Contacts of the strand formed by residues 257 - 262 (chain B) in PDB entry 3BFO
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 HIS 257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B PRO* 6.3 0.4 - - - +
255B ILE* 3.5 16.4 + - + +
256B PRO* 1.3 73.0 + - - +
258B TYR* 1.3 66.9 + - - +
292B VAL* 3.3 8.7 - - - +
293B TYR* 2.8 72.9 + + + +
294B ASN* 4.6 6.5 - - + -
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Residues in contact with TYR 258 (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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248B CYS 3.4 23.1 - - - -
249B VAL* 4.0 0.3 - - - -
250B ALA* 2.9 39.6 + - - +
256B PRO* 3.5 26.2 - - + +
257B HIS* 1.3 76.9 - - - +
259B GLN* 1.3 64.6 + - - +
260B TRP* 5.2 0.2 - - - +
271B THR* 3.2 44.9 + - - +
272B LYS* 4.2 4.9 - - - +
273B LYS* 3.6 36.6 - - + +
290B CYS* 3.8 21.8 - - - -
291B HIS 3.3 7.0 - - - -
292B VAL* 3.8 19.3 - - + -
293B TYR* 4.4 6.5 + - - -
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Residues in contact with GLN 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B TYR* 1.3 75.7 - - - +
260B TRP* 1.3 84.5 + - - +
261B PHE* 3.3 31.8 - - + -
266B PRO* 3.9 9.5 - - + +
267B LEU 2.9 27.1 + - - +
268B THR* 5.0 0.4 - - - +
269B HIS 5.0 2.4 + - - -
270B GLU 3.5 6.6 + - - -
271B THR* 3.3 20.4 - - - +
290B CYS* 3.4 4.4 - - - -
291B HIS* 2.9 36.7 + - + +
293B TYR* 4.8 8.7 - - + +
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Residues in contact with TRP 260 (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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233B PRO* 4.1 13.5 - - + -
246B LEU* 3.7 39.0 - - + -
247B GLN 3.9 13.2 - - - -
248B CYS* 3.7 13.5 - - + -
259B GLN* 1.3 90.4 + - - +
261B PHE* 1.3 64.1 + - - +
266B PRO* 3.6 2.4 - - - +
267B LEU* 2.9 28.9 + - + -
270B GLU* 3.0 30.3 + - + +
271B THR 5.2 0.2 - - - -
272B LYS 2.8 27.2 + - - -
273B LYS 3.5 19.2 + - - -
274B LEU 4.7 0.9 - - - -
275B TYR* 3.9 24.6 - - + +
288B TYR* 4.7 4.0 - + + -
289B TRP* 3.5 29.2 - - - -
290B CYS* 3.8 23.9 - - + -
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Residues in contact with PHE 261 (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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259B GLN* 3.3 40.8 - - + -
260B TRP* 1.3 72.8 - - - +
262B LYS* 1.3 61.7 + - - +
264B GLU 4.5 4.0 - - - -
265B LEU* 3.3 12.6 - - - +
266B PRO* 3.4 36.3 - - + -
267B LEU* 4.1 3.4 - - - +
287B THR 4.5 0.2 - - - -
288B TYR* 3.2 10.7 - - - +
289B TRP* 2.8 80.4 + + + +
291B HIS* 3.8 18.2 - + + -
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Residues in contact with LYS 262 (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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261B PHE* 1.3 74.5 - - - +
263B ASN* 1.3 93.6 + - - +
264B GLU 3.1 2.2 - - - -
265B LEU* 2.9 23.7 + - - +
267B LEU* 4.0 21.4 - - + +
275B TYR* 5.8 0.2 - - - +
283B GLU 2.9 28.3 + - - +
284B HIS* 4.1 2.5 - - + -
285B GLN 3.0 23.2 + - - -
286B GLY* 5.0 0.4 - - - -
287B THR 3.4 5.6 - - - +
288B TYR* 3.7 37.0 - - + +
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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