Contacts of the helix formed by residues 278 - 285 (chain A) in PDB entry 3FPL
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 ARG 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A VAL 3.5 4.1 + - - +
277A PRO* 1.3 71.3 - - - +
279A LEU* 1.3 84.4 + - + +
281A TRP* 3.2 9.5 + - - +
283A CYS* 2.8 68.4 + - - +
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Residues in contact with LEU 279 (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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277A PRO 3.6 0.2 - - - -
278A ARG* 1.3 107.4 - - - +
280A GLU* 1.3 69.5 + - - +
282A GLY* 2.9 22.0 + - - -
283A CYS* 4.2 12.0 - - - +
357A PGE 3.7 26.7 + - - +
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Residues in contact with GLU 280 (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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224A GLU* 4.8 2.1 - - - +
253A VAL* 3.6 4.4 - - + +
254A LYS* 3.6 36.3 + - + +
277A PRO* 3.5 21.9 + - + +
278A ARG 3.4 0.4 - - - -
279A LEU* 1.3 83.6 + - - +
281A TRP* 1.3 56.0 + - - +
282A GLY 3.2 2.4 + - - -
286A ALA* 4.5 0.2 - - - +
288A LYS* 2.8 32.9 + - - +
357A PGE 3.3 57.1 - - - +
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Residues in contact with TRP 281 (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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253A VAL* 3.9 13.9 - - + -
276A VAL* 3.6 21.1 - - + -
277A PRO 3.0 19.8 + - - +
278A ARG* 3.9 4.0 - - - +
279A LEU 3.2 0.8 - - - -
280A GLU* 1.3 75.1 - - - +
282A GLY* 1.3 56.8 + - - +
283A CYS 3.2 1.6 - - - -
284A GLY* 3.0 49.9 + - - -
285A MET 3.2 8.3 + - - -
286A ALA* 3.3 13.0 + - - -
287A HIS 6.2 0.2 - - - -
288A LYS* 2.8 46.6 + - + +
289A THR* 5.8 0.7 - - - -
290A ILE* 3.8 21.8 - - + +
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Residues in contact with GLY 282 (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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279A LEU 2.9 12.5 + - - -
280A GLU 3.2 2.8 - - - -
281A TRP* 1.3 72.8 - - - +
283A CYS* 1.3 72.8 + - - +
284A GLY 3.0 2.0 - - - -
285A MET* 3.0 25.2 + - - +
286A ALA* 3.6 15.7 - - - +
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Residues in contact with CYS 283 (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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278A ARG* 2.8 58.0 + - + +
279A LEU* 3.9 18.1 + - - -
282A GLY* 1.3 79.2 - - - +
284A GLY* 1.3 55.0 + - - +
285A MET* 4.1 17.1 - - + +
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Residues in contact with GLY 284 (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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278A ARG* 4.4 0.6 + - - +
281A TRP* 3.0 46.2 + - - -
283A CYS* 1.3 74.7 - - - +
285A MET* 1.3 65.0 + - - +
286A ALA 3.8 0.7 - - - -
287A HIS 5.6 0.2 + - - -
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Residues in contact with MET 285 (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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282A GLY* 3.0 23.4 + - - +
283A CYS* 4.1 15.7 - - + +
284A GLY* 1.3 84.7 - - - +
286A ALA* 1.3 61.9 + - - +
287A HIS* 3.3 19.5 + - - -
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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