Contacts of the strand formed by residues 249 - 256 (chain B) in PDB entry 4BVH
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 GLY 249 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229B ASN 4.2 6.6 - - - +
230B ILE* 4.2 9.2 - - - +
246B GLU* 3.1 28.9 + - - +
247B ALA 3.4 1.0 + - - -
248B HIS* 1.3 79.6 - - - +
250B THR* 1.3 65.2 + - - -
290B ASP 3.4 9.9 - - - -
291B ILE* 4.3 1.8 - - - -
292B VAL* 4.0 3.2 - - - +
299B PRO* 4.1 8.0 - - - +
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Residues in contact with THR 250 (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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230B ILE 4.9 4.4 + - - -
232B GLY* 5.6 5.9 - - - -
246B GLU* 3.8 19.9 + - - +
249B GLY* 1.3 77.9 - - - -
251B PHE* 1.4 58.4 + - - +
252B ALA* 2.9 33.0 + - + +
253B SER* 3.5 14.6 - - - +
290B ASP* 3.0 36.4 + - + +
291B ILE* 3.7 9.8 - - - +
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Residues in contact with PHE 251 (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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192B PHE* 4.4 15.3 - + - -
196B ALA* 4.9 4.3 - - + -
199B LEU* 3.7 29.8 - - + -
200B TYR* 3.4 39.3 + + + -
201B PRO* 3.7 31.2 - - + -
230B ILE* 3.2 54.0 + - + -
250B THR* 1.4 69.9 + - - +
252B ALA* 1.3 63.2 + - - +
253B SER 3.2 8.4 + - - +
265B GLY* 3.3 15.8 - - - -
289B PRO* 3.6 31.3 - - + +
291B ILE* 4.1 4.9 - - + -
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Residues in contact with ALA 252 (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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235B ARG* 3.9 26.0 - - - +
250B THR* 2.9 20.9 + - + +
251B PHE* 1.3 77.7 - - - +
253B SER* 1.3 59.9 + - - +
264B PRO* 3.8 1.9 - - - +
265B GLY* 2.8 18.4 + - - -
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Residues in contact with SER 253 (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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250B THR* 3.5 13.1 - - - +
251B PHE 3.7 6.6 - - - +
252B ALA* 1.3 80.4 - - - +
254B ALA* 1.3 64.0 + - - +
262B PRO* 6.5 0.7 - - - -
263B PHE 3.5 14.1 - - - -
264B PRO* 5.1 0.7 - - - -
265B GLY* 3.7 3.1 - - - +
289B PRO* 3.8 1.7 - - - +
290B ASP* 2.5 43.4 + - - +
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Residues in contact with ALA 254 (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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253B SER* 1.3 78.5 - - - +
255B THR* 1.3 66.3 + - - +
256B CYS 4.3 0.2 - - - -
262B PRO* 3.6 5.5 - - - +
263B PHE* 3.1 27.7 + - + +
264B PRO 4.4 11.0 - - - +
265B GLY* 5.1 1.6 - - - -
268B ILE* 4.4 9.2 - - + -
287B VAL* 3.6 20.4 - - + -
288B LYS 3.2 15.5 - - - +
289B PRO* 3.8 7.6 - - + -
290B ASP* 3.3 5.8 - - - +
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Residues in contact with THR 255 (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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254B ALA* 1.3 74.5 + - - +
256B CYS* 1.3 78.2 + - - +
257B THR* 3.3 2.0 + - - -
260B GLN* 3.9 26.2 - - + +
261B ARG 3.5 7.4 - - - +
262B PRO* 5.3 1.0 - - - +
287B VAL* 4.1 1.6 - - - -
288B LYS* 2.8 36.0 + - - +
290B ASP* 2.5 24.6 + - - -
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Residues in contact with CYS 256 (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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255B THR* 1.3 77.3 - - - +
257B THR* 1.3 63.3 + - - +
258B VAL* 2.8 29.6 - - - -
260B GLN* 3.1 28.2 - - - +
261B ARG 3.1 10.6 + - - +
263B PHE* 3.7 24.0 - - + -
280B CYS* 3.4 14.8 - - + -
285B GLY 4.3 5.8 - - - -
287B VAL* 4.0 10.3 - - + +
1396B ZN 2.3 37.7 - - - -
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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