Contacts of the helix formed by residues 279 - 285 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ALA 5.6 2.2 - - - +
106A MET* 3.3 14.4 - - + +
271A GLY 5.8 0.2 - - - +
272A ASP 4.8 0.6 + - - +
277C PRO 3.4 0.2 - - - -
278C ARG* 1.3 106.9 - - + +
280C GLU* 1.3 77.1 + - + +
281C TRP 3.2 0.2 - - - -
282C GLY* 3.0 17.2 + - - -
283C CYS* 4.6 7.4 - - - +
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Residues in contact with GLU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 3.6 7.9 - - - +
253C VAL* 3.6 12.0 - - + +
254C LYS* 3.7 45.3 - - + +
277C PRO* 3.2 20.3 + - + +
278C ARG 3.4 0.2 - - - -
279C VAL* 1.3 88.7 + - + +
281C TRP* 1.3 57.0 + - - +
282C GLY 3.1 6.7 + - - -
288C LYS* 2.9 32.7 + - - +
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Residues in contact with TRP 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A MET* 6.3 0.9 - - + -
249A LEU* 5.7 2.2 - - + -
264A ASN* 4.4 11.9 - - + -
274A LEU* 4.0 31.9 - - + -
290A ILE* 3.9 30.1 - - + -
291A LYS 4.1 18.6 - - - -
292A GLY* 4.4 4.3 - - - -
253C VAL* 3.8 13.0 - - + +
276C ILE* 3.5 25.1 - - + -
277C PRO 3.1 19.4 + - - +
278C ARG* 3.1 4.0 + - - +
280C GLU* 1.3 75.9 - - - +
282C GLY* 1.3 57.4 - - - +
283C CYS 3.1 0.9 - - - -
284C GLY* 2.8 49.7 + - - -
285C MET 3.3 7.1 + - - -
286C ALA* 3.5 11.4 + - + -
288C LYS* 2.9 45.3 + - + +
290C ILE* 4.0 11.1 - - + +
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Residues in contact with GLY 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 3.6 22.2 - - - -
107A LEU* 3.9 9.3 - - - +
279C VAL 3.0 13.8 + - - -
280C GLU 3.1 3.2 + - - -
281C TRP* 1.3 77.7 - - - +
283C CYS* 1.3 71.8 + - - +
285C MET* 2.9 25.5 + - - +
286C ALA* 3.8 6.7 - - - -
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Residues in contact with CYS 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA 4.4 8.1 - - - -
49A ILE* 4.8 8.1 - - - -
107A LEU* 5.6 2.0 - - - -
266A ASN 3.4 4.2 - - - +
267A TYR* 3.7 23.8 - - + -
268A HIS* 3.2 42.5 + - - +
274A LEU* 5.7 0.9 - - - -
278C ARG* 2.9 54.7 + - - +
279C VAL* 4.0 7.6 + - - -
281C TRP* 4.7 1.1 - - - -
282C GLY* 1.3 78.1 - - - +
284C GLY* 1.3 55.9 + - - +
285C MET* 4.3 1.9 - - + +
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Residues in contact with GLY 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ASN* 3.0 21.5 + - - -
268A HIS* 4.6 1.3 - - - -
292A GLY* 3.0 23.0 - - - -
293A GLY 3.4 1.2 + - - -
281C TRP* 2.8 40.1 + - - -
283C CYS* 1.3 77.2 - - - +
285C MET* 1.3 61.2 + - - +
286C ALA 3.7 0.9 - - - -
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Residues in contact with MET 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A HIS* 3.1 15.8 - - - -
107A LEU* 3.8 26.7 - - + -
110A TRP* 4.5 11.0 - - + -
265A ILE 4.6 9.4 - - - +
266A ASN 4.4 8.5 - - - +
267A TYR* 3.7 44.2 - - + -
292A GLY 3.5 2.0 - - - -
293A GLY 4.1 4.0 - - - +
294A LEU* 2.9 47.9 + - + +
282C GLY 2.9 16.2 + - - +
283C CYS* 4.3 0.9 - - + +
284C GLY* 1.3 84.1 - - - +
286C ALA* 1.3 57.8 + - - +
287C HIS 3.2 7.0 + - - -
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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