Contacts of the strand formed by residues 257 - 262 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A PRO* 6.3 1.1 - - + -
255A ILE* 3.6 14.4 + - + -
256A PRO* 1.3 73.2 - - - +
258A TYR* 1.3 67.8 - - - +
292A VAL* 3.2 10.0 - - - +
293A TYR* 2.8 71.1 + + + +
294A ASN* 4.6 6.0 - - + -
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Residues in contact with TYR 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A CYS 3.4 22.7 - - - -
250A ALA* 2.9 37.2 + - - +
256A PRO* 3.5 26.6 - - + +
257A HIS* 1.3 77.6 - - - +
259A GLN* 1.3 64.2 + - - +
260A TRP* 5.1 0.2 - - - +
271A THR* 3.1 45.6 + - - +
272A LYS* 4.0 8.1 - - - +
273A LYS* 3.3 34.5 - - + -
290A CYS* 3.8 14.6 - - - -
291A HIS 3.3 6.5 - - - -
292A VAL* 3.8 28.7 - - + -
293A TYR* 4.4 6.3 + - - -
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Residues in contact with GLN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A TYR* 1.3 76.5 - - - +
260A TRP* 1.3 79.6 + - - +
261A PHE* 3.3 27.7 - - + -
266A PRO* 3.9 8.2 - - + +
267A LEU 2.9 31.6 + - - +
268A THR* 5.0 0.4 - - - +
269A HIS 5.0 2.3 + - - -
270A GLU 3.4 6.5 + - - -
271A THR* 3.3 20.5 - - + +
290A CYS* 3.9 4.0 - - - -
291A HIS 2.8 35.2 + - - +
293A TYR* 4.7 0.7 - - + -
295D ASP* 3.5 42.5 - - + +
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Residues in contact with TRP 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A PRO* 4.1 13.2 - - + -
246A LEU* 3.7 41.7 - - + -
247A GLN 3.9 7.0 - - - -
248A CYS* 3.7 26.2 - - + -
259A GLN* 1.3 90.8 + - - +
261A PHE* 1.3 62.4 + - - +
266A PRO* 3.6 2.4 - - - +
267A LEU* 2.9 28.9 + - + -
270A GLU* 3.0 30.1 + - + +
272A LYS 2.8 27.7 + - - -
273A LYS 3.5 19.6 + - - -
274A LEU 4.8 0.9 - - - -
275A TYR* 3.9 21.4 - - + +
288A TYR* 4.7 4.0 - + + -
289A TRP* 3.5 29.6 - - - -
290A CYS* 3.8 18.5 - - + -
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Residues in contact with PHE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A GLN* 3.3 36.8 - - + -
260A TRP* 1.3 72.6 - - - +
262A LYS* 1.3 61.1 + - - +
264A GLU 4.5 3.1 - - - -
265A LEU* 3.3 12.3 - - - +
266A PRO* 3.4 37.2 - - + -
267A LEU* 4.1 3.4 - - - +
288A TYR* 3.2 10.0 - - - +
289A TRP* 2.8 75.1 + + + +
291A HIS* 3.8 9.4 - - + -
295D ASP* 3.6 23.8 - - - -
296D ARG* 3.7 29.6 - - + -
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A PHE* 1.3 75.8 - - - +
263A ASN* 1.3 90.2 + - - +
264A GLU 3.1 2.7 - - - -
265A LEU* 2.9 24.2 + - - +
267A LEU* 4.1 23.8 - - + +
275A TYR* 5.1 2.2 + - - -
283A GLU* 3.5 22.1 + - - -
284A HIS* 4.3 7.7 + - - +
285A GLN 4.0 12.8 - - - +
287A THR 3.4 9.2 - - - +
288A TYR* 3.2 45.5 + - + +
289A TRP* 5.6 0.2 - - - -
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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