Contacts of the strand formed by residues 479 - 490 (chain C) in PDB entry 3RBH
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 MSE 479 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C GLU* 4.5 2.9 - - + -
54C ASN 3.5 6.3 - - - -
55C ASP 3.4 25.4 - - - +
56C ARG* 4.3 10.3 - - - -
58C LEU* 3.6 21.1 - - + -
369C ALA* 3.9 14.6 - - - +
414C GLY 3.9 10.1 - - - +
415C ILE* 3.8 15.0 - - + -
464C LEU* 3.4 6.4 - - - +
465C PHE* 2.6 46.9 + - + +
478C THR* 1.3 78.2 - - - +
480C HIS* 1.3 81.7 + - - +
481C ARG* 3.5 38.6 - - + +
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Residues in contact with HIS 480 (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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52C SER* 2.7 41.5 + - - -
53C GLU* 3.6 0.2 - - - -
54C ASN* 2.9 63.4 + - + +
463C GLY 3.2 12.8 - - - +
464C LEU* 4.2 12.6 - - + -
479C MSE 1.3 87.8 - - - +
481C ARG* 1.3 68.3 + - - +
482C ALA* 4.0 9.9 - - + -
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Residues in contact with ARG 481 (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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51C GLU* 3.6 21.2 + - - +
52C SER 3.3 9.0 - - - +
53C GLU* 2.5 30.7 + - + +
56C ARG* 3.1 16.9 - - - +
100C GLU* 4.9 0.4 + - - -
368C GLU* 3.3 21.3 + - - +
369C ALA* 2.7 32.7 + - - +
371C ARG* 3.7 35.2 - - - +
414C GLY* 2.8 27.4 + - - -
462C GLY* 3.5 1.4 - - - -
463C GLY* 2.9 30.8 + - - +
479C MSE 3.5 10.9 - - + +
480C HIS* 1.3 76.3 - - - +
482C ALA* 1.3 63.4 - - - +
483C PHE* 3.8 10.5 - - + -
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Residues in contact with ALA 482 (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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50C GLY 3.9 0.2 - - - +
51C GLU* 3.4 4.0 - - - +
52C SER* 2.8 37.9 + - - +
460C PHE* 4.1 18.8 - - + -
461C ARG 3.2 10.1 - - - +
462C GLY* 4.0 7.9 - - - -
463C GLY 5.0 0.4 - - - +
480C HIS* 4.2 13.0 - - + -
481C ARG* 1.3 79.4 - - - +
483C PHE* 1.3 66.3 + - - +
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Residues in contact with PHE 483 (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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49C THR* 4.0 14.6 - - + -
50C GLY 3.2 5.2 - - - +
51C GLU* 3.3 50.3 - - + -
100C GLU* 3.8 21.1 - - + -
368C GLU* 3.9 5.2 - - + -
371C ARG* 3.7 22.7 - - - -
459C ARG 4.4 0.2 - - - -
460C PHE* 3.4 7.9 - - - -
461C ARG* 2.7 84.4 + - + +
481C ARG* 3.8 15.3 - - + -
482C ALA* 1.3 76.9 - - - +
484C VAL* 1.3 70.9 + - - +
485C ASP* 4.5 2.7 - - - +
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Residues in contact with VAL 484 (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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48C ILE 3.8 1.3 - - - +
49C THR* 3.3 6.4 - - - -
50C GLY* 3.0 35.7 + - - +
458C ILE* 4.4 23.1 - - + -
459C ARG 3.3 8.5 - - - +
460C PHE* 4.0 20.0 - - + -
483C PHE* 1.3 78.0 - - - +
485C ASP* 1.3 66.9 + - - +
486C PHE* 5.0 1.6 - - + +
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Residues in contact with ASP 485 (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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47C LYS* 3.5 20.9 - - + -
48C ILE 3.7 2.0 - - - -
49C THR* 2.7 37.2 + - - +
101C THR* 5.9 0.2 - - - -
457C LEU* 3.8 1.3 - - + +
458C ILE* 3.2 6.8 - - - +
459C ARG* 2.8 55.1 + - + +
461C ARG* 3.0 33.8 + - - +
483C PHE* 4.5 2.5 - - - +
484C VAL* 1.3 75.1 - - - +
486C PHE* 1.3 61.0 + - - +
487C ILE* 4.9 7.9 - - + -
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Residues in contact with PHE 486 (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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46C VAL* 5.3 3.4 - - + -
47C LYS* 3.2 5.2 - - - +
48C ILE* 2.8 66.3 + - + +
438C PHE* 4.0 23.6 - + - -
457C LEU 3.5 7.4 - - - -
458C ILE* 4.5 17.3 - - + -
484C VAL* 5.0 2.2 - - + +
485C ASP* 1.3 73.9 - - - +
487C ILE* 1.3 72.0 + - - +
488C TRP* 4.1 36.1 - + + -
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Residues in contact with ILE 487 (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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45C ASP* 5.5 4.3 - - + -
46C VAL 3.2 10.5 - - - +
47C LYS* 4.0 19.1 - - + -
452C ASP 4.6 0.4 - - - +
453C GLU* 3.2 47.6 - - + +
455C SER 4.5 6.7 - - - +
456C ALA* 3.2 7.9 - - - +
457C LEU* 2.9 59.8 + - + +
459C ARG* 4.9 2.5 - - - +
485C ASP* 4.9 3.6 - - + -
486C PHE* 1.3 86.7 - - - +
488C TRP* 1.3 71.8 + - - +
489C ARG* 4.6 10.1 - - - +
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Residues in contact with TRP 488 (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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45C ASP* 3.6 1.0 - - - -
46C VAL* 2.7 50.1 + - + +
438C PHE* 4.2 12.8 - + + -
440C GLN* 3.5 40.4 - - + -
441C GLY* 6.5 0.2 - - - -
456C ALA* 3.4 28.7 - - + -
486C PHE* 4.1 28.4 - + + -
487C ILE* 1.3 79.9 - - - +
489C ARG* 1.3 78.8 + - - +
490C PHE* 3.5 39.7 - + + -
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Residues in contact with ARG 489 (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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44C LEU 3.6 3.4 - - - +
45C ASP* 2.6 41.3 + - - +
76C TRP* 4.8 4.9 - - + +
441C GLY* 2.8 47.9 + - - -
443C LEU* 3.6 40.0 - - - +
449C GLN* 4.0 1.6 - - - +
453C GLU* 2.8 40.6 + - - +
455C SER* 3.8 10.5 - - - +
456C ALA* 4.9 4.1 - - - +
487C ILE* 4.6 7.3 - - - +
488C TRP* 1.3 93.3 + - - +
490C PHE* 1.3 74.6 + - - +
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Residues in contact with PHE 490 (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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42C PHE 4.5 2.6 - - - +
43C GLY* 3.3 11.8 - - - -
44C LEU* 2.9 50.1 + - + +
46C VAL* 3.8 31.0 - - + -
76C TRP* 5.4 0.3 - - - -
488C TRP* 3.5 33.9 - + + -
489C ARG* 1.3 81.3 - - - +
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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