Contacts of the strand formed by residues 461 - 466 (chain C) in PDB entry 4ICU
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 LEU 461 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449C LYS* 3.4 3.8 - - - +
450C ILE* 2.8 49.7 + - + +
452C TYR* 3.5 24.0 - - - +
459C LYS* 3.8 2.0 - - - +
460C VAL* 1.3 92.3 - - + +
462C GLU* 1.3 65.0 + - - +
463C LYS* 3.7 32.1 - - + -
478C LEU* 6.0 2.0 - - + -
481C LEU* 4.3 18.8 - - + -
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Residues in contact with GLU 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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447C THR* 3.6 21.9 - - + +
448C LEU 3.3 9.0 - - - +
449C LYS* 3.7 36.6 + - + +
461C LEU* 1.3 81.3 - - - +
463C LYS* 1.3 68.0 + - - +
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Residues in contact with LYS 463 (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 LEU 3.4 2.8 - - - +
447C THR* 4.5 1.3 - - - -
448C LEU* 2.9 33.7 + - - +
450C ILE* 4.0 15.2 - - + +
461C LEU* 3.7 22.4 - - + -
462C GLU* 1.3 74.2 - - - +
464C GLN* 1.3 67.1 + - - +
465C LEU* 3.6 27.7 + - + +
477C LEU* 4.5 27.1 - - + +
478C LEU* 6.6 0.2 - - + -
481C LEU* 6.2 2.2 - - - -
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Residues in contact with GLN 464 (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 LEU* 3.7 37.2 + - + +
446C LEU 3.3 3.8 - - - +
447C THR* 3.5 27.8 + - + +
463C LYS* 1.3 75.2 - - - +
465C LEU* 1.3 65.9 + - - +
466C PRO* 4.4 3.3 - - - +
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Residues in contact with LEU 465 (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 LEU* 3.7 3.3 - - - +
446C LEU* 2.9 34.0 + - - +
448C LEU* 3.8 23.1 - - + -
450C ILE* 5.6 1.8 - - + -
463C LYS* 4.2 23.6 - - + +
464C GLN* 1.3 79.7 - - - +
466C PRO* 1.4 70.7 - - + +
467C GLY 3.5 0.2 + - - -
469C MET* 3.7 23.1 - - + -
474C VAL* 4.4 20.0 - - + -
477C LEU* 3.8 25.8 - - + -
512C LEU* 4.1 17.4 - - + +
523C LEU* 4.8 5.4 - - + -
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Residues in contact with PRO 466 (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 GLN 4.3 2.2 - - - +
445C LEU* 3.6 19.9 - - + -
464C GLN 4.4 2.0 - - - +
465C LEU* 1.4 88.0 - - + +
467C GLY* 1.3 65.0 + - - +
468C SER* 4.3 13.5 - - - +
469C MET* 3.0 39.0 + - + +
512C LEU* 3.9 5.0 - - - +
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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