Contacts of the helix formed by residues 246 - 257 (chain B) in PDB entry 1F4J
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 SER 246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B ASN 4.0 1.8 + - - -
245B LEU* 1.3 76.6 - - - +
247B VAL* 1.3 58.6 + - - +
248B GLU* 3.4 22.6 + - - -
249B ASP* 3.3 31.8 + - - +
250B ALA* 2.9 26.2 + - - +
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Residues in contact with VAL 247 (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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127B ARG* 3.6 27.6 - - - +
205B ILE* 4.4 7.2 - - + -
245B LEU 3.9 0.2 + - - -
246B SER* 1.3 69.3 - - - +
248B GLU* 1.3 88.7 + - + +
250B ALA* 3.8 7.6 - - - +
251B ALA* 3.0 25.3 + - - +
462B ASN* 3.9 16.4 - - - +
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Residues in contact with GLU 248 (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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246B SER* 3.4 18.1 + - - +
247B VAL* 1.3 109.5 + - + +
249B ASP* 1.3 67.6 + - - +
251B ALA* 3.2 5.1 + - - +
252B ARG* 3.0 21.6 + - - +
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Residues in contact with ASP 249 (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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245B LEU* 4.6 15.0 - - + +
246B SER* 3.3 26.5 + - - +
248B GLU* 1.3 80.2 - - - +
250B ALA* 1.3 67.7 + - - +
252B ARG* 2.9 36.3 + - - +
253B LEU* 2.7 29.9 + - + +
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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
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125B THR* 3.0 35.6 + - - +
126B VAL* 5.3 0.2 - - - -
205B ILE* 3.8 32.8 - - + -
245B LEU* 4.3 5.5 - - + +
246B SER 2.9 21.5 + - - +
247B VAL 3.8 3.6 - - - +
249B ASP* 1.3 71.6 - - - +
251B ALA* 1.3 52.1 + - - +
253B LEU* 4.5 1.3 - - - -
254B SER* 2.8 30.7 + - - -
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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
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247B VAL 3.0 18.2 + - - +
248B GLU* 3.4 6.1 - - - +
250B ALA* 1.3 75.0 - - - +
252B ARG* 1.3 66.7 + - - +
254B SER* 2.6 26.1 + - - -
255B GLN 3.5 1.2 + - - -
255C GLN* 3.2 32.3 - - - +
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Residues in contact with ARG 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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248B GLU 3.0 11.9 + - - +
249B ASP* 2.9 39.2 + - - +
251B ALA* 1.3 75.8 - - - +
253B LEU* 1.3 76.7 + - - +
255B GLN* 3.2 12.4 + - - +
256B GLU* 3.0 65.5 + - + +
255C GLN* 5.3 1.8 - - - +
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Residues in contact with LEU 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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125B THR* 3.4 20.9 - - + +
245B LEU* 3.9 21.3 - - + -
249B ASP* 2.7 21.9 + - + +
250B ALA 3.7 0.2 - - - +
252B ARG* 1.3 97.4 - - - +
254B SER* 1.3 56.8 + - - +
255B GLN 2.8 11.2 + - - -
256B GLU* 4.1 10.5 - - + +
257B ASP* 2.9 33.8 + - + +
260B TYR* 3.4 48.5 - - + +
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Residues in contact with SER 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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123B ALA* 3.7 27.1 - - - +
125B THR* 3.4 12.1 + - - -
126B VAL* 4.5 6.7 - - - -
250B ALA 2.8 19.0 + - - -
251B ALA* 2.6 20.5 + - - -
253B LEU* 1.3 72.6 - - - +
255B GLN* 1.3 56.7 + - - +
257B ASP 4.7 0.4 - - - -
258B PRO* 3.5 18.6 - - - +
254C SER 5.0 5.0 - - - +
255C GLN* 3.3 19.0 + - - +
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Residues in contact with GLN 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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251B ALA 4.1 0.7 - - - +
252B ARG* 3.2 11.5 + - - +
253B LEU 2.8 0.4 - - - -
254B SER* 1.3 80.9 + - - +
256B GLU* 1.3 85.5 + - - +
257B ASP 3.5 1.1 - - - -
258B PRO* 4.3 7.7 - - - +
251C ALA* 3.2 33.5 + - + +
252C ARG* 5.1 2.0 - - - +
254C SER* 3.1 25.4 + - - +
255C GLN* 3.5 24.3 - - + +
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Residues in contact with GLU 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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252B ARG* 3.0 60.5 + - - +
253B LEU* 4.1 8.1 - - + +
255B GLN* 1.3 96.2 + - - +
257B ASP* 1.3 64.3 + - + +
258B PRO* 4.0 3.0 - - - +
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Residues in contact with ASP 257 (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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124B ASP 5.3 0.2 + - - -
125B THR* 5.0 1.0 + - - -
253B LEU* 2.9 19.7 + - + +
254B SER* 4.7 0.2 - - - -
256B GLU* 1.3 83.1 - - + +
258B PRO* 1.3 66.3 - - - +
259B ASP* 3.0 15.1 + - - +
260B TYR* 3.2 43.9 + - + +
263B ARG* 2.7 47.8 + - - -
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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