Contacts of the helix formed by residues 281 - 285 (chain A) in PDB entry 3FTN
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 TRP 281 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A VAL* 3.8 15.7 - - + +
276A ILE* 3.5 25.4 - - + -
277A PRO 3.0 19.2 + - - +
278A ARG 3.9 2.9 - - - +
279A VAL 3.1 0.2 - - - -
280A GLU* 1.3 74.8 - - - +
282A GLY* 1.3 57.2 + - - +
283A CYS 3.1 1.3 - - - -
284A GLY* 2.8 49.2 + - - -
285A MET 3.3 6.9 + - - -
286A ALA* 3.5 10.4 + - + -
288A LYS* 2.7 48.8 + - + +
290A ILE* 4.0 12.4 - - + +
241C MET* 6.3 0.2 - - + -
249C LEU* 5.6 1.8 - - + -
264C ASN* 4.5 9.6 - - + -
274C LEU* 3.8 28.3 - - + -
290C ILE* 3.7 32.3 - - + -
291C LYS 4.2 9.2 - - - -
292C GLY* 4.3 15.5 - - - -
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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
----------------------------------------------------------
279A VAL 3.0 13.0 + - - -
280A GLU 3.1 4.8 + - - -
281A TRP* 1.3 77.4 - - - +
283A CYS* 1.3 69.5 + - - +
284A GLY 2.8 1.7 + - - -
285A MET* 2.9 23.9 + - - +
286A ALA* 3.9 6.5 - - - -
106C MET* 3.6 19.4 - - - -
107C LEU* 4.2 13.0 - - - +
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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
----------------------------------------------------------
278A ARG* 2.7 58.3 + - - -
279A VAL* 4.0 8.0 + - - -
281A TRP* 4.9 0.7 - - - -
282A GLY* 1.3 72.7 - - - +
284A GLY* 1.3 56.3 + - - +
285A MET* 4.4 1.5 - - + +
48C ALA 3.9 13.5 - - - -
49C ILE* 4.5 7.0 - - - -
107C LEU* 5.7 2.0 - - - -
266C ASN 3.3 5.0 - - - +
267C TYR* 3.8 21.6 - - + -
268C HIS* 3.0 45.1 + - - +
274C LEU* 5.8 0.4 - - - -
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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
----------------------------------------------------------
281A TRP* 2.8 34.3 + - - -
283A CYS* 1.3 78.2 - - - +
285A MET* 1.3 58.0 + - - +
286A ALA 3.7 0.7 - - - -
264C ASN* 2.8 30.7 + - - +
268C HIS* 4.4 2.5 - - - -
292C GLY* 2.9 21.9 - - - -
293C GLY 3.3 0.5 + - - -
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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 2.9 14.4 + - - +
283A CYS* 4.4 3.4 - - + +
284A GLY* 1.3 84.5 - - - +
286A ALA* 1.3 58.1 + - - +
287A HIS 3.2 5.6 + - - -
102C HIS* 3.2 15.6 - - - -
107C LEU* 3.9 22.0 - - + -
110C TRP* 4.6 10.3 - - + -
264C ASN* 5.0 0.4 - - - +
265C ILE 4.7 9.2 - - - +
266C ASN 4.5 6.7 - - - +
267C TYR* 3.4 50.5 - - + -
292C GLY 3.6 2.2 - - - -
293C GLY* 3.8 3.8 - - - +
294C LEU* 3.0 51.4 + - + +
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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