Contacts of the strand formed by residues 456 - 462 (chain C) in PDB entry 2NT0
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 ALA 456 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C LEU* 4.4 10.3 - - + -
449C LEU 3.7 6.7 - - - +
450C MET* 4.8 1.1 - - - +
451C HIS* 5.0 1.5 + - - -
454C GLY 3.9 0.8 + - - -
455C SER* 1.3 75.0 + - - +
457C VAL* 1.3 63.4 + - - +
492C TYR 4.4 0.4 - - - -
493C LEU* 3.3 6.9 - - - +
494C TRP* 3.0 74.0 + - + +
496C ARG* 4.0 12.9 - - - +
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Residues in contact with VAL 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C PHE* 3.6 17.5 - - + +
427C ILE* 4.3 8.5 - - + -
447C VAL 4.1 0.2 - - - +
448C ALA* 3.3 2.8 - - - -
449C LEU* 2.9 58.7 + - + +
451C HIS* 3.6 30.3 - - + +
456C ALA* 1.3 74.6 - - - +
458C VAL* 1.3 67.5 + - - +
459C VAL* 4.5 7.2 - - + -
491C THR* 3.5 29.2 - - + -
492C TYR 3.2 6.1 - - - +
493C LEU* 4.3 3.8 - - + -
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Residues in contact with VAL 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 5.1 1.1 - - + -
69C LEU* 4.8 2.7 - - + -
436C LEU* 3.9 24.7 - - + -
447C VAL 3.3 10.8 - - - +
448C ALA* 3.8 17.7 - - + -
457C VAL* 1.3 79.6 - - - +
459C VAL* 1.3 65.8 + - - +
460C VAL* 3.7 23.6 - - + -
472C ILE* 4.3 11.9 - - + -
491C THR* 3.5 1.6 - - - -
492C TYR* 2.8 41.6 + - + +
494C TRP* 3.5 33.0 - - + -
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Residues in contact with VAL 459 (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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368C ILE* 4.7 2.8 - - + +
422C HIS 3.6 20.6 - - - +
423C PHE* 3.5 44.9 - - + -
427C ILE* 4.7 5.8 - - + -
445C ASP 3.9 0.4 - - - +
446C ALA* 3.2 26.7 - - - +
447C VAL* 3.0 18.0 + - + +
449C LEU* 5.5 0.9 - - + +
457C VAL* 4.5 6.7 - - + -
458C VAL* 1.3 74.4 - - - +
460C VAL* 1.3 65.3 + - - +
461C LEU 4.2 0.4 - - - -
489C ILE* 3.9 17.3 - - + -
490C HIS 3.4 9.6 - - - +
491C THR* 3.8 12.6 - - + +
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Residues in contact with VAL 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 4.5 3.4 - - + -
444C LEU* 3.7 32.1 - - + -
445C ASP 3.5 6.7 - - - +
446C ALA* 4.4 8.3 - - + -
458C VAL* 3.7 19.7 - - + -
459C VAL* 1.3 78.1 - - - +
461C LEU* 1.3 61.7 + - - +
462C ASN 4.2 0.6 + - - -
470C LEU* 4.2 16.8 - - + -
472C ILE* 4.5 1.6 - - + -
484C SER* 4.0 14.1 + - - +
488C SER* 4.7 0.3 + - - -
489C ILE* 3.4 4.6 - - - -
490C HIS* 2.8 42.6 + - + +
492C TYR* 4.1 23.1 - - + -
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Residues in contact with LEU 461 (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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361C MET* 4.1 5.8 - - + +
364C SER* 3.4 30.7 - - - +
365C HIS* 3.5 25.8 - - - +
368C ILE* 3.9 12.3 - - + +
419C HIS* 4.0 8.7 - - + -
444C LEU* 3.5 8.0 - - - +
445C ASP* 2.7 54.4 + - + +
459C VAL 4.2 0.2 - - - -
460C VAL* 1.3 73.4 - - - +
462C ASN* 1.3 62.0 + - - +
463C ARG* 3.7 23.1 + - + -
488C SER 3.5 16.8 - - - +
489C ILE* 3.9 15.5 - - + +
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Residues in contact with ASN 462 (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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361C MET* 4.5 2.3 - - - +
443C ASP 4.6 1.9 - - - +
444C LEU* 3.5 13.4 - - + +
461C LEU* 1.3 72.5 - - - +
463C ARG* 1.3 58.3 + - - +
464C SER* 2.6 35.9 + - - -
466C LYS 2.9 24.2 + - - -
468C VAL* 3.7 8.1 - - - +
484C SER* 3.0 38.7 + - - +
485C PRO 3.3 16.0 + - - +
487C TYR* 3.2 24.8 + - - -
488C SER* 3.0 16.0 + - - +
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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