Contacts of the strand formed by residues 441 - 446 (chain D) in PDB entry 6RKU
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 GLN 441 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408D ALA 4.0 0.2 - - - +
409D ASP 3.7 3.5 - - - +
410D CYS* 3.2 24.0 + - - +
419D GLU* 2.9 35.2 + - - +
421D TYR* 3.1 24.8 + - + -
436D ARG* 3.9 19.1 + - + +
437D ASN* 3.4 45.0 + - + +
439D LYS 3.8 0.2 - - - -
440D ASN* 1.3 97.2 + - - +
442D ALA* 1.3 63.1 + - - +
443D ILE* 6.1 0.2 - - + -
751D TRP* 5.1 8.5 - - + -
755D MET* 5.2 7.1 + - - +
757D PRO* 5.5 7.7 - - - +
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Residues in contact with ALA 442 (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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407D LEU* 4.8 1.8 - - + -
408D ALA 3.5 12.6 - - - +
409D ASP* 4.2 4.3 - - - -
410D CYS* 4.9 1.1 - - - +
419D GLU 2.9 16.6 + - - +
420D LEU* 3.6 18.1 - - + -
421D TYR* 3.2 27.4 + - - -
436D ARG* 5.4 0.4 - - - +
441D GLN* 1.3 78.2 + - - +
443D ILE* 1.3 68.5 + - - +
490D TYR* 3.8 22.2 - - + +
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Residues in contact with ILE 443 (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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406D LYS 3.9 0.7 - - - +
407D LEU* 3.5 9.6 - - - +
408D ALA* 3.5 28.1 + - + +
420D LEU* 4.5 0.9 - - - -
421D TYR* 4.1 17.9 - - + +
423D VAL* 4.7 11.4 - - + -
429D GLY* 4.9 2.2 - - - -
432D ALA* 3.5 47.3 - - + +
433D LYS* 3.5 21.5 - - + +
436D ARG* 3.5 24.0 - - + -
441D GLN* 6.1 0.2 - - + -
442D ALA* 1.3 81.4 - - - +
444D LEU* 1.3 62.7 + - - +
445D PRO* 3.8 21.7 - - + +
496D MET* 6.0 1.1 - - + -
755D MET* 6.3 1.3 - - + -
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Residues in contact with LEU 444 (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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402D GLY 5.5 0.7 - - - +
406D LYS* 4.4 13.9 - - + -
407D LEU* 4.4 12.3 - - + +
420D LEU* 4.5 10.8 - - + -
421D TYR 3.2 9.1 + - - +
422D LEU* 3.5 45.8 - - + +
423D VAL 3.8 1.1 + - - -
443D ILE* 1.3 77.3 - - - +
445D PRO* 1.3 79.7 - - + +
446D LEU* 4.2 2.4 - - + +
466D GLU* 4.7 10.8 - - + +
467D VAL* 4.3 28.0 - - + +
470D LEU* 3.7 34.1 - - + -
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Residues in contact with PRO 445 (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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406D LYS* 3.9 45.6 - - + +
423D VAL* 3.9 10.5 - - + +
424D GLU 5.0 0.2 - - - +
425D GLY* 3.4 27.1 - - - +
429D GLY* 4.9 4.5 - - - -
433D LYS* 4.8 11.0 - - - +
443D ILE* 3.8 17.5 - - + +
444D LEU* 1.3 100.3 - - - +
446D LEU* 1.3 69.0 + - - +
466D GLU* 5.2 2.9 - - - +
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Residues in contact with LEU 446 (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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422D LEU* 4.4 22.4 - - + -
423D VAL 3.1 20.8 + - - +
424D GLU* 4.2 3.6 - - - +
425D GLY* 2.8 25.2 + - - +
444D LEU* 4.2 8.3 - - + +
445D PRO* 1.3 83.0 - - - +
447D LYS* 1.3 70.6 + - - +
448D GLY 4.1 5.4 + - - +
450D ILE* 4.6 20.4 - - + -
467D VAL* 4.4 22.0 - - + -
506D ILE* 5.9 4.3 - - + -
510D LEU* 4.5 19.5 - - + -
16G T 5.6 1.4 - - - +
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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