Contacts of the strand formed by residues 469 - 479 (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 ILE 469 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461C ALA* 5.7 1.3 - - + -
462C ALA 3.6 11.4 - - - +
463C VAL* 4.2 11.2 - - + -
467C GLY 3.3 10.7 + - - +
468C ASP* 1.3 70.1 - - - +
470C LEU* 1.3 64.8 + - - +
471C TYR* 4.0 5.4 - - - +
472C ILE* 3.7 38.1 - - + -
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Residues in contact with LEU 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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441C LEU* 3.6 28.7 - - + -
462C ALA* 2.6 18.6 + - + +
463C VAL 4.0 11.7 - - - -
464C ASP* 4.0 21.8 - - + +
468C ASP* 3.4 0.9 + - + +
469C ILE* 1.3 76.0 - - - +
471C TYR* 1.3 60.0 + - - +
496C ALA 5.1 0.4 - - - +
499C LYS* 3.6 31.7 - - + +
500C TYR* 4.0 23.8 - - + +
503C LYS* 3.7 38.4 - - + +
504C PHE* 4.5 0.9 - - + -
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Residues in contact with TYR 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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460C ILE* 3.7 23.3 - - + -
461C ALA* 3.4 0.9 - - - -
462C ALA* 2.8 29.1 + - + +
469C ILE* 3.5 1.9 - - - -
470C LEU* 1.3 83.1 - - - +
472C ILE* 1.3 79.8 + - - +
473C GLY* 3.4 16.3 - - - -
492C GLU* 2.3 40.9 + - - -
495C LYS* 3.2 35.3 + - + +
496C ALA* 4.0 20.2 - - + -
499C LYS* 3.7 33.9 - - + -
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Residues in contact with ILE 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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459C CYS* 4.6 10.8 - - - -
460C ILE 3.4 8.7 - - - +
461C ALA* 4.4 12.3 - - + -
469C ILE* 3.7 31.4 - - + -
471C TYR* 1.3 95.6 - - - +
473C GLY* 1.3 67.0 + - - +
474C LYS* 5.3 3.4 - - + -
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Residues in contact with GLY 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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458C LEU* 5.6 0.4 - - - +
459C CYS* 3.2 6.2 - - - -
460C ILE* 2.8 37.0 + - - +
471C TYR* 3.4 21.2 - - - -
472C ILE* 1.3 75.4 - - - +
474C LYS* 1.3 61.4 + - - -
475C HIS* 5.1 1.3 - - - -
492C GLU* 3.6 13.5 - - - -
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Residues in contact with LYS 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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458C LEU 3.4 9.6 - - - +
459C CYS* 4.3 16.2 - - + -
472C ILE* 5.3 4.3 - - + -
473C GLY* 1.3 75.7 - - - +
475C HIS* 1.3 80.3 + - - +
476C LYS* 4.0 32.3 - - + +
492C GLU* 5.0 0.4 - - - -
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Residues in contact with HIS 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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457C ASN* 3.6 2.2 - - - +
458C LEU* 2.8 46.0 + - + +
473C GLY 5.1 0.2 - - - -
474C LYS* 1.3 82.3 + - - +
476C LYS* 1.3 65.6 + - - +
478C LEU* 3.7 28.8 - - + +
488C ILE* 3.6 27.7 - - + +
491C LYS* 6.0 4.5 - - + +
492C GLU* 2.4 41.0 + - + +
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Residues in contact with LYS 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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457C ASN* 3.5 14.8 - - + +
474C LYS* 4.0 31.1 - - + +
475C HIS* 1.3 78.3 - - - +
477C ASN* 1.3 88.0 + - - +
478C LEU* 3.3 8.9 + - - +
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Residues in contact with ASN 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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455C LYS* 4.3 30.2 + - + +
456C THR 3.4 2.6 + - - -
457C ASN* 3.0 17.4 + - - +
476C LYS* 1.3 95.0 + - - +
478C LEU* 1.3 64.8 + - - +
479C GLU 4.0 0.7 + - - -
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Residues in contact with LEU 478 (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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455C LYS* 3.1 6.4 - - - -
456C THR* 2.6 55.7 + - - +
458C LEU* 4.7 11.7 - - + -
475C HIS* 3.7 35.7 - - + +
476C LYS 4.3 7.9 - - - +
477C ASN* 1.3 80.1 - - - +
479C GLU* 1.3 60.7 + - - +
485C ASN* 4.0 11.4 - - + +
488C ILE* 3.6 39.9 - - + -
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Residues in contact with GLU 479 (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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453C ALA 4.3 0.2 - - - +
454C ARG* 2.6 28.2 - - + +
455C LYS* 2.2 35.6 + - - -
456C THR* 4.1 0.2 - - - -
477C ASN 4.0 1.0 + - - -
478C LEU* 1.3 73.2 - - - +
480C LEU* 1.3 63.5 + - - +
481C ASN* 2.8 10.3 + - + -
484C MET* 3.6 27.1 - - + +
485C ASN* 3.2 16.1 + - - -
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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