Contacts of the strand formed by residues 271 - 275 (chain B) in PDB entry 5FI2
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 ARG 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLY* 2.9 14.5 + - - +
168B ARG* 3.4 61.6 - - + +
223B PHE* 3.1 14.8 - - - -
263B SER* 6.0 0.2 - - - -
264B VAL 3.3 9.9 + - - -
265B CYS* 3.7 16.8 - - - +
269B GLY 3.3 20.6 - - - +
270B GLN* 1.3 78.5 - - - +
272B HIS* 1.3 63.0 + - - +
368B GLU* 2.9 40.6 + - - -
424B GLU* 3.4 22.0 + - - +
427B SER* 4.1 1.8 + - - -
428B VAL* 3.4 13.9 - - - +
441B ILE* 3.8 14.1 - - + +
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Residues in contact with HIS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 6.1 0.4 - - - -
223B PHE* 4.0 5.8 - - + -
226B PHE* 6.4 0.2 - - + -
227B THR* 3.4 43.2 - - + +
230B ILE* 4.0 21.8 - - + -
231B ASP* 2.9 35.1 + - - -
262B VAL 3.9 0.9 - - - +
263B SER* 3.3 2.3 - - - -
264B VAL* 2.6 45.5 + - + +
271B ARG* 1.3 78.5 + - - +
273B SER* 1.3 81.5 + - - +
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 4.6 5.5 + - - -
262B VAL 3.3 5.4 - - - -
263B SER* 3.0 19.6 + - - -
272B HIS* 1.3 91.2 + - - +
274B THR* 1.3 64.3 + - - +
277B THR* 3.4 20.9 - - - -
424B GLU* 3.3 20.2 + - - +
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Residues in contact with THR 274 (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* 4.6 4.7 - - + -
231B ASP* 3.4 25.5 + - - +
234B TYR* 3.0 48.7 - - + -
235B GLU* 5.1 1.6 + - - -
262B VAL* 3.0 40.2 + - + +
272B HIS* 4.3 0.7 - - - -
273B SER* 1.3 76.2 - - - +
275B GLY* 1.3 65.6 + - - +
277B THR* 3.4 0.8 - - - +
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Residues in contact with GLY 275 (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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234B TYR* 3.1 23.1 - - - -
260B TRP 3.4 0.4 - - - -
274B THR* 1.3 78.1 + - - +
276B ASP* 1.3 64.0 + - - -
277B THR* 2.8 14.4 + - - -
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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