Contacts of the strand formed by residues 455 - 461 (chain C) in PDB entry 1RQQ
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 LYS 455 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1162B PTR 3.1 38.7 + - + +
424C LEU* 3.7 3.1 - - - -
451C ASN* 3.5 1.0 - - - -
452C PHE* 2.6 52.1 + - - +
453C GLN* 3.2 40.3 + - - +
454C GLY* 1.3 76.6 - - - +
456C ALA* 1.3 62.9 + - - +
457C LYS* 3.8 16.3 + - - +
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Residues in contact with ALA 456 (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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1159B GLU 4.1 5.4 - - - +
1160B THR* 4.6 6.9 - - - +
1162B PTR 6.1 0.3 - - - -
420C ALA* 3.9 24.5 - - + -
423C VAL* 4.5 2.7 - - + -
424C LEU* 3.6 30.6 - - + +
449C THR* 5.1 1.1 - - + -
450C PHE 3.4 6.3 - - - +
455C LYS* 1.3 74.8 - - - +
457C LYS* 1.3 68.5 + - - +
458C HIS* 4.5 9.1 + - + -
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Residues in contact with LYS 457 (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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1159B GLU 3.5 3.8 - - - +
1160B THR* 3.6 22.1 - - + +
1162B PTR 2.9 42.0 + - - -
448C LEU 3.6 0.7 - - - +
449C THR* 3.2 4.9 - - - +
450C PHE* 2.8 63.2 + - + +
452C PHE* 4.1 15.3 - - + -
455C LYS* 4.0 25.2 - - - +
456C ALA* 1.3 80.9 + - - +
458C HIS* 1.3 64.8 + - - +
459C LEU 4.2 0.4 - - - -
471D VAL* 4.0 12.1 - - + +
474D LEU* 4.2 21.2 - - + +
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Residues in contact with HIS 458 (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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1158B PTR 4.2 16.2 - - + +
1159B GLU* 2.8 53.7 + - - +
1160B THR* 5.2 1.3 - - - -
416C ARG* 3.7 38.8 + - + +
420C ALA* 4.2 13.6 - - + +
437C ARG* 2.9 18.4 + - - +
447C VAL* 3.8 9.6 - - + -
448C LEU 3.5 3.8 - - - -
449C THR* 2.9 40.5 + - + +
456C ALA* 4.5 9.2 - - + -
457C LYS* 1.3 76.9 - - - +
459C LEU* 1.3 60.8 + - - +
460C ARG 4.1 0.9 + - - -
471D VAL* 5.0 0.2 - - - -
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Residues in contact with LEU 459 (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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1159B GLU* 4.4 9.4 - - + +
447C VAL* 3.3 4.3 - - - +
448C LEU* 2.7 59.3 + - + +
450C PHE* 4.2 5.6 - - + -
458C HIS* 1.3 74.1 - - - +
460C ARG* 1.3 67.8 + - - +
461C LEU* 3.5 8.0 + - + +
468D GLN 6.0 0.7 - - - +
471D VAL* 3.2 33.4 - - + -
472D GLN* 3.7 38.8 - - + +
475D TRP* 3.9 22.4 - - + -
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Residues in contact with ARG 460 (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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1156B ASP* 2.6 32.9 + - - -
1158B PTR 3.0 48.0 - - + +
1159B GLU* 4.0 22.2 + - - +
442C ARG* 2.9 45.4 - - - +
445C GLU* 4.8 9.2 - - + +
446C CYS 3.9 7.0 - - - +
447C VAL* 4.5 4.9 - - + -
458C HIS 4.1 0.2 + - - -
459C LEU* 1.3 75.4 - - - +
461C LEU* 1.3 62.9 + - - +
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Residues in contact with LEU 461 (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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436C ILE* 4.4 6.1 - - + -
445C GLU* 3.8 16.9 - - - +
446C CYS* 2.9 35.6 + - + +
447C VAL 4.0 5.2 - - - -
448C LEU* 3.8 35.7 - - + +
459C LEU* 3.7 14.8 - - + +
460C ARG* 1.3 80.1 - - - +
462C SER* 1.3 65.0 + - - +
463C LEU* 3.6 21.2 + - + +
472C GLN* 4.5 8.1 - - - +
476C PHE* 4.3 21.1 - - + -
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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