Contacts of the strand formed by residues 225 - 230 (chain C) in PDB entry 4FJV
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 TYR 225 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C THR* 3.0 26.7 + - - +
51C CYS* 3.5 19.4 - - - +
52C PHE* 3.9 26.9 - + + -
55C ALA* 4.3 2.1 - - + +
175C CYS* 3.6 18.8 - - - -
180C ILE* 3.3 21.0 - - + +
193C VAL* 4.0 17.9 - - + -
218C LEU* 4.0 29.2 - - + -
219C LEU 3.4 3.4 - - - -
220C TYR* 3.5 37.7 - + + -
224C HIS* 1.3 80.4 + - - +
226C ASN* 1.3 62.6 + - - +
73D LEU* 2.7 33.4 + - - +
75D GLY* 3.9 6.3 - - - -
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Residues in contact with ASN 226 (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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18C ILE* 5.9 0.4 - - - +
42C ILE* 4.0 19.8 - - + +
43C ARG 3.3 8.5 - - - +
44C LYS* 3.3 27.4 - - - +
45C THR* 3.0 25.1 + - - +
218C LEU* 3.2 10.0 - - - +
219C LEU* 2.8 39.2 + - + +
221C LYS* 5.9 5.1 - - - +
224C HIS* 3.0 27.2 + - - -
225C TYR* 1.3 71.9 - - - +
227C ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 227 (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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9C ILE* 4.4 5.8 - - + -
42C ILE* 3.2 9.4 - - - +
43C ARG* 2.9 47.6 + - + +
45C THR* 4.2 11.4 - - + -
55C ALA* 3.8 39.3 - - + +
58C TYR* 3.9 23.1 - - + -
59C SER* 3.7 22.2 - - - +
217C TYR 3.8 5.6 - - - +
218C LEU* 4.0 5.2 - - + -
226C ASN* 1.3 74.6 - - - +
228C LEU* 1.3 68.7 + - - +
229C TYR* 3.8 22.6 - - + +
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Residues in contact with LEU 228 (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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15C ILE* 3.8 28.9 - - + -
35C LEU* 4.8 4.9 - - + -
39C PHE* 3.8 28.7 - - + -
41C ALA 3.6 4.7 - - - +
42C ILE* 4.6 5.4 - - + -
59C SER* 5.3 0.7 + - - -
194C GLU* 3.8 22.0 - - + -
217C TYR* 2.9 30.7 + - + +
218C LEU* 3.7 26.9 - - - +
219C LEU* 3.7 27.8 - - + +
227C ILE* 1.3 79.5 - - - +
229C TYR* 1.3 66.9 + - - +
230C ALA 4.2 0.2 - - - -
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Residues in contact with TYR 229 (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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12C LYS* 3.7 41.7 - - + +
39C PHE* 3.3 6.0 - - - -
40C THR* 2.9 32.1 + - - +
41C ALA* 3.0 30.8 + - + +
42C ILE 4.1 0.4 - - - -
43C ARG* 2.8 38.3 + - + -
58C TYR* 4.0 1.9 - - - -
59C SER* 5.9 0.9 - - - -
62C GLU* 2.6 33.1 + - - -
217C TYR* 5.5 0.2 - - - -
227C ILE* 3.8 25.6 - - + +
228C LEU* 1.3 77.3 - - - +
230C ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 230 (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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38C ARG 3.5 10.1 - - - +
39C PHE* 3.5 11.2 - - + -
40C THR* 4.3 4.0 + - - -
217C TYR* 3.9 33.0 - - + +
228C LEU 4.2 0.6 + - - -
229C TYR* 1.3 76.1 - - - +
231C ALA* 1.3 71.3 + - - +
232C ASP* 4.5 2.8 - - - +
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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