Contacts of the strand formed by residues 292 - 301 (chain B) in PDB entry 3VBB
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 ILE 292 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B ILE* 5.4 5.8 - - + -
280B HIS* 4.4 9.6 - - + +
285B LEU* 3.9 27.1 - - + -
289B ASP* 3.4 26.7 - - + +
290B LEU* 3.8 20.2 - - + -
291B PRO* 1.3 70.6 - - - +
293B LYS* 1.3 62.3 + - - +
294B TYR* 3.6 38.8 + - + +
327B PHE 3.8 1.4 - - - +
328B VAL* 3.4 2.4 - - - -
329B TYR* 2.9 38.9 + - + +
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Residues in contact with LYS 293 (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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218B ARG 3.3 24.7 + - - -
219B GLY* 4.1 12.5 + - - +
220B TYR* 3.4 40.0 - - + +
221B ILE* 2.9 27.3 + - - +
291B PRO* 4.0 19.0 + - + +
292B ILE* 1.3 78.4 - - - +
294B TYR* 1.3 66.5 + - - +
327B PHE 3.5 4.0 - - - -
328B VAL* 4.0 16.6 - - + -
340B MET* 4.4 13.1 - - + +
343B GLU* 3.3 20.2 + - - +
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Residues in contact with TYR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LYS* 5.1 11.5 + - - -
220B TYR* 3.3 10.9 - - - -
221B ILE* 3.4 33.0 - - + +
223B ILE* 4.0 23.8 - - + -
276B ILE* 3.6 27.8 - - + -
279B LEU* 3.3 25.7 - - + +
280B HIS* 2.6 36.3 + + - -
292B ILE* 3.6 20.6 - - + +
293B LYS* 1.3 78.2 - - - +
295B ALA* 1.3 60.3 + - - +
296B GLY 3.8 0.2 - - - -
325B GLU 3.6 0.9 - - - +
327B PHE* 2.8 33.9 + - + +
329B TYR* 3.8 13.2 - + - -
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Residues in contact with ALA 295 (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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212B LEU* 5.3 5.6 - - + +
215B LEU* 3.3 33.0 - - + -
216B GLY 5.7 0.4 - - - +
220B TYR* 4.0 11.4 - - + +
221B ILE 2.9 8.9 + - - -
222B PRO* 3.3 16.6 - - + +
223B ILE* 2.8 28.2 + - - +
294B TYR* 1.3 71.7 - - - +
296B GLY* 1.3 63.4 + - - +
297B LEU* 3.6 1.7 + - - +
324B ILE* 4.9 3.6 - - + -
325B GLU 3.2 5.4 - - - -
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Residues in contact with GLY 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ILE 3.6 5.6 - - - -
225B THR* 4.8 0.2 - - - -
272B SER* 3.8 13.7 - - - -
276B ILE* 3.8 22.4 - - - +
294B TYR 3.8 2.0 - - - -
295B ALA* 1.3 72.3 - - - +
297B LEU* 1.3 60.6 + - - +
323B LYS 3.4 0.7 - - - +
324B ILE* 3.1 10.8 - - - +
325B GLU 2.6 39.6 + - - -
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Residues in contact with LEU 297 (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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201A VAL* 3.8 30.3 - - + -
205A GLN* 4.1 16.8 - - - +
208B ILE* 4.2 16.2 - - + -
212B LEU* 3.8 18.4 - - + -
222B PRO* 6.2 0.2 - - + -
223B ILE 2.8 15.1 + - - +
224B TYR* 3.5 18.8 - - + -
225B THR* 3.3 19.6 + - - +
272B SER* 3.8 0.8 + - - -
295B ALA 4.6 2.2 - - - +
296B GLY* 1.3 73.9 - - - +
298B SER* 1.3 67.8 + - - +
322B GLU* 5.6 4.9 - - + -
323B LYS 3.7 2.0 - - - +
324B ILE* 3.3 27.4 - - + -
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Residues in contact with SER 298 (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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224B TYR* 5.4 0.4 - - - -
225B THR* 3.6 18.2 - - - -
227B PHE* 3.7 9.2 - - - -
269B ILE* 3.7 9.5 - - - +
272B SER* 2.7 25.4 + - - -
297B LEU* 1.3 78.4 - - - +
299B THR* 1.3 60.7 + - - +
300B CYS* 3.1 22.2 + - - -
322B GLU* 3.3 8.9 - - - +
323B LYS 3.0 32.6 + - - +
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Residues in contact with THR 299 (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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227A PHE* 3.5 17.2 - - + -
299A THR* 4.2 1.4 + - - -
227B PHE* 3.4 36.7 - - - -
269B ILE* 3.9 15.4 - - - +
298B SER* 1.3 73.8 - - - +
300B CYS* 1.3 62.5 + - - +
301B PHE* 3.7 30.7 - - + -
320B GLN* 4.0 12.3 - - + -
321B PHE 3.4 11.4 - - - +
322B GLU* 3.0 25.5 + - - +
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Residues in contact with CYS 300 (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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269B ILE* 3.6 4.5 - - - -
270B ALA 3.5 15.9 - - - +
271B THR* 3.8 18.2 - - - -
298B SER* 3.1 26.0 - - - -
299B THR* 1.3 73.5 - - - +
301B PHE* 1.3 65.4 + - - +
319B HIS 3.6 0.3 - - - +
320B GLN* 3.5 5.7 - - - -
321B PHE* 2.7 50.9 + - + +
323B LYS* 3.4 30.1 - - - -
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Residues in contact with PHE 301 (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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227A PHE* 4.3 17.0 - + + -
228A PHE* 3.6 35.4 - + - -
268A LEU* 5.4 1.3 - - + -
301A PHE* 5.2 7.2 - + - -
227B PHE* 4.7 10.3 - + + -
247B LEU* 4.8 2.9 - - - -
248B TYR* 3.8 19.0 - - + -
268B LEU* 3.8 37.8 - - + +
269B ILE 3.1 11.2 + - - +
270B ALA* 3.5 20.3 + - - +
299B THR* 3.7 36.3 - - + -
300B CYS* 1.3 75.7 - - - +
302B ARG* 1.3 62.5 + - - +
319B HIS 3.1 12.3 - - - +
320B GLN* 3.9 21.5 - - + -
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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