Contacts of the strand formed by residues 479 - 490 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B GLU* 4.5 3.6 - - + -
54B ASN 3.5 6.5 - - - -
55B ASP 3.5 24.5 - - - +
56B ARG* 4.3 9.9 - - - -
58B LEU* 3.6 20.4 - - + -
369B ALA* 3.9 7.4 - - - +
414B GLY 4.0 1.3 - - - +
415B ILE* 3.8 23.3 - - + -
464B LEU* 3.4 6.6 - - - +
465B PHE* 2.6 53.2 + - + +
478B THR* 1.3 81.1 + - - +
480B HIS* 1.3 81.1 + - - +
481B ARG* 3.5 38.4 - - + +
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Residues in contact with HIS 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B SER* 2.7 43.5 + - - -
53B GLU* 3.6 0.3 - - - -
54B ASN* 2.9 63.5 + - + -
463B GLY 3.2 14.1 - - - +
464B LEU* 4.2 11.9 - - + -
479B MSE 1.3 90.9 - - - +
481B ARG* 1.3 65.1 + - - +
482B ALA* 4.0 9.9 - - + -
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Residues in contact with ARG 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU* 3.7 19.9 + - - +
52B SER 3.3 7.6 - - - +
53B GLU* 2.6 30.4 + - + +
56B ARG* 3.1 17.1 - - - +
100B GLU* 4.7 0.6 + - - -
368B GLU* 3.3 20.0 + - - +
369B ALA* 2.7 33.3 + - - +
371B ARG* 3.7 36.7 - - - +
414B GLY* 2.8 27.6 + - - -
461B ARG 4.3 0.2 - - - +
462B GLY* 3.4 1.2 - - - -
463B GLY* 2.8 30.6 + - - +
479B MSE 3.5 10.2 - - + +
480B HIS* 1.3 74.8 - - - +
482B ALA* 1.3 64.1 + - - +
483B PHE* 3.8 10.8 - - + -
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Residues in contact with ALA 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLY 3.9 0.2 - - - +
51B GLU* 3.4 4.3 - - - +
52B SER* 2.8 38.1 + - - +
460B PHE* 4.2 17.9 - - + -
461B ARG 3.2 9.4 - - - +
462B GLY* 4.0 7.6 - - - -
463B GLY 4.9 0.2 - - - +
480B HIS* 4.2 13.5 - - + -
481B ARG* 1.3 77.9 - - - +
483B PHE* 1.3 64.7 + - - +
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Residues in contact with PHE 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B THR* 4.0 14.1 - - + -
50B GLY 3.2 5.2 - - - +
51B GLU* 3.4 48.0 - - + -
100B GLU* 3.6 23.1 - - + -
368B GLU* 3.8 5.4 - - - -
371B ARG* 3.7 28.0 - - - -
459B ARG 4.4 0.2 - - - -
460B PHE* 3.4 7.8 - - - -
461B ARG* 2.7 78.4 + - + +
481B ARG* 3.8 15.3 - - + -
482B ALA* 1.3 77.8 - - - +
484B VAL* 1.3 69.7 + - - +
485B ASP* 4.5 2.9 - - - +
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Residues in contact with VAL 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ILE 3.8 1.3 - - - +
49B THR* 3.3 6.2 - - - -
50B GLY* 3.0 34.7 + - - +
458B ILE* 4.3 23.6 - - + -
459B ARG 3.3 9.0 - - - +
460B PHE* 4.0 19.7 - - + -
483B PHE* 1.3 78.6 - - - +
485B ASP* 1.3 66.1 + - - +
486B PHE* 5.0 1.6 - - + +
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Residues in contact with ASP 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LYS* 3.4 22.2 - - + -
48B ILE 3.7 1.8 - - - -
49B THR* 2.7 36.6 + - - +
101B THR 5.8 0.2 - - - -
457B LEU* 3.9 1.3 - - + +
458B ILE* 3.2 7.5 - - - +
459B ARG* 2.8 50.1 + - + +
461B ARG* 3.0 33.5 + - - +
483B PHE* 4.5 2.4 - - - +
484B VAL* 1.3 74.3 - - - +
486B PHE* 1.3 59.4 + - - +
487B ILE* 4.2 8.7 - - + -
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Residues in contact with PHE 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 5.4 2.9 - - + -
47B LYS* 3.3 5.9 - - - +
48B ILE* 2.9 65.2 + - + +
438B PHE* 4.0 22.9 - + - -
457B LEU 3.5 8.5 - - - -
458B ILE* 4.5 17.9 - - + +
484B VAL* 5.0 1.5 - - + +
485B ASP* 1.3 73.9 - - - +
487B ILE* 1.3 71.0 + - - +
488B TRP* 4.1 36.8 - + + -
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Residues in contact with ILE 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ASP* 5.6 4.5 - - + -
46B VAL 3.3 10.8 - - - +
47B LYS* 4.0 25.4 - - + +
452B ASP 4.6 2.5 - - - +
453B GLU* 3.6 33.9 - - + -
455B SER 4.5 6.3 - - - +
456B ALA* 3.2 8.1 - - - +
457B LEU* 2.9 57.6 + - + +
459B ARG* 5.0 3.4 - - - +
485B ASP* 5.0 3.4 - - + -
486B PHE* 1.3 85.7 - - - +
488B TRP* 1.3 73.8 + - - +
489B ARG* 4.5 10.1 - - - +
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Residues in contact with TRP 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU 4.0 0.5 - - - +
45B ASP* 3.7 1.0 - - - -
46B VAL* 2.7 48.9 + - + +
438B PHE* 4.3 13.0 - + + -
440B GLN* 3.5 40.8 - - + -
441B GLY 6.1 0.2 - - - -
456B ALA* 3.4 28.0 - - + -
486B PHE* 4.1 29.7 - + + -
487B ILE* 1.3 78.1 - - - +
489B ARG* 1.3 77.4 + - - +
490B PHE* 3.5 40.1 - + + -
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Residues in contact with ARG 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU 3.7 3.8 - - - +
45B ASP* 2.7 39.1 + - - +
76B TRP* 5.0 11.8 - - + +
441B GLY* 2.8 46.3 + - - -
442B LEU 5.7 0.2 - - - -
443B LEU* 3.7 21.0 - - - +
449B GLN* 4.9 4.8 - - - +
453B GLU* 2.8 40.7 + - - +
455B SER* 3.8 10.3 - - - +
456B ALA* 4.9 4.1 - - - +
487B ILE* 4.5 8.2 - - + +
488B TRP* 1.3 91.4 + - - +
490B PHE* 1.3 74.8 + - - +
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Residues in contact with PHE 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B PHE 4.6 1.4 - - - +
43B GLY* 3.5 11.2 - - - -
44B LEU* 3.1 47.0 + - + +
46B VAL* 3.9 30.5 - - + -
76B TRP* 5.6 0.2 - - - -
488B TRP* 3.5 33.7 - + - -
489B ARG* 1.3 81.4 - - - +
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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