Contacts of the helix formed by residues 279 - 285 (chain B) 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 VAL 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277B PRO 3.6 0.2 - - - -
278B ARG* 1.3 100.7 - - + +
280B GLU* 1.3 72.0 + - + +
282B GLY* 2.9 18.2 + - - -
283B CYS* 4.2 9.6 - - - -
106D MET* 3.3 16.6 - - + +
272D ASP 4.9 0.2 + - - -
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B VAL* 3.6 11.1 - - + +
254B LYS* 3.6 50.9 + - + +
277B PRO* 3.5 16.4 + - + +
278B ARG 3.3 0.6 - - - -
279B VAL* 1.3 89.8 + - + +
281B TRP* 1.3 56.3 + - - +
282B GLY 3.1 3.3 + - - -
288B LYS* 2.8 33.3 + - - +
106D MET* 3.7 7.6 - - - +
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Residues in contact with TRP 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B VAL* 3.9 15.7 - - + -
276B ILE* 3.5 30.7 - - + -
277B PRO 3.1 19.0 + - - +
278B ARG* 3.7 3.6 - - - +
279B VAL 3.1 0.4 - - - -
280B GLU* 1.3 78.4 - - - +
282B GLY* 1.3 56.6 + - - +
283B CYS 3.0 1.6 - - - -
284B GLY* 2.8 52.1 + - - -
285B MET 3.4 6.6 + - - -
286B ALA* 3.7 10.3 + - + +
288B LYS* 2.8 46.6 + - + +
289B THR* 5.9 0.4 - - - -
290B ILE* 4.2 17.5 - - + +
241D MET* 6.4 0.4 - - + -
249D LEU* 5.8 4.5 - - + -
264D ASN* 4.6 19.5 - - + -
274D LEU* 4.2 25.8 - - + -
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Residues in contact with GLY 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B VAL 2.9 13.6 + - - -
280B GLU 3.1 4.2 + - - -
281B TRP* 1.3 76.5 - - - +
283B CYS* 1.3 69.3 + - - +
284B GLY 2.9 1.7 + - - -
285B MET* 3.0 23.4 + - - +
286B ALA* 3.9 6.7 - - - -
106D MET* 3.6 22.6 - - - -
107D LEU* 4.0 10.7 - - - +
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Residues in contact with CYS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ARG* 2.8 56.0 + - - -
279B VAL* 4.2 12.8 - - - -
281B TRP* 4.7 1.3 - - - -
282B GLY* 1.3 78.0 - - - +
284B GLY* 1.3 55.9 + - - +
285B MET* 4.5 1.7 - - + +
48D ALA 5.2 2.7 - - - -
107D LEU* 5.9 0.9 - - + -
266D ASN 3.5 4.2 - - - +
267D TYR* 3.3 28.8 - - + -
268D HIS* 3.0 43.9 + - - +
274D LEU* 5.7 0.4 - - - -
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Residues in contact with GLY 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B TRP* 2.8 37.7 + - - -
283B CYS* 1.3 76.4 - - - +
285B MET* 1.3 62.3 + - - +
286B ALA 3.8 1.6 - - - -
287B HIS 5.5 0.4 + - - -
264D ASN* 3.1 36.8 + - - +
268D HIS* 4.3 1.1 - - - -
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Residues in contact with MET 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLY 3.0 16.2 + - - +
283B CYS 4.5 1.3 - - - +
284B GLY* 1.3 84.2 - - - +
286B ALA* 1.3 57.5 + - - +
287B HIS* 3.3 13.4 + - - -
102D HIS* 3.0 20.6 + - - -
107D LEU* 3.4 26.4 - - + +
110D TRP* 5.1 8.1 - - + -
265D ILE* 4.8 13.2 - - - +
266D ASN 4.5 5.6 - - - +
267D TYR* 3.8 48.7 - - + -
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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