Contacts of the strand formed by residues 320 - 330 (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 GLN 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A TYR* 3.4 18.6 + - - +
225A THR 3.5 5.0 - - - +
226A PRO* 3.7 11.7 - - - +
227A PHE* 2.9 59.4 + - - +
228A PHE* 4.4 10.3 - - + +
189B ALA* 5.9 0.2 - - - +
194B TYR* 2.6 39.9 + - + +
299B THR* 4.0 11.0 - - + -
300B CYS 3.5 3.8 - - - -
301B PHE* 3.9 15.1 - - + -
318B VAL* 3.2 5.4 - - - +
319B HIS* 1.3 82.6 - - + +
321B PHE* 1.3 59.1 + - - +
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Residues in contact with PHE 321 (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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224A TYR* 4.4 1.1 - - - -
194B TYR* 4.1 4.5 - - - -
270B ALA 4.7 1.1 - - - -
299B THR* 3.4 2.2 - - - -
300B CYS* 2.7 52.7 + - + +
302B ARG* 4.0 40.2 - - + -
318B VAL* 3.4 26.0 - - + -
319B HIS 4.4 2.0 - - - -
320B GLN* 1.3 80.8 - - - +
322B GLU* 1.3 70.4 + - - +
323B LYS* 3.4 39.0 - - + -
432B ALA* 4.5 12.1 - - + -
433B THR* 4.9 0.7 - - - +
434B THR* 3.7 27.8 - - + +
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A TYR* 2.7 40.4 + - - -
227A PHE* 4.1 2.1 - - - -
194B TYR* 5.1 0.5 + - - -
204B GLU* 3.2 20.6 - - - +
208B ILE* 4.6 15.3 - - + -
297B LEU* 5.6 6.3 - - + -
298B SER 3.3 13.2 - - - +
299B THR* 3.0 23.8 + - - +
321B PHE* 1.3 75.5 - - - +
323B LYS* 1.3 64.4 + - - +
432B ALA* 3.7 2.9 - - - -
433B THR* 3.1 44.8 + - + +
434B THR* 5.9 0.2 - - - +
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Residues in contact with LYS 323 (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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270B ALA 4.3 3.5 + - - +
271B THR* 4.0 12.5 - - - +
272B SER* 4.9 0.2 + - - -
296B GLY 3.4 3.1 - - - +
297B LEU* 4.3 0.5 - - - +
298B SER* 3.0 29.7 + - - +
300B CYS* 3.4 28.7 - - + -
302B ARG* 5.9 2.0 - - - +
321B PHE* 3.4 33.4 - - + -
322B GLU* 1.3 74.2 - - - +
324B ILE* 1.3 69.3 + - - +
325B GLU* 3.5 19.4 + - + +
429B THR* 2.9 44.4 + - - +
431B CYS 3.4 6.1 - - - +
432B ALA* 4.6 11.4 - - + +
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Residues in contact with ILE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 4.2 20.0 - - + -
211B ALA* 4.1 24.5 - - + -
212B LEU* 3.9 20.0 - - + -
215B LEU* 3.9 26.2 - - + -
295B ALA* 4.9 1.3 - - + -
296B GLY 3.1 7.9 - - - +
297B LEU* 3.3 33.4 - - + -
322B GLU* 5.9 0.2 - - + -
323B LYS* 1.3 73.8 - - - +
325B GLU* 1.3 60.4 + - - +
429B THR* 3.9 1.0 - - - -
430B MET* 3.0 25.8 + - + +
431B CYS* 2.9 31.4 + - + +
433B THR* 5.2 2.0 - - + -
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Residues in contact with GLU 325 (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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215B LEU* 4.9 1.6 - - - -
271B THR* 2.9 16.8 - - - -
272B SER* 2.6 50.0 + - - -
273B GLU* 4.0 14.1 + - - +
276B ILE* 5.8 1.1 - - + -
295B ALA* 3.2 7.6 - - - +
296B GLY* 2.6 37.7 + - - +
323B LYS* 3.5 18.9 - - + +
324B ILE* 1.3 76.8 - - - +
326B GLN* 1.3 65.2 + - - +
327B PHE* 6.0 0.9 - - + -
427B ASN* 4.9 2.9 - - - +
428B ALA 3.3 11.7 + - - +
429B THR* 3.1 26.5 - - + +
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Residues in contact with GLN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 4.2 19.6 - - + +
220B TYR* 2.3 49.0 + - + -
294B TYR 3.6 4.7 - - - -
325B GLU* 1.3 75.8 - - - +
327B PHE* 1.3 60.4 + - - +
328B VAL 4.3 0.2 - - - -
344B MET* 3.0 42.3 + - + +
347B THR* 4.2 6.0 - - - +
348B ALA* 4.2 11.4 + - - +
427B ASN* 3.2 6.2 - - - +
428B ALA* 2.6 49.8 + - + +
430B MET* 4.2 14.4 - - + +
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Residues in contact with PHE 327 (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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273B GLU* 3.6 44.9 - - + -
276B ILE* 3.6 28.0 - - + -
277B ALA* 3.7 10.1 - - + -
292B ILE 3.8 0.9 - - - +
293B LYS* 3.5 2.3 - - - -
294B TYR* 2.8 40.6 + - + +
325B GLU* 3.9 1.5 + - + -
326B GLN* 1.3 74.2 - - - +
328B VAL* 1.3 75.3 + - - +
329B TYR* 3.5 40.4 - + - -
402B GLN* 5.2 0.4 - - - -
425B MET* 3.6 31.9 - - + -
426B LEU 3.5 4.3 - - - -
427B ASN* 3.8 18.8 - - + -
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Residues in contact with VAL 328 (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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220B TYR* 4.3 8.7 - - + +
291B PRO* 4.1 8.1 - - + -
292B ILE 3.4 5.8 - - - +
293B LYS* 4.0 17.9 - - + -
327B PHE* 1.3 83.2 - - - +
329B TYR* 1.3 80.3 + - - +
330B SER* 4.2 1.8 - - - +
340B MET* 3.6 31.4 - - + -
344B MET* 3.8 30.1 - - + -
424B HIS 3.8 0.3 - - - +
425B MET* 3.5 5.4 - - - -
426B LEU* 2.9 36.5 + - + +
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Residues in contact with TYR 329 (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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276B ILE 2.5 26.0 + - - -
277B ALA* 3.1 15.8 + - - -
280B HIS* 3.5 30.4 - + + +
285B LEU* 4.0 27.8 - - + -
290B LEU* 3.8 7.9 - - + +
291B PRO* 3.1 29.1 - - - +
292B ILE* 2.9 21.4 + - + +
294B TYR* 3.8 16.2 - + - -
327B PHE* 3.5 19.7 - + - -
328B VAL* 1.3 74.7 - - - +
330B SER* 1.3 58.7 + - - +
408B ILE* 3.9 22.0 - - + -
423B VAL* 4.4 7.0 - - + -
424B HIS 3.6 1.8 - - - -
425B MET* 3.8 22.4 - - + -
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Residues in contact with SER 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 4.3 5.2 - - - -
291B PRO* 4.6 7.0 - - - +
328B VAL* 4.5 4.7 - - - -
329B TYR* 1.3 75.0 - - - +
331B SER* 1.3 70.0 + - - +
336B LYS* 3.6 8.3 + - - +
337B SER* 3.5 30.7 + - - -
340B MET* 4.6 3.8 - - - +
423B VAL* 3.4 8.1 - - - +
424B HIS* 2.7 42.5 + - - -
426B LEU* 4.0 12.1 - - - -
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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