Contacts of the strand formed by residues 445 - 451 (chain D) 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 445 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444D GLN* 1.3 84.9 + - - +
446D LEU* 1.3 64.1 + - - +
447D THR* 3.8 3.1 + - - -
464D GLN* 4.0 38.5 + - + +
465D LEU 3.7 11.4 - - - +
466D PRO* 3.7 31.0 - - + -
519D ASN* 4.0 6.8 - - - +
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Residues in contact with LEU 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D GLN 4.5 13.0 - - - +
445D LEU* 1.3 75.6 - - - +
447D THR* 1.3 60.4 + - - +
448D LEU* 3.4 18.0 + - + +
463D LYS 3.2 5.9 - - - +
464D GLN* 3.3 1.9 - - - -
465D LEU* 2.9 41.6 + - - +
467D GLY* 3.8 26.0 - - - -
512D LEU* 4.1 21.1 - - + -
513D GLN* 4.8 2.5 - - + +
517D VAL* 3.8 26.2 - - + +
518D GLU* 3.9 3.4 - - - -
519D ASN* 3.7 27.4 - - + +
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Residues in contact with THR 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445D LEU 3.8 1.8 + - - -
446D LEU* 1.3 68.3 - - - +
448D LEU* 1.3 61.4 + - - +
449D LYS* 4.2 4.1 + - + +
462D GLU* 3.4 32.8 - - + +
463D LYS 3.6 6.5 - - - +
464D GLN* 3.7 25.6 + - + +
519D ASN* 2.7 23.2 + - - -
520D GLY* 2.8 33.7 + - - -
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Residues in contact with LEU 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446D LEU* 4.0 17.7 - - + +
447D THR* 1.3 78.6 - - - +
449D LYS* 1.3 63.8 - - - +
450D ILE* 3.9 14.3 - - + +
462D GLU* 3.3 3.4 - - - -
463D LYS 2.8 40.0 + - - +
465D LEU* 4.0 20.9 - - + -
512D LEU* 4.1 19.3 - - + -
517D VAL* 3.8 25.1 - - + -
518D GLU 3.4 26.0 - - - +
521D ASP* 3.6 13.9 - - + +
522D CYS 6.0 0.2 - - - -
523D LEU* 4.8 16.2 - - + -
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Residues in contact with LYS 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D THR* 5.1 4.9 - - - +
448D LEU* 1.3 75.0 - - - +
450D ILE* 1.3 55.4 + - - +
459D LYS* 3.8 40.6 - - + +
461D LEU 3.4 7.4 - - - +
462D GLU* 3.4 34.9 + - + +
520D GLY* 4.6 17.5 - - - +
521D ASP 3.1 11.7 + - - +
522D CYS* 3.3 4.6 - - - -
523D LEU 2.7 32.4 + - - -
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Residues in contact with ILE 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D LEU* 3.9 16.4 - - + +
449D LYS* 1.3 81.4 - - - +
451D LYS* 1.3 58.7 + - - +
452D TYR* 3.8 16.6 - - + -
459D LYS* 3.6 4.3 - - - -
460D VAL* 2.8 33.1 + - - -
461D LEU* 2.7 47.8 + - + +
463D LYS* 4.8 8.3 - - + -
465D LEU* 5.3 2.7 - - + -
478D LEU* 4.4 11.2 - - + -
523D LEU* 3.4 31.2 - - + +
525D VAL* 3.6 27.8 - - + -
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Residues in contact with LYS 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D LYS 4.2 0.2 + - - -
450D ILE* 1.3 73.6 - - - +
452D TYR* 1.3 67.4 + - - +
453D PRO* 3.3 19.3 - - + +
456D LEU 3.9 10.1 - - - +
457D ASP* 3.3 35.1 + - - +
458D GLN 4.0 9.6 - - - +
459D LYS* 4.5 13.4 - - + +
460D VAL* 4.6 3.8 - - - +
494D GLU* 4.5 13.9 + - - -
522D CYS* 4.0 21.3 - - - -
523D LEU 2.8 11.3 + - - +
524D LEU* 4.0 21.2 - - + +
525D VAL* 2.8 31.2 + - - +
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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