Contacts of the strand formed by residues 455 - 461 (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 LYS 455 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1162A PTR 3.3 38.5 + - + +
1164A ARG* 5.1 2.0 - - - +
424D LEU* 3.7 2.7 - - - -
451D ASN* 3.5 1.2 - - - -
452D PHE* 2.7 46.6 + - + +
453D GLN* 4.2 18.6 - - + +
454D GLY* 1.3 80.5 - - - +
456D ALA* 1.3 61.9 + - - +
457D LYS* 3.8 16.9 + - - +
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Residues in contact with ALA 456 (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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1159A GLU 4.1 4.7 - - - +
1160A THR* 4.6 7.6 - - - +
420D ALA* 3.8 26.2 - - + -
423D VAL* 4.4 2.9 - - + -
424D LEU* 3.6 29.4 - - + +
449D THR* 5.1 0.4 - - + -
450D PHE 3.4 6.5 - - - +
455D LYS* 1.3 73.0 - - - +
457D LYS* 1.3 69.4 + - - +
458D HIS* 4.6 10.5 + - + +
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Residues in contact with LYS 457 (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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1159A GLU 3.4 3.6 - - - -
1160A THR* 3.8 23.3 - - + +
1162A PTR 3.3 36.8 + - - -
471C VAL* 3.9 8.5 - - + -
474C LEU* 4.2 18.9 - - + +
448D LEU 3.6 0.7 - - - +
449D THR* 3.2 5.4 - - - +
450D PHE* 2.8 73.9 + - + +
452D PHE* 4.1 15.5 - - + -
455D LYS* 4.0 30.4 - - - +
456D ALA* 1.3 79.3 + - - +
458D HIS* 1.3 65.0 + - - +
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Residues in contact with HIS 458 (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 3.7 15.9 - - + +
1159A GLU* 3.0 42.3 + - - +
1160A THR* 5.4 1.1 - - - -
1161A ASP* 5.1 2.2 - - - -
471C VAL* 5.0 0.7 - - - -
416D ARG* 3.5 52.4 + - - +
420D ALA* 4.3 12.2 - - + +
437D ARG* 3.1 13.5 + - - -
447D VAL* 4.0 10.3 - - + -
448D LEU 3.5 3.1 - - - -
449D THR* 2.9 38.7 + - + +
456D ALA* 4.6 9.0 + - + +
457D LYS* 1.3 77.3 - - - +
459D LEU* 1.3 63.6 + - - +
460D ARG 4.1 0.9 + - - -
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Residues in contact with LEU 459 (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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1159A GLU* 3.7 18.6 - - - +
468C GLN 6.0 0.9 - - - +
471C VAL* 3.6 26.9 - - + +
472C GLN* 3.7 40.8 - - + +
475C TRP* 4.0 20.2 - - + -
447D VAL* 3.3 5.0 - - - +
448D LEU* 2.7 59.2 + - + +
450D PHE* 4.3 4.7 - - + -
457D LYS 4.2 0.2 - - - -
458D HIS* 1.3 72.5 - - - +
460D ARG* 1.3 68.8 + - - +
461D LEU* 3.5 8.5 + - + +
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Residues in contact with ARG 460 (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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1156A ASP* 2.7 30.9 + - - -
1158A PTR 3.6 54.7 - - + +
1159A GLU* 3.6 26.3 + - - +
439D SER* 6.1 0.2 - - - -
441D THR* 5.7 0.9 - - - -
442D ARG* 5.8 5.4 - - - -
445D GLU* 4.4 15.9 - - - +
446D CYS 3.9 5.6 - - - +
447D VAL* 4.5 5.4 - - + +
458D HIS 4.1 0.6 + - - +
459D LEU* 1.3 78.0 - - - +
461D LEU* 1.3 63.4 + - - +
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Residues in contact with LEU 461 (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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436D ILE* 3.8 31.6 - - + -
445D GLU* 3.5 18.0 - - - +
446D CYS* 2.9 33.8 + - + +
447D VAL 4.1 4.0 - - - -
448D LEU* 3.9 22.9 - - + +
459D LEU* 3.7 15.7 - - + +
460D ARG* 1.3 77.3 - - - +
462D SER* 1.3 66.8 + - - +
463D LEU* 3.5 12.1 + - + -
472D GLN* 4.7 7.4 - - - +
476D PHE* 4.3 22.4 - - + -
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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