Contacts of the strand formed by residues 446 - 452 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410D PHE* 4.3 14.1 - - - -
436D ILE* 4.1 9.9 - - + -
437D ARG 3.1 19.3 - - - +
438D GLN* 4.2 3.8 - - - -
439D SER 3.9 0.7 - - - +
445D GLU* 1.3 79.2 - - - +
447D VAL* 1.3 70.3 + - - +
460D ARG* 3.9 0.9 - - - +
461D LEU* 2.9 32.7 + - + +
463D LEU* 4.0 31.2 - - + +
464D ASN* 3.2 33.7 - - - -
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Residues in contact with VAL 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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1158A PTR 3.6 28.7 - - + +
436D ILE* 3.4 4.5 - - - +
437D ARG* 2.7 65.6 + - + +
439D SER* 3.7 21.8 - - - +
446D CYS* 1.3 81.8 - - - +
448D LEU* 1.3 67.5 + - - +
458D HIS* 4.0 8.5 - - + -
459D LEU 3.3 25.4 - - - +
460D ARG* 4.6 6.3 - - + -
461D LEU* 4.1 4.5 - - - -
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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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475C TRP* 3.7 46.0 - - + +
434D PHE* 3.5 34.8 - - + -
436D ILE* 3.4 28.0 - - + -
447D VAL* 1.3 71.6 - - - +
449D THR* 1.3 63.2 + - - +
450D PHE* 3.9 7.7 + - + -
457D LYS 3.6 1.0 - - - +
458D HIS* 3.5 1.2 - - - -
459D LEU* 2.7 55.0 + - + +
461D LEU* 3.9 12.9 - - + +
476D PHE* 4.5 7.6 - - + -
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Residues in contact with THR 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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419D ALA* 4.0 24.9 - - - +
420D ALA* 4.1 2.0 - - - +
423D VAL* 3.8 13.1 - - + +
434D PHE* 3.2 3.5 - - - +
435D VAL* 3.0 44.1 + - - -
437D ARG* 3.0 23.4 + - - -
447D VAL 3.8 0.6 + - - -
448D LEU* 1.3 74.0 - - - +
450D PHE* 1.3 64.3 + - - +
457D LYS 3.2 6.3 - - - +
458D HIS* 2.9 36.5 + - + -
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Residues in contact with PHE 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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471C VAL* 3.6 30.1 - - + -
474C LEU* 4.2 4.7 - - + -
475C TRP* 3.7 44.0 - + + -
478C SER* 4.7 4.0 - - - -
423D VAL* 4.0 7.4 - - - +
432D GLY 4.9 0.9 - - - +
433D LEU 3.4 11.4 - - - +
434D PHE* 3.7 11.4 - - + -
448D LEU* 3.9 16.8 - - + -
449D THR* 1.3 76.7 - - - +
451D ASN* 1.3 70.5 + - - +
452D PHE* 3.8 12.7 + + + -
455D LYS 3.6 0.7 - - - +
456D ALA* 3.4 4.0 - - - -
457D LYS* 2.8 76.6 + - + -
459D LEU* 4.3 9.4 - - + -
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Residues in contact with ASN 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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478C SER* 5.1 0.3 - - - -
423D VAL* 2.7 33.1 + - + +
424D LEU* 3.5 16.5 - - + +
427D GLY 3.1 24.4 + - - -
430D SER* 3.2 20.7 + - - +
431D HIS* 3.6 5.9 + - - -
432D GLY* 2.9 28.6 + - - -
433D LEU 3.0 10.5 + - - +
450D PHE* 1.3 77.5 - - - +
452D PHE* 1.3 59.6 + - - +
453D GLN 3.5 1.9 + - - -
454D GLY 2.7 26.9 + - - -
455D LYS 3.5 3.4 - - - -
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Residues in contact with PHE 452 (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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474C LEU* 3.6 59.2 - - + -
477C GLN* 4.4 13.7 - - + -
478C SER* 4.1 11.2 - - - -
481C ASP* 4.8 1.8 - - - -
431D HIS* 3.5 19.3 - + - -
450D PHE* 3.8 14.5 + + + -
451D ASN* 1.3 72.8 + - - +
453D GLN* 1.3 101.7 + - + +
454D GLY 3.1 0.2 - - - -
455D LYS* 2.7 35.1 + - + +
457D LYS* 4.1 13.9 - - + -
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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