Contacts of the strand formed by residues 296 - 301 (chain C) in PDB entry 1FBA
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 ALA 296 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C VAL* 3.8 42.2 - - + +
265C THR 3.9 6.7 + - - +
267C VAL* 3.0 30.0 + - - +
295C TRP* 1.3 75.4 - - - +
297C LEU* 1.3 60.8 + - - +
298C THR* 3.9 4.7 - - + +
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Residues in contact with LEU 297 (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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253C VAL* 4.7 2.7 - - + -
256C LEU* 3.8 22.4 - - + -
267C VAL* 3.6 14.8 - - + -
269C PHE* 3.8 25.4 - - + -
283C LEU* 3.5 4.7 - - - +
286C ILE* 3.9 16.4 - - + +
287C ASN* 2.8 47.6 + - - +
293C ARG* 3.7 41.5 - - + +
295C TRP* 3.4 21.1 + - + +
296C ALA* 1.3 70.8 - - - +
298C THR* 1.3 61.8 + - - +
338C ALA* 3.8 7.2 + - - +
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Residues in contact with THR 298 (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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22C ILE 5.2 0.4 - - - +
23C VAL* 4.0 19.3 - - + -
27C LYS 2.6 28.5 + - - +
28C GLY* 3.5 2.2 - - - -
267C VAL 2.9 11.2 + - - +
268C THR* 3.8 25.1 - - + -
269C PHE* 3.0 32.1 + - - +
283C LEU* 3.9 8.7 - - - +
296C ALA* 5.2 2.5 - - + -
297C LEU* 1.3 75.2 - - - +
299C PHE* 1.3 80.5 + - - +
338C ALA* 3.5 12.9 - - - +
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Residues in contact with PHE 299 (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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27C LYS 4.1 0.4 - - - -
28C GLY* 3.4 36.9 - - - -
29C ILE* 2.8 41.2 + - - +
72C ASN 3.5 10.5 - - - -
73C ILE* 3.9 14.8 - - + -
268C THR* 3.9 8.2 - - - -
269C PHE 3.8 4.5 - - - -
283C LEU* 3.9 7.0 - - + -
298C THR* 1.3 92.1 + - - +
300C SER* 1.3 59.0 + - - +
301C TYR* 3.6 32.5 - + + -
305C LEU* 3.9 13.2 - - + -
331C ALA 4.4 3.4 - - - -
334C ASN* 3.4 49.4 - - + -
335C GLY* 3.8 6.7 - - - -
338C ALA* 4.5 0.2 - - + -
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Residues in contact with SER 300 (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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29C ILE* 3.4 30.3 - - - +
31C ALA* 4.4 1.6 - - - +
77C ILE* 3.8 5.2 - - - +
185C ILE* 5.2 0.3 - - - +
229C LYS* 3.0 44.9 + - - +
268C THR* 3.7 23.8 - - - -
269C PHE 2.9 14.0 + - - +
270C LEU* 4.0 3.5 - - - -
271C SER 4.9 0.2 + - - -
299C PHE* 1.3 74.4 - - - +
301C TYR* 1.3 62.6 + - - +
302C GLY 4.1 0.9 + - - -
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Residues in contact with TYR 301 (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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29C ILE 3.2 8.5 + - - +
30C LEU* 3.8 4.0 - - - +
31C ALA* 2.9 23.9 + - - +
232C MET* 3.3 17.3 - - - +
269C PHE* 3.0 30.3 - - - +
270C LEU 4.0 1.3 - - - -
271C SER* 3.9 21.1 - - - +
279C ALA* 2.9 37.0 + - + +
283C LEU* 3.9 7.7 - - + +
299C PHE* 3.6 20.3 - + + +
300C SER* 1.3 76.7 - - - +
302C GLY* 1.3 62.1 + - - +
304C ALA* 3.8 22.7 - - + -
305C LEU* 3.9 21.4 - - + +
334C ASN* 3.5 36.3 - - - -
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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