Contacts of the helix formed by residues 247 - 255 (chain B) in PDB entry 1F0K
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 ASP 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ARG* 4.6 2.0 - - - +
166B ASP* 4.7 3.7 - - - +
216B TRP* 5.4 1.4 - - - -
245B ILE* 3.4 10.0 - - - +
246B ASP* 1.3 88.5 + - - +
248B MET* 1.3 60.5 + - - +
249B ALA* 3.3 12.5 + - - +
250B ALA* 2.9 39.4 + - + +
251B ALA 3.2 8.8 + - - -
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Residues in contact with MET 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ARG* 3.3 26.7 - - - +
167B VAL* 5.3 0.4 - - + -
187B LEU* 4.8 0.4 - - - -
189B VAL* 3.8 32.1 - - + -
218B GLN* 4.6 5.2 - - - +
245B ILE* 3.4 50.5 - - + +
246B ASP 3.5 4.4 + - - -
247B ASP* 1.3 71.6 - - - +
249B ALA* 1.3 60.0 + - - +
251B ALA* 3.2 4.9 + - - +
252B TYR* 2.8 65.0 + - + -
269B GLU* 4.5 8.3 - - - +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ARG* 4.2 3.0 - - - +
166B ASP* 3.6 47.6 - - + +
167B VAL* 4.1 10.9 - - + +
170B LEU* 3.6 11.9 - - + +
247B ASP* 3.2 8.9 - - - +
248B MET* 1.3 78.3 - - - +
250B ALA* 1.3 56.8 + - - +
252B TYR* 3.4 4.0 + - - +
253B ALA* 3.0 29.6 + - - +
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PRO* 4.3 24.5 - - + +
216B TRP* 5.8 0.4 - - + -
247B ASP* 2.9 35.8 + - + +
249B ALA* 1.3 77.9 - - - +
251B ALA* 1.3 60.9 + - - +
253B ALA* 3.5 8.3 + - - +
254B TRP* 3.3 20.8 + - - +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 3.9 23.9 - - + +
216B TRP* 3.8 33.1 - - + -
245B ILE* 4.0 12.8 - - + -
247B ASP 3.2 7.2 + - - +
248B MET* 3.2 8.8 + - - +
250B ALA* 1.3 78.0 - - - +
252B TYR* 1.3 59.0 + - - +
254B TRP* 3.2 6.5 + - - +
255B ALA* 3.0 29.1 + - - +
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Residues in contact with TYR 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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167B VAL* 4.1 13.9 - - + -
170B LEU* 4.0 11.9 - - + -
176B ARG* 4.3 3.0 - - - -
187B LEU* 3.7 22.0 - - + -
189B VAL* 5.0 4.5 - - + +
248B MET* 2.8 34.4 + - + +
249B ALA 3.7 4.5 - - - +
251B ALA* 1.3 76.0 - - - +
253B ALA* 1.3 61.6 + - - +
254B TRP 3.4 0.3 + - - -
255B ALA* 3.5 7.2 + - - +
258B VAL* 4.0 7.0 - - + +
266B THR* 4.8 6.4 - - - +
269B GLU* 2.6 44.5 + - + +
270B ILE* 3.4 32.8 - - + +
273B ALA* 4.0 14.1 - - + -
275B LEU* 3.3 42.4 - - + +
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Residues in contact with ALA 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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170B LEU* 3.8 17.2 - - + +
171B PRO* 5.8 1.6 - - + -
176B ARG* 3.3 23.2 - - - +
180B ARG* 2.9 21.8 + - - -
249B ALA 3.0 17.9 + - - +
250B ALA* 3.7 9.0 - - - +
251B ALA 3.2 0.4 - - - -
252B TYR* 1.3 76.7 - - - +
254B TRP* 1.3 59.0 + - - +
255B ALA 4.3 0.2 - - - +
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Residues in contact with TRP 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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237A PRO* 5.8 1.3 - - + -
238A GLN* 3.3 52.2 - - + +
180B ARG* 2.9 20.3 + - - +
185B ARG* 2.9 73.8 + - + +
186B VAL 3.8 16.2 - - - -
187B LEU* 4.1 7.6 - - + -
214B THR* 3.8 28.2 - - + +
215B ILE 4.2 1.1 - - - -
216B TRP* 3.6 41.1 - + + -
250B ALA 3.3 9.1 + - - +
251B ALA* 3.2 14.2 + - - +
253B ALA* 1.3 80.0 - - - +
255B ALA* 1.3 73.2 + - + +
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Residues in contact with ALA 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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176B ARG* 4.2 4.2 + - - -
177B LEU* 4.8 0.2 - - - +
180B ARG* 3.2 12.1 + - - -
185B ARG* 3.9 3.4 - - - +
187B LEU* 3.7 30.1 - - + -
251B ALA 3.0 16.2 + - - +
252B TYR 3.5 8.9 + - - +
253B ALA 4.3 0.3 - - - +
254B TRP* 1.3 87.2 - - + +
256B ASP* 1.3 59.6 + - - +
257B VAL 4.0 9.2 - - - +
275B LEU* 3.5 22.3 - - + +
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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
------------------------------------------------------------
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