Contacts of the strand formed by residues 446 - 452 (chain R) in PDB entry 6CNC
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 LYS 446 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399R THR* 5.0 4.3 - - - +
400R VAL 3.4 7.6 - - - +
401R THR* 3.3 35.9 - - + +
441R ILE* 3.7 3.8 - - - +
442R PHE* 2.9 37.7 + - + +
444R SER* 3.6 10.6 + - - +
445R GLY* 1.3 80.0 - - - +
447R MET* 1.3 65.6 + - - +
18X T 3.2 28.1 + - - +
19X A 3.4 27.1 + - - -
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Residues in contact with MET 447 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399R THR* 2.6 28.5 + - - -
400R VAL* 2.8 55.4 + - + +
402R LEU* 3.6 42.6 - - + -
439R ALA* 5.6 3.6 - - - -
440R LEU 3.0 27.1 - - - +
441R ILE* 4.1 7.2 - - + +
442R PHE* 3.9 6.4 - - - -
446R LYS* 1.3 79.9 - - - +
448R VAL* 1.3 66.7 + - - +
449R VAL* 4.9 4.3 - - + -
462R SER* 4.5 16.8 - - - +
465R TYR* 5.4 9.0 - - + -
466R ALA* 5.6 3.6 - - + +
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Residues in contact with VAL 448 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397R VAL* 3.5 15.5 - - + -
398R ALA 3.2 4.7 - - - +
439R ALA* 3.0 3.9 - - - +
440R LEU* 2.7 46.5 + - + +
442R PHE* 3.5 27.8 - - + -
447R MET* 1.3 78.3 - - - +
449R VAL* 1.3 65.9 + - - +
450R THR* 4.2 4.9 - - + -
484R GLN* 3.4 18.4 - - - +
17X G 3.6 32.1 - - + +
18X T 3.6 11.2 - - - +
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Residues in contact with VAL 449 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396R ILE 3.1 7.3 - - - +
397R VAL* 2.7 36.2 - - - +
398R ALA* 2.9 34.2 + - + +
399R THR* 4.1 2.9 - - - +
400R VAL* 4.4 10.3 - - + -
437R THR* 6.4 0.4 - - + -
439R ALA* 3.7 10.3 - - + +
447R MET* 4.9 4.5 - - + -
448R VAL* 1.3 77.3 - - - +
450R THR* 1.3 68.4 + - - +
452R ALA* 4.4 3.4 - - + -
458R SER* 3.2 28.9 - - - +
461R ALA* 6.3 1.3 - - + -
462R SER* 3.3 25.1 - - - +
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Residues in contact with THR 450 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395R ASN* 3.6 10.5 - - - +
396R ILE 3.9 1.3 - - - -
397R VAL* 4.0 15.7 - - + -
437R THR* 3.6 5.7 - - - -
438R THR* 3.3 15.0 + - - +
439R ALA* 2.8 48.7 + - - +
448R VAL* 4.2 13.0 - - + -
449R VAL* 1.3 84.3 - - - +
451R GLY* 1.3 63.0 + - - +
452R ALA* 3.1 7.9 + - - -
16X A 4.9 0.2 - - + -
17X G 4.6 1.3 - - - +
47Y C 4.2 21.2 + - + +
48Y T 3.9 13.5 - - + +
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Residues in contact with GLY 451 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394R GLN 5.6 0.7 - - - -
395R ASN* 2.7 20.4 + - - +
435R PRO 4.1 2.4 - - - +
436R LYS 2.9 25.9 - - - +
437R THR* 3.2 12.4 - - - +
438R THR* 4.2 2.4 - - - -
450R THR* 1.3 76.3 - - - +
452R ALA* 1.3 57.4 + - - -
453R LYS* 3.6 3.3 + - - +
48Y T 4.6 13.5 + - - -
49Y A 5.6 3.8 - - - -
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Residues in contact with ALA 452 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394R GLN 4.5 0.2 - - - -
395R ASN* 2.6 9.9 + - - +
396R ILE* 2.7 48.6 + - + +
437R THR* 4.1 8.7 - - + -
449R VAL* 4.4 6.7 - - + -
450R THR 3.1 1.9 - - - +
451R GLY* 1.3 71.6 - - - +
453R LYS* 1.3 60.8 + - - +
454R SER 3.7 6.3 - - - +
457R ASP* 4.8 1.8 - - - -
458R SER* 3.6 37.2 - - - +
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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