Contacts of the helix formed by residues 455 - 462 (chain B) in PDB entry 4I5L
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 455 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A GLU* 4.2 36.6 - - + +
101A GLU* 3.4 20.4 + - + +
393B ILE* 4.2 12.3 - - + -
394B GLU* 4.2 22.9 - - + -
397B PHE* 3.3 49.3 - - + -
406B GLY 4.4 0.8 + - - -
454B THR* 1.3 73.3 - - - +
456B GLN* 1.3 63.7 + - - +
458B LEU* 3.0 5.9 + - - +
459B LYS* 3.0 40.1 + - + +
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Residues in contact with GLN 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 6.0 0.2 - - - +
63A ASP* 3.4 38.0 + - - +
64A GLU 5.2 0.7 + - - -
101A GLU* 3.7 4.8 + - - +
448B ARG* 3.4 36.4 + - - +
454B THR* 3.3 8.5 + - - +
455B LEU* 1.3 78.3 - - - +
457B ASP* 1.3 72.0 + - - +
459B LYS* 3.3 9.2 + - + +
460B ARG* 3.0 77.4 + - + +
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Residues in contact with ASP 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B VAL* 4.3 14.7 - - + +
446B LYS 4.6 1.4 - - - +
447B PRO* 3.5 13.7 - - + +
448B ARG* 2.7 39.4 + - - +
449B THR 5.0 0.5 + - - -
452B LYS 3.4 14.6 - - - +
453B ILE* 4.8 0.7 - - + -
454B THR* 2.9 38.5 + - - +
456B GLN* 1.3 80.5 + - - +
458B LEU* 1.3 65.3 + - - +
460B ARG* 3.4 4.9 + - - +
461B CYS* 3.2 26.6 + - - +
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Residues in contact with LEU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B ILE* 3.9 15.8 - - + +
397B PHE* 3.6 28.3 - - + -
408B LEU* 4.0 18.2 - - + -
445B VAL* 3.8 30.7 - - + -
453B ILE* 4.1 9.6 - - + -
454B THR 3.1 10.0 + - - +
455B LEU* 3.0 8.5 + - - +
457B ASP* 1.3 79.2 - - - +
459B LYS* 1.3 59.2 + - - +
461B CYS* 3.7 13.4 + - - -
462B LYS 4.2 1.4 + - - -
464B ALA* 3.5 22.7 - - + +
467B PHE* 4.1 17.3 - - + -
468B PHE* 4.2 22.4 - - + -
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Residues in contact with LYS 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP 5.8 2.0 + - - -
100A GLU* 5.5 1.2 - - - +
275B ARG* 4.4 2.8 - - - +
390B PRO* 4.1 19.3 - - + -
393B ILE* 4.0 24.9 - - + +
394B GLU* 2.7 41.3 + - - +
455B LEU* 3.0 33.4 + - + +
456B GLN* 3.3 10.3 + - + +
458B LEU* 1.3 78.8 - - - +
460B ARG* 1.3 64.6 + - + +
461B CYS 3.4 0.3 + - - -
462B LYS* 4.0 10.4 + - - +
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Residues in contact with ARG 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 3.0 31.3 + - - +
64A GLU* 6.1 1.4 - - - +
448B ARG* 4.3 15.0 - - - +
456B GLN* 3.0 60.3 + - + +
457B ASP* 4.0 4.5 - - - +
458B LEU 3.4 0.2 - - - -
459B LYS* 1.3 78.8 - - + +
461B CYS* 1.3 62.6 + - - +
462B LYS* 3.5 14.8 + - - +
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Residues in contact with CYS 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B LEU* 3.8 18.3 - - - +
445B VAL* 3.5 34.1 - - - +
457B ASP 3.2 13.6 + - - +
458B LEU* 3.7 16.2 - - - -
459B LYS 3.3 1.2 - - - -
460B ARG* 1.3 78.3 - - - +
462B LYS* 1.3 73.8 + - - +
463B LEU* 3.3 23.9 + - - +
464B ALA* 3.7 10.5 - - - -
135C ARG* 5.3 0.5 + - - -
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Residues in contact with LYS 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B LYS* 4.9 11.4 - - - +
458B LEU 4.2 2.6 + - - -
459B LYS 4.0 9.7 + - - +
460B ARG 3.5 14.7 - - - +
461B CYS* 1.3 78.8 - - - +
463B LEU* 1.3 68.2 + - - +
464B ALA* 3.6 2.7 - - - +
465B ASN* 4.4 3.5 - - - +
135C ARG* 3.0 47.8 + - + +
136C LYS* 3.9 20.1 + - + +
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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