Contacts of the helix formed by residues 263 - 272 (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 SER 263 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261E PHE 3.8 1.2 + - - -
262E SER* 1.3 73.1 - - - +
264E ASP* 1.3 57.2 + - - +
266E LYS* 3.5 14.7 - - - +
267E ASP* 3.1 26.2 + - - +
270E ARG* 4.1 8.0 + - - +
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Residues in contact with ASP 264 (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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144E ARG* 5.5 0.9 + - - -
262E SER* 3.8 8.3 - - - +
263E SER* 1.3 78.2 + - - +
265E LEU* 1.4 65.6 + - - +
267E ASP* 3.0 16.8 + - - +
268E LEU* 3.0 11.6 + - - +
294E HIS* 3.4 7.9 - - - -
295E LYS* 3.5 56.7 + - - +
296E TRP* 3.6 22.5 + - + +
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Residues in contact with LEU 265 (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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140E GLU* 3.9 20.0 - - + +
228E ILE* 3.9 15.5 - - + -
232E ALA* 4.2 14.1 - - + -
261E PHE* 4.3 9.4 - - + -
262E SER* 3.0 19.3 + - - +
264E ASP* 1.4 75.1 - - - +
266E LYS* 1.3 67.3 + - - +
268E LEU* 3.1 10.2 + - + -
269E LEU* 2.9 49.7 + - + +
296E TRP* 3.3 40.4 - - + +
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Residues in contact with LYS 266 (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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257E PHE* 3.6 46.4 - - + -
258E PRO 3.9 12.1 + - - -
259E SER* 4.9 4.3 + - - +
261E PHE* 3.0 30.3 + - + -
262E SER 3.0 13.7 + - - +
263E SER* 3.5 9.8 - - - +
265E LEU* 1.3 77.3 - - - +
267E ASP* 1.3 64.9 + - - +
269E LEU* 3.3 3.7 + - - +
270E ARG* 2.8 57.2 + - - +
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Residues in contact with ASP 267 (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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263E SER 3.1 11.2 + - - +
264E ASP* 3.0 13.5 + - - +
266E LYS* 1.3 81.5 - - - +
268E LEU* 1.3 58.7 + - - +
270E ARG* 3.2 21.7 + - - +
271E ASN* 2.3 38.1 + - - +
281E PHE* 5.5 1.0 - - - -
294E HIS* 3.1 23.0 + - + +
295E LYS* 6.4 0.4 - - - -
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Residues in contact with LEU 268 (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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228E ILE* 4.5 14.1 - - + -
264E ASP 3.0 8.8 + - - +
265E LEU* 3.1 12.5 + - + +
267E ASP* 1.3 72.4 - - - +
269E LEU* 1.3 66.7 + - + +
271E ASN* 2.8 18.9 + - - +
272E LEU* 3.0 36.8 + - + +
281E PHE* 4.4 8.1 - - + -
291E ILE* 4.8 7.0 - - + -
294E HIS* 3.5 39.5 - - + +
296E TRP* 3.6 22.7 - - + -
297E PHE* 3.5 32.3 - - + -
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Residues in contact with LEU 269 (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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225E GLY* 3.6 28.5 - - - +
228E ILE* 3.8 18.2 - - + -
229E TYR* 4.2 9.6 - - + +
257E PHE* 3.6 31.9 - - + -
261E PHE* 3.8 16.8 - - + -
265E LEU* 2.9 43.6 + - + +
266E LYS 3.9 0.2 - - - +
268E LEU* 1.3 75.6 - - + +
270E ARG* 1.3 54.2 + - - +
272E LEU* 4.3 7.9 - - + +
273E LEU* 2.6 46.7 + - + +
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Residues in contact with ARG 270 (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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255E VAL* 6.1 1.8 - - + -
257E PHE* 4.0 26.4 - - + -
263E SER* 4.1 11.3 + - - +
266E LYS* 2.8 60.8 + - - +
267E ASP* 3.4 19.8 + - - +
269E LEU* 1.3 75.1 - - - +
271E ASN* 1.3 61.4 + - - +
273E LEU* 3.7 4.4 - - - +
274E GLN* 3.5 21.7 + - - +
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Residues in contact with ASN 271 (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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267E ASP* 2.3 42.6 + - - +
268E LEU* 2.8 7.7 + - - +
270E ARG* 1.3 79.5 - - - +
272E LEU* 1.3 62.4 + - - +
274E GLN* 3.4 11.7 - - - +
279E LYS 5.1 3.8 + - - -
280E ARG* 3.4 6.9 - - - +
281E PHE* 3.1 68.9 + - + -
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Residues in contact with LEU 272 (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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221E TRP* 4.0 14.8 - - + +
222E TRP* 3.6 14.2 - - - -
224E LEU* 4.4 9.0 - - + -
225E GLY* 3.7 32.5 - - - +
228E ILE* 4.2 16.2 - - + -
268E LEU* 3.0 43.6 + - + +
269E LEU* 3.9 5.4 - - + +
271E ASN* 1.3 75.0 - - - +
273E LEU* 1.3 61.4 + - - +
274E GLN 3.0 8.4 + - - -
280E ARG* 3.5 21.6 - - - +
281E PHE* 3.5 26.2 - - + +
291E ILE* 4.0 14.8 - - + -
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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