Contacts of the helix formed by residues 268 - 278 (chain A) in PDB entry 1F0C
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 THR 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A MET* 4.1 4.5 - - - +
39A ARG* 4.2 13.9 + - - +
266A ASN* 2.9 14.8 + - - -
267A LEU* 1.3 78.3 + - - +
269A ASP* 1.3 61.9 + - + +
270A THR* 3.1 28.9 - - - +
271A ASN* 3.0 14.7 + - - +
272A PHE* 2.6 38.0 + - - +
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Residues in contact with ASP 269 (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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35A MET* 4.1 21.9 + - - +
36A ASP* 5.0 2.4 + - - +
268A THR* 1.3 74.6 - - + +
270A THR* 1.3 64.9 + - - +
272A PHE* 3.9 7.1 - - - +
273A LYS* 3.2 24.1 + - - +
382B ILE* 4.1 19.6 - - - +
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Residues in contact with THR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 3.0 14.4 - - - +
269A ASP* 1.3 80.5 - - - +
271A ASN* 1.3 67.7 + - - +
273A LYS* 3.4 4.2 + - - +
274A LYS* 3.2 20.7 + - + +
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Residues in contact with ASN 271 (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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234A GLU* 6.0 0.2 - - - -
235A PHE* 4.0 18.4 + - - -
266A ASN* 3.0 27.4 + - - +
268A THR* 3.0 16.5 + - - +
270A THR* 1.3 83.5 - - - +
272A PHE* 1.3 65.0 + - - +
274A LYS* 3.0 29.9 + - - +
275A TRP* 3.0 41.7 + - + -
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Residues in contact with PHE 272 (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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35A MET* 4.4 6.5 - - + -
239A ILE* 4.5 1.6 - - + -
251A VAL* 3.7 31.6 - - + -
253A ILE* 4.1 20.2 - - + -
267A LEU* 4.2 14.4 - - + -
268A THR 2.6 22.8 + - - +
269A ASP* 3.9 7.0 - - - +
271A ASN* 1.3 72.5 - - - +
273A LYS* 1.3 61.6 + - + +
275A TRP* 3.5 14.5 + + - +
276A CYS* 3.0 45.2 + - - +
373B VAL* 4.0 29.4 - - + -
375B ARG* 3.6 28.7 - - - -
382B ILE* 4.4 15.0 - - + -
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Residues in contact with LYS 273 (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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269A ASP 3.2 18.4 + - - +
270A THR* 3.9 4.7 - - - +
272A PHE* 1.3 80.4 - - + +
274A LYS* 1.3 61.3 + - - +
276A CYS* 3.2 5.9 + - + +
277A ASP* 2.7 73.3 + - - +
375B ARG* 5.4 9.2 - - - +
378B ASP 6.1 0.9 - - - -
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Residues in contact with LYS 274 (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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234A GLU* 2.8 31.8 + - - -
270A THR* 3.2 10.8 + - + +
271A ASN* 3.0 20.8 + - - +
273A LYS* 1.3 78.7 - - - +
275A TRP* 1.3 79.6 + - - +
277A ASP* 3.1 13.4 + - + +
278A SER* 3.1 22.4 + - - -
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Residues in contact with TRP 275 (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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230A ALA* 4.4 1.6 - - - +
232A VAL* 4.0 21.0 - - + +
234A GLU* 3.5 17.4 + - - -
235A PHE* 3.8 25.6 - - - -
237A PHE* 3.5 32.5 - + - -
239A ILE* 3.9 15.0 - - + +
253A ILE* 4.2 16.2 - - + -
263A ILE* 4.8 6.7 - - + -
266A ASN 3.9 13.2 - - - -
267A LEU* 4.1 24.5 - - + -
271A ASN* 3.0 30.9 + - + +
272A PHE* 3.6 20.2 - + - +
274A LYS* 1.3 90.7 - - - +
276A CYS* 1.3 62.1 + - - +
278A SER* 2.7 24.0 + - - -
279A MET* 3.3 12.4 - - - +
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Residues in contact with CYS 276 (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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239A ILE* 4.9 1.8 - - - -
251A VAL* 4.3 12.1 - - - -
272A PHE* 3.0 41.1 + - - +
273A LYS* 3.2 10.3 + - + +
275A TRP* 1.3 75.4 - - - +
277A ASP* 1.3 66.4 + - - +
279A MET* 3.1 35.0 + - - +
375B ARG* 3.1 34.5 - - - +
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Residues in contact with ASP 277 (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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273A LYS* 2.7 61.5 + - - +
274A LYS* 3.3 12.9 - - + +
276A CYS* 1.3 77.8 - - - +
278A SER* 1.3 59.4 + - - +
279A MET 3.5 4.5 + - - +
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Residues in contact with SER 278 (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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229A HIS 4.4 0.2 - - - +
230A ALA* 3.5 17.8 - - - +
232A VAL* 4.9 3.5 - - - +
274A LYS 3.1 10.5 + - - -
275A TRP* 2.7 21.3 + - - -
277A ASP* 1.3 76.3 - - - +
279A MET* 1.3 62.6 + - - +
280A ASP* 3.6 11.2 + - - +
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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