Contacts of the strand formed by residues 440 - 450 (chain C) in PDB entry 5I4A
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 ASN 440 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437C LYS* 3.5 31.9 + - - +
438C GLU 3.0 8.4 + - - +
439C LYS* 1.3 90.8 - - - +
441C LEU* 1.3 60.3 + - - +
442C TYR* 3.2 42.8 + - + +
464C ASP* 4.7 7.3 - - - -
465C ASN 4.8 0.2 + - - -
500C TYR* 3.8 7.8 - - - -
510C ASN* 2.9 34.7 + - - +
512C PHE* 4.0 18.4 - - + -
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Residues in contact with LEU 441 (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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439C LYS 4.2 0.4 + - - -
440C ASN* 1.3 71.7 - - - +
442C TYR* 1.3 60.3 + - - +
443C ILE* 3.7 24.4 + - + -
462C ALA* 4.0 17.9 - - + -
463C VAL 4.2 2.0 - - - +
470C LEU* 3.6 30.3 - - + -
496C ALA 4.2 3.1 - - - +
497C PHE* 3.9 29.4 - - + -
500C TYR* 4.1 7.4 - - + -
508C PRO* 3.7 32.3 - - + +
510C ASN 2.9 9.1 + - - +
511C VAL* 3.5 6.3 - - + +
512C PHE 2.8 32.7 + - - +
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Residues in contact with TYR 442 (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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434C MET* 3.6 25.2 - - + +
437C LYS* 3.4 20.3 - - - +
440C ASN* 3.2 42.2 + - + -
441C LEU* 1.3 71.2 - - - +
443C ILE* 1.3 60.1 + - - +
461C ALA 3.8 0.5 - - - +
462C ALA* 3.3 3.3 - - - +
463C VAL* 2.9 60.4 + - + +
464C ASP 4.2 9.0 - - - -
465C ASN* 4.2 4.9 - - - -
512C PHE* 3.5 49.0 - + + -
514C LEU* 5.3 10.3 - - + -
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Residues in contact with ILE 443 (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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441C LEU* 3.7 28.9 - - + -
442C TYR* 1.3 78.2 - - - +
444C GLY* 1.3 63.0 + - - +
445C ILE* 3.6 25.8 - - + -
460C ILE* 4.4 13.5 - - + -
461C ALA 3.2 7.9 - - - +
462C ALA* 4.0 8.5 - - + -
493C TYR* 3.6 37.9 - - + -
496C ALA* 4.3 8.1 - - + -
511C VAL* 4.0 2.5 - - + -
512C PHE 2.9 12.7 + - - +
513C ILE* 3.8 10.8 - - + -
514C LEU* 2.8 34.9 + - - +
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Residues in contact with GLY 444 (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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443C ILE* 1.3 71.7 - - - +
445C ILE* 1.3 65.9 + - - +
446C ASP 4.2 0.2 - - - -
459C CYS 4.0 0.2 - - - +
460C ILE* 3.1 6.6 - - - -
461C ALA* 2.8 39.3 + - - -
514C LEU* 3.3 11.2 - - - -
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Residues in contact with ILE 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C ILE* 3.6 17.9 - - + -
444C GLY* 1.3 83.6 - - - +
446C ASP* 1.3 61.9 + - - +
447C LEU* 3.9 8.1 - - + -
458C LEU* 4.1 22.7 - - + -
459C CYS 3.7 1.3 - - - -
460C ILE* 3.5 17.7 - - + -
489C LEU* 4.3 18.4 - - + -
493C TYR* 6.4 1.3 - - + -
513C ILE* 4.1 22.7 - - + -
514C LEU 2.8 17.8 + - - +
515C ARG* 3.7 23.8 - - - +
516C ASP* 2.9 29.2 + - - +
519C PHE* 5.8 2.0 - - + -
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Residues in contact with ASP 446 (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 GLY 4.2 0.2 - - - -
445C ILE* 1.3 72.3 - - - +
447C LEU* 1.3 64.9 + - - +
448C SER* 4.4 9.2 + - - -
457C ASN 3.7 1.6 - - - +
458C LEU* 3.4 3.3 - - - +
459C CYS* 2.8 51.1 + - + +
516C ASP* 3.9 23.5 - - + +
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Residues in contact with LEU 447 (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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445C ILE* 3.9 6.0 + - + -
446C ASP* 1.3 76.9 + - - +
448C SER* 1.3 61.6 + - - +
449C HIS* 3.7 22.2 - - + +
456C THR* 4.8 5.8 - - - +
457C ASN 3.5 16.2 - - - +
458C LEU* 3.9 29.2 - - + -
485C ASN* 5.4 10.1 - - + +
489C LEU* 4.5 17.0 - - + -
515C ARG* 3.3 32.4 + - - +
516C ASP* 5.2 4.2 + - - +
521C GLU* 3.3 35.0 - - + +
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Residues in contact with SER 448 (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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446C ASP* 4.2 9.5 + - - -
447C LEU* 1.3 74.7 - - - +
449C HIS* 1.3 67.3 + - - +
456C THR* 3.4 3.5 - - - -
457C ASN* 2.9 53.3 + - - +
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Residues in contact with HIS 449 (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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447C LEU* 3.7 28.7 - - + +
448C SER* 1.3 76.5 + - - +
450C ASP* 1.3 62.0 + - - +
451C THR* 3.6 5.2 + - - +
455C LYS 3.7 2.5 - - - -
456C THR* 3.2 21.2 - - + +
480C LEU* 3.7 23.1 - - + +
482C GLU* 5.0 2.9 + - - -
485C ASN* 3.7 20.0 - - + -
515C ARG* 5.1 0.9 - - - -
520C ILE* 5.7 7.9 - - + -
521C GLU* 3.0 30.9 + - + +
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Residues in contact with ASP 450 (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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448C SER 4.3 0.4 - - - -
449C HIS* 1.3 70.0 - - - +
451C THR* 1.3 54.9 + - - +
452C TYR* 3.0 42.9 + - - -
453C ALA* 3.2 22.3 + - + +
454C ARG* 2.7 35.0 + - - -
455C LYS* 2.6 27.6 + - + +
457C ASN* 5.6 6.5 - - - +
480C LEU* 3.2 3.8 - - - +
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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