Contacts of the strand formed by residues 488 - 494 (chain C) 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 SER 488 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C SER 3.2 12.8 - - - -
43C THR* 4.1 7.4 - - - -
357C TRP* 4.0 4.4 - - - +
460C VAL 4.1 0.6 + - - +
461C LEU* 3.6 7.1 - - - +
462C ASN 2.9 28.3 + - - -
484C SER* 3.8 7.4 + - - -
485C PRO* 2.8 49.3 + - - +
486C GLY 3.9 0.9 - - - -
487C TYR* 1.3 78.8 - - - +
489C ILE* 1.3 60.9 + - - +
490C HIS* 3.9 7.7 + - - -
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Residues in contact with ILE 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C SER* 2.8 45.9 + - - +
364C SER* 3.5 32.8 - - - +
419C HIS* 3.8 24.0 - - + +
422C HIS* 3.3 46.8 - - + +
423C PHE* 3.9 7.6 - - + -
459C VAL* 4.0 7.6 - - + -
460C VAL 3.4 9.0 - - - +
461C LEU* 4.0 11.9 - - + -
488C SER* 1.3 75.6 - - - +
490C HIS* 1.3 73.4 + - - +
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Residues in contact with HIS 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG* 3.8 17.6 - - + -
40C TYR 3.2 6.7 - - - +
41C GLU* 2.9 39.4 + - + +
422C HIS* 3.8 2.2 - - - -
458C VAL 4.4 0.2 - - - -
459C VAL* 3.4 6.2 - - - +
460C VAL* 2.8 37.1 + - + +
483C ILE 3.3 24.9 + - - -
484C SER* 4.3 5.9 - - - -
485C PRO* 3.5 11.1 - - + +
488C SER* 3.9 7.8 + - - -
489C ILE* 1.3 85.9 - - - +
491C THR* 1.3 62.6 + - - +
492C TYR* 2.7 41.3 + - + -
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Residues in contact with THR 491 (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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38C SER 3.7 0.7 - - - +
39C ARG* 3.5 3.5 - - - -
40C TYR* 3.0 34.5 + - - +
422C HIS* 2.7 44.7 + - - +
426C PHE* 3.8 19.3 - - + -
457C VAL* 3.7 26.2 - - + -
458C VAL 3.2 9.4 - - - +
459C VAL* 3.9 5.4 - - + +
490C HIS* 1.3 74.7 + - - +
492C TYR* 1.3 65.2 + - - +
493C LEU* 4.0 5.5 + - + +
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Residues in contact with TYR 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 3.9 12.8 - + - -
38C SER 3.3 5.8 - - - +
39C ARG* 3.4 21.9 + - + -
456C ALA 4.3 0.3 - - - -
457C VAL* 3.1 7.1 - - - +
458C VAL* 2.7 43.9 + - + +
460C VAL* 4.2 13.7 - - + -
470C LEU* 5.1 1.8 - - + +
472C ILE* 4.1 16.2 - - + -
480C LEU* 3.8 29.4 - - + -
482C THR* 2.6 36.8 + - + +
483C ILE 4.2 0.5 + - - -
484C SER* 5.6 0.2 - - - -
490C HIS* 2.7 40.7 + - + -
491C THR* 1.3 74.8 - - - +
493C LEU* 1.3 62.9 + - - +
494C TRP* 4.0 21.4 - - + -
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Residues in contact with LEU 493 (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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32C PRO* 6.1 0.2 - - - +
37C PHE* 3.3 1.6 - - - +
38C SER* 2.8 45.6 + - - +
40C TYR* 3.7 28.9 - - + +
426C PHE* 3.8 26.7 - - + +
455C SER* 6.0 1.3 - - - +
456C ALA 3.4 6.7 - - - +
457C VAL* 3.6 26.7 - - + -
491C THR* 4.0 7.2 - - + +
492C TYR* 1.3 82.4 - - - +
494C TRP* 1.3 66.7 + - - +
495C HIS* 6.5 0.4 - - + -
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Residues in contact with TRP 494 (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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32C PRO* 6.4 1.6 - - - -
36C THR 3.7 11.9 - - - +
37C PHE* 3.9 1.8 - - + -
56C ILE* 3.6 30.3 - - + -
69C LEU* 4.2 10.5 - - + -
455C SER* 3.4 3.6 - - - -
456C ALA* 3.0 50.9 + - + +
458C VAL* 3.5 33.4 - - + -
472C ILE* 3.7 20.9 - - + -
474C ASP* 2.7 42.5 + - + +
477C VAL* 4.3 4.0 - - + -
480C LEU* 4.0 22.7 - - + -
492C TYR* 4.0 16.8 - - + -
493C LEU* 1.3 82.5 - - - +
495C HIS* 1.3 81.5 + - - +
496C ARG* 3.8 1.1 + - + -
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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