Contacts of the strand formed by residues 290 - 297 (chain B) in PDB entry 3VS5
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 THR 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ILE* 4.0 17.8 - - + +
98B HIS* 5.8 0.5 + - - -
253B LYS* 6.4 2.5 - - + -
255B TRP* 4.1 23.1 - - + -
285B THR* 4.4 5.6 + - - +
286B TYR* 2.9 48.8 + - - +
288B LYS 3.9 0.8 - - - -
289B HIS* 1.3 82.3 + - - +
291B LYS* 1.3 73.6 + - - +
292B VAL* 3.4 1.3 + - + +
326B HIS* 6.1 1.3 - - + -
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Residues in contact with LYS 291 (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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283B MET* 3.7 30.0 - - - +
284B ALA 3.6 9.2 - - - +
285B THR* 4.6 6.0 + - - +
289B HIS 4.3 0.6 + - - -
290B THR* 1.3 75.2 - - - +
292B VAL* 1.3 67.3 + - - +
326B HIS* 5.8 0.7 - - - -
339B GLU* 5.4 0.7 - - - -
340B PHE* 3.6 52.8 + - + +
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B TRP* 3.8 23.8 - - + -
267B LEU* 4.5 5.4 - - + -
283B MET* 3.8 2.6 - - - -
284B ALA* 2.8 56.4 + - + +
285B THR 4.4 0.4 - - - -
286B TYR* 4.1 12.1 - - + +
290B THR* 4.0 9.4 - - + +
291B LYS* 1.3 81.5 - - - +
293B ALA* 1.3 56.8 - - - +
294B VAL* 4.5 1.6 - - + -
326B HIS* 4.1 6.5 - - + +
337B ILE* 3.7 29.2 - - + -
338B THR 3.5 12.3 - - - +
339B GLU* 5.3 0.2 - - - -
340B PHE* 4.1 12.5 - - - +
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Residues in contact with ALA 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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273B LEU* 5.2 0.4 - - + -
281B VAL* 5.2 2.0 - - + -
282B TRP 3.3 9.0 - - - +
292B VAL* 1.3 76.7 - - - +
294B VAL* 1.3 62.8 + - - +
336B ILE 3.4 1.6 - - - +
337B ILE* 3.6 1.6 - - - -
338B THR* 3.0 35.8 + - - +
339B GLU 4.1 2.7 - - - +
340B PHE* 3.9 13.2 - - + +
601B VSG 3.3 43.8 - - + +
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 4.3 5.6 - - + -
269B LEU* 3.6 16.4 - - + -
280B GLU 3.7 0.7 - - - +
281B VAL* 3.3 6.6 - - - -
282B TRP* 2.8 41.2 + - + +
284B ALA* 3.5 28.3 - - + -
292B VAL* 4.5 2.7 - - + -
293B ALA* 1.3 76.9 - - - +
295B LYS* 1.3 63.6 + - - +
296B THR* 3.8 9.7 + - + +
335B TYR* 3.8 37.5 - - + -
336B ILE 3.2 9.0 - - - +
337B ILE* 4.2 14.8 - - + -
601B VSG 5.3 0.2 - - - -
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Residues in contact with LYS 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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279B GLY 6.0 0.7 - - - -
280B GLU 3.4 9.2 - - - +
281B VAL* 3.9 19.4 - - + +
293B ALA 4.1 0.4 + - - -
294B VAL* 1.3 72.0 - - - +
296B THR* 1.3 63.3 + - - +
297B MET* 3.8 19.9 + - - -
334B ILE 3.6 2.1 - - - +
335B TYR* 3.4 4.2 - - - -
336B ILE* 2.8 51.8 + - + +
404B ASP* 3.2 35.6 + - - +
407B LEU* 3.7 20.9 - - + -
601B VSG 3.6 34.6 - - + +
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Residues in contact with THR 296 (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 LEU* 3.8 13.2 - - + -
279B GLY* 3.1 16.5 - - - -
280B GLU* 2.8 34.0 + - - +
282B TRP* 3.7 26.5 - - + +
294B VAL* 4.0 5.6 - - + +
295B LYS* 1.3 73.4 - - - +
297B MET* 1.3 65.3 + - - +
298B LYS* 3.5 0.9 + - - +
333B PRO* 5.6 1.6 - - - -
334B ILE 3.7 5.6 - - - -
335B TYR* 3.5 29.2 - - + +
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Residues in contact with MET 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 3.7 29.4 - - + +
279B GLY* 5.2 1.8 - - - -
295B LYS* 3.9 34.3 - - + -
296B THR* 1.3 71.0 - - - +
298B LYS* 1.3 66.5 + - - +
299B PRO 3.8 0.2 - - - -
302B MET* 5.7 13.0 - - + -
307B PHE* 5.4 8.3 - - + -
333B PRO* 3.3 23.6 - - - +
334B ILE* 3.1 29.8 + - + +
336B ILE* 4.7 13.5 - - + -
407B LEU* 4.6 20.0 - - + -
411B ILE* 5.9 4.7 - - + -
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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