Contacts of the strand formed by residues 444 - 450 (chain D) in PDB entry 3RIK
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 LEU 444 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D LEU* 4.1 11.4 - - + -
67D LEU* 5.3 4.0 - - + -
442D ASN* 2.9 22.3 + - - +
443D ASP* 1.3 82.3 - - - +
445D ASP* 1.3 68.3 + - - +
446D ALA* 5.5 2.7 - - + -
460D VAL* 3.7 22.7 - - + -
461D LEU 3.5 4.0 - - - +
462D ASN* 3.5 44.2 - - + +
468D VAL* 4.0 30.3 - - + -
470D LEU* 4.1 21.5 - - + -
484D SER* 3.9 4.0 - - - +
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Residues in contact with ASP 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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365D HIS* 3.4 17.6 + - + -
368D ILE* 3.8 25.7 - - + +
443D ASP 4.8 0.9 - - - +
444D LEU* 1.3 78.6 - - - +
446D ALA* 1.3 62.7 + - - +
459D VAL 3.8 0.5 - - - +
460D VAL* 3.5 1.2 - - - +
461D LEU* 2.7 48.7 + - + +
463D ARG* 2.8 43.3 + - - -
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Residues in contact with ALA 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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67D LEU* 4.0 18.6 - - + -
368D ILE* 4.2 5.2 - - - +
372D LEU* 3.9 20.3 - - - +
436D LEU* 3.6 24.1 - - + +
444D LEU* 4.2 2.6 + - + -
445D ASP* 1.3 76.9 - - - +
447D VAL* 1.3 64.0 + - - +
458D VAL* 4.8 0.2 - - + -
459D VAL 3.1 11.9 - - - +
460D VAL* 4.2 9.2 - - + -
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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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368D ILE* 4.1 22.7 - - + -
371D LEU* 3.9 40.2 - - + -
372D LEU* 3.9 20.9 - - + -
423D PHE* 4.3 1.6 - - + -
433D ARG* 4.0 15.5 - - + +
436D LEU* 4.2 5.2 - - - -
446D ALA* 1.3 77.5 - - - +
448D ALA* 1.3 64.2 + - - +
449D LEU* 4.3 9.4 - - + +
458D VAL* 3.3 5.0 - - - +
459D VAL* 3.0 41.2 + - + -
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Residues in contact with ALA 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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69D LEU* 3.6 30.7 - - + -
433D ARG* 3.5 3.6 - - - +
434D VAL* 2.8 32.8 + - + +
435D GLY 4.2 0.2 - - - +
436D LEU* 3.9 21.6 - - + +
447D VAL* 1.3 77.7 - - - +
449D LEU* 1.3 67.3 + - - +
457D VAL 3.6 3.6 - - - -
458D VAL* 3.9 10.8 - - + -
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Residues in contact with LEU 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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69D LEU* 5.8 1.2 - - - +
78D VAL* 3.9 16.4 - - + -
371D LEU* 4.6 9.9 - - + -
427D ILE* 3.5 46.7 - - + -
431D SER* 4.7 4.0 - - - -
432D GLN 3.3 9.4 - - - +
433D ARG* 3.8 26.0 - - + +
434D VAL* 4.2 4.4 - - - +
447D VAL* 4.3 19.3 - - + +
448D ALA* 1.3 81.0 - - - +
450D MET* 1.3 65.4 + - - +
456D ALA* 3.7 4.3 - - - +
457D VAL* 2.9 48.3 + - + +
459D VAL* 5.3 0.7 - - + -
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Residues in contact with MET 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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69D LEU* 5.9 2.7 - - + -
71D PRO* 4.5 10.3 - - + +
74D LYS* 3.8 26.7 - - - +
430D GLY 4.7 0.2 - - - +
431D SER* 3.2 4.0 - - - -
432D GLN* 2.7 44.4 + - + +
434D VAL* 4.0 17.2 - - + +
449D LEU* 1.3 74.4 - - - +
451D HIS* 1.3 67.3 + - - +
454D GLY* 3.8 31.4 - - - +
455D SER 3.3 10.5 - - - +
456D ALA* 5.0 2.2 - - + -
457D VAL* 5.0 0.2 - - - -
496D ARG* 4.4 20.6 - - - +
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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