Contacts of the strand formed by residues 446 - 452 (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 CYS 446 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404C LEU* 4.3 12.1 - - - -
410C PHE* 4.2 21.1 - - - -
436C ILE* 4.1 11.7 - - + -
437C ARG 3.1 15.5 - - - +
438C GLN* 4.3 5.2 - - - -
439C SER 3.9 0.2 - - - +
444C GLY 4.2 0.6 + - - -
445C GLU* 1.3 81.1 - - - +
447C VAL* 1.3 71.5 + - - +
460C ARG* 3.9 0.9 - - - +
461C LEU* 2.9 32.4 + - + +
463C LEU* 4.0 31.2 - - + +
464C ASN* 4.9 4.0 - - - -
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Residues in contact with VAL 447 (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 3.5 31.0 - - + +
436C ILE* 3.4 3.6 - - - -
437C ARG* 2.8 67.8 + - + +
439C SER* 3.8 18.4 - - - -
446C CYS* 1.3 80.7 - - - +
448C LEU* 1.3 65.7 + - - +
449C THR* 4.1 0.4 - - - +
458C HIS* 3.8 20.2 - - + -
459C LEU 3.3 14.6 - - - +
460C ARG* 4.5 5.2 - - + -
461C LEU* 4.0 4.5 - - - -
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Residues in contact with LEU 448 (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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434C PHE* 3.3 45.5 - - + -
435C VAL 3.6 4.0 - - - +
436C ILE* 4.1 7.6 - - + -
447C VAL* 1.3 71.2 - - - +
449C THR* 1.3 60.0 + - - +
450C PHE* 3.9 7.7 + - + -
457C LYS 3.6 1.2 - - - +
458C HIS* 3.5 1.2 - - - -
459C LEU* 2.7 55.8 + - + +
461C LEU* 3.8 17.8 - - + +
476C PHE* 4.2 12.8 - - + -
475D TRP* 3.6 43.5 - - + +
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Residues in contact with THR 449 (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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419C ALA* 4.0 24.0 - - - +
420C ALA* 4.1 2.7 - - - +
423C VAL* 3.8 14.1 - - + +
434C PHE* 3.2 4.0 - - - +
435C VAL* 2.9 44.5 + - - -
437C ARG* 3.0 19.6 + - - -
447C VAL* 3.8 0.8 + - - +
448C LEU* 1.3 72.9 - - - +
450C PHE* 1.3 63.8 + - - +
456C ALA* 5.1 0.2 - - + -
457C LYS 3.2 6.7 - - - +
458C HIS* 2.9 39.3 - - + +
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Residues in contact with PHE 450 (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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423C VAL* 4.0 7.8 - - - +
432C GLY 4.8 0.7 - - - +
433C LEU 3.4 11.4 - - - +
434C PHE* 3.7 11.4 - - + -
448C LEU* 4.1 12.8 - - + -
449C THR* 1.3 75.2 - - - +
451C ASN* 1.3 69.9 + - - +
452C PHE* 3.7 22.3 + + + -
455C LYS 3.5 1.2 - - - +
456C ALA* 3.4 4.0 - - - -
457C LYS* 2.8 67.2 + - + -
459C LEU* 4.2 8.1 - - + -
471D VAL* 3.6 19.3 - - + -
474D LEU* 4.1 4.5 - - + -
475D TRP* 3.5 59.7 - + + -
478D SER* 4.5 4.9 - - - -
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Residues in contact with ASN 451 (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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423C VAL* 2.9 32.3 + - + +
424C LEU* 3.6 16.4 - - + +
427C GLY 3.1 25.9 + - - -
430C SER* 3.4 21.0 + - - +
431C HIS* 3.2 9.5 + - - -
432C GLY* 2.9 28.1 + - - -
433C LEU 3.0 11.0 + - - +
450C PHE* 1.3 77.8 - - - +
452C PHE* 1.3 60.7 + - - +
453C GLN 3.4 0.3 + - - -
454C GLY* 2.9 22.1 + - - -
455C LYS 3.5 3.6 - - - -
478D SER* 5.0 0.3 - - - -
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Residues in contact with PHE 452 (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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1162B PTR 5.9 0.2 - - - -
431C HIS* 3.8 20.6 - + - -
450C PHE* 3.7 14.1 + + + -
451C ASN* 1.3 73.2 + - - +
453C GLN* 1.3 93.6 + - + +
454C GLY 3.1 0.2 - - - -
455C LYS* 2.6 47.7 + - - +
457C LYS* 4.1 13.5 - - + -
474D LEU* 3.6 64.4 - - + -
477D GLN* 4.6 12.1 - - + -
478D SER* 4.3 9.6 - - - -
481D ASP* 4.9 1.3 - - - -
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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