Contacts of the helix formed by residues 243 - 252 (chain E) in PDB entry 1FMO
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 PRO 243 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202E PRO* 4.3 16.8 - - + -
241E ASP 4.3 3.6 - - - +
242E GLN* 1.3 84.5 - - + +
244E ILE* 1.3 59.9 + - + +
246E ILE* 2.9 18.7 + - + +
247E TYR* 2.8 60.4 + - + +
15I ARG* 4.4 17.3 - - - +
22I ILE* 5.8 3.8 - - + -
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Residues in contact with ILE 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E GLN* 4.5 17.0 - - + +
243E PRO* 1.3 88.3 - - + +
245E GLN* 1.3 70.9 + - + +
247E TYR* 3.0 29.4 + - + +
248E GLU* 3.1 31.1 + - + +
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Residues in contact with GLN 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E ALA* 3.0 15.5 - - + +
241E ASP* 2.9 34.0 - - - +
242E GLN* 2.7 46.4 + - + +
244E ILE* 1.3 81.4 - - + +
246E ILE* 1.3 60.1 + - - +
248E GLU* 3.7 12.4 + - - +
249E LYS* 2.9 29.8 + - + +
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Residues in contact with ILE 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E PRO* 4.0 13.9 - - + +
203E GLU* 3.9 15.7 - - + +
238E PHE* 3.6 22.9 - - + +
239E PHE* 4.2 1.3 - - - -
240E ALA* 3.8 22.4 - - - +
242E GLN 3.6 6.7 - - - +
243E PRO* 2.9 26.1 + - + +
245E GLN* 1.3 79.1 - - - +
247E TYR* 1.3 63.7 + - + +
249E LYS* 2.9 18.4 + - - +
250E ILE* 3.1 27.6 + - + +
15I ARG* 3.8 30.5 - - - +
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Residues in contact with TYR 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E LEU* 5.7 4.0 - - + +
202E PRO* 4.0 26.8 - - + +
205E LEU* 4.4 7.9 - - + -
210E ILE* 3.3 42.2 - - + -
243E PRO* 2.8 40.0 + - + +
244E ILE* 3.2 20.6 - - + +
246E ILE* 1.3 73.8 - - - +
248E GLU* 1.3 64.2 + - + +
249E LYS 3.1 0.3 + - - -
250E ILE* 3.2 7.5 + - + +
251E VAL* 3.1 29.1 + - - +
22I ILE* 3.7 26.6 - - + +
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Residues in contact with GLU 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E ILE* 3.1 31.5 + - + +
245E GLN* 4.1 10.8 - - - +
246E ILE 3.2 0.2 - - - -
247E TYR* 1.3 77.8 - - + +
249E LYS* 1.3 54.9 + - + +
251E VAL* 3.5 11.9 - - - +
252E SER* 2.3 32.1 + - - +
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Residues in contact with LYS 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E PHE* 3.8 26.3 - - + -
239E PHE 4.0 25.0 + - - +
240E ALA* 5.1 2.0 - - + -
245E GLN* 2.9 21.5 - - + +
246E ILE* 2.9 7.3 + - - +
248E GLU* 1.3 77.2 - - + +
250E ILE* 1.3 61.7 + - - +
252E SER* 2.8 30.9 + - - -
253E GLY 3.2 3.3 + - - -
254E LYS 4.4 2.0 + - - +
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Residues in contact with ILE 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E PRO 3.4 25.8 - - - +
203E GLU 4.4 4.0 - - - +
205E LEU 3.5 24.7 - - - +
207E PRO* 3.8 18.4 - - + -
210E ILE* 4.0 17.3 - - + -
222E TRP* 3.7 19.8 - - + +
238E PHE* 3.8 29.5 - - + -
246E ILE* 3.1 23.9 + - + +
247E TYR* 3.6 6.3 - - + +
249E LYS* 1.3 73.7 - - - +
251E VAL* 1.3 62.6 + - - +
252E SER 3.0 1.4 + - - -
253E GLY* 3.0 15.2 + - - -
275E VAL* 4.1 8.5 - - - +
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Residues in contact with VAL 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E PRO* 4.2 19.3 - - + -
210E ILE* 4.4 13.2 - - + -
211E LEU* 4.0 40.2 - - + -
247E TYR 3.1 15.5 + - - +
248E GLU* 3.5 18.4 - - - +
250E ILE* 1.3 73.3 - - - +
252E SER* 1.3 59.7 + - - +
253E GLY* 3.2 0.6 + - - -
275E VAL* 4.7 8.3 - - - +
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Residues in contact with SER 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E GLU* 2.3 29.0 + - - +
249E LYS* 2.8 19.0 + - - -
251E VAL* 1.3 77.9 - - - +
253E GLY* 1.3 66.8 - - - +
254E LYS* 4.0 22.8 - - - +
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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