER* 1.3 77.4 - - - +
469C ASP* 1.3 76.8 + - - +
470C TYR* 3.7 38.8 - - + +
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Residues in contact with ASP 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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82C VAL* 3.1 30.9 + - - +
110C ALA* 4.0 15.0 - - + +
111C GLN* 4.7 5.4 - - - +
114C ALA* 3.3 29.6 - - - +
406C CYS* 3.4 0.9 - - - -
407C HIS* 2.7 62.7 + - + +
468C LEU* 1.3 79.9 - - - +
470C TYR* 1.3 58.8 + - - +
471C ASN* 3.8 10.4 - - - +
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Residues in contact with TYR 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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81C HIS* 4.3 12.7 + + - -
82C VAL* 3.4 33.7 - - + +
83C ASP* 3.8 13.6 + - - -
294C GLN* 3.3 33.0 + - - -
345C LEU* 3.9 24.3 + - + +
346C LEU* 5.6 0.4 - - + -
404C ALA* 4.4 2.5 - - + -
405C GLU 3.3 4.3 - - - +
406C CYS* 3.8 19.7 - - - -
447C MET* 3.9 21.1 - - + -
450C VAL* 4.0 22.7 - - + -
451C VAL* 5.4 2.2 - - + +
455C PHE* 6.4 2.9 - + + -
468C LEU* 3.7 23.3 - - + -
469C ASP* 1.3 76.8 + - - +
471C ASN* 1.3 67.0 + - - +
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Residues in contact with ASN 471 (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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82C VAL* 4.1 11.3 - - + +
85C SER* 6.0 1.6 - - - +
294C GLN* 5.6 1.8 - - - -
404C ALA* 4.5 3.1 - - - -
405C GLU* 2.9 48.6 + - - +
407C HIS* 4.5 7.0 - - - -
447C MET* 4.5 3.6 - - - -
469C ASP* 3.8 15.2 - - - +
470C TYR* 1.3 80.5 - - - +
472C PHE* 1.3 73.8 + - - +
473C LYS* 5.5 0.6 - - - +
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Residues in contact with PHE 472 (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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294C GLN* 5.1 3.6 + - - +
402C PRO* 4.1 17.3 - - + -
403C ILE 4.1 5.6 - - - -
447C MET* 4.1 17.1 - - + +
471C ASN* 1.3 85.3 + - - +
473C LYS* 1.3 66.2 + - - +
474C ARG* 3.3 36.3 - - - -
475C PHE* 3.6 42.2 - + - -
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Residues in contact with LYS 473 (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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403C ILE* 3.1 15.0 + - + +
404C ALA 4.6 0.2 - - - -
405C GLU* 3.6 48.0 + - + +
444C GLU* 3.5 24.7 - - - +
471C ASN* 5.8 0.4 - - - +
472C PHE* 1.3 86.2 - - - +
474C ARG* 1.3 68.3 + - + +
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Residues in contact with ARG 474 (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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403C ILE* 2.8 47.5 + - + +
444C GLU* 2.6 39.2 + - - -
472C PHE* 3.3 17.2 - - - -
473C LYS* 1.3 85.9 - - + +
475C PHE* 1.3 77.6 + - - +
476C GLN* 2.5 34.9 + - - -
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Residues in contact with PHE 475 (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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371C VAL* 3.4 28.7 - - + -
373C GLU* 3.4 51.1 - - + +
383C TYR* 3.8 30.5 - + - -
400C ARG* 4.0 11.7 - - + -
401C GLU 3.5 4.3 - - - -
402C PRO* 3.7 22.4 - - + -
472C PHE* 3.6 29.1 - + - -
474C ARG* 1.3 88.5 - - - +
476C GLN* 1.3 61.8 + - - +
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Residues in contact with GLN 476 (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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400C ARG* 3.5 6.7 - - - +
401C GLU* 2.6 41.7 + - - +
403C ILE* 3.7 20.6 - - + +
474C ARG* 2.5 43.9 + - - +
475C PHE* 1.3 74.7 - - - +
477C ALA* 1.3 77.5 + - + +
478C SER* 3.5 1.2 + - - -
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Residues in contact with ALA 477 (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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398C GLU* 3.5 36.3 - - + +
399C LEU 3.8 3.4 - - - -
400C ARG* 3.4 12.8 - - - +
476C GLN* 1.3 88.1 - - + +
478C SER* 1.3 62.1 + - - +
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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