Contacts of the strand formed by residues 228 - 233 (chain C) in PDB entry 5FFO
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 PHE 228 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C SER* 3.5 27.8 - - - -
81C ARG* 3.6 39.5 - - + -
82C VAL 3.4 14.4 - - - +
83C LEU* 3.6 18.6 - - + -
106C PHE* 4.8 1.6 - - - -
126C LEU* 3.7 5.8 - - - +
127C ARG* 3.1 45.4 + - + +
166C TRP* 3.6 34.1 - + - -
225C ASN 5.1 2.5 - - - -
226C ARG 4.3 6.3 - - - -
227C PRO* 1.3 74.6 - - + +
229C LEU* 1.3 57.9 + - - +
230C LEU* 3.7 32.3 + - + -
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Residues in contact with LEU 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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81C ARG* 3.6 1.7 - - - -
82C VAL* 3.0 35.7 + - + +
106C PHE* 4.4 13.6 - - + -
111C LEU* 4.4 20.4 - - + -
124C ALA 4.5 2.5 - - - -
125C GLU 3.8 4.7 - - - +
126C LEU* 3.7 39.0 - - + +
171C VAL* 4.0 12.8 - - + -
175C VAL* 3.9 23.1 - - + -
178C TRP* 6.1 1.8 - - + -
188C PHE* 5.2 10.1 - - + -
228C PHE* 1.3 73.2 - - - +
230C LEU* 1.3 63.5 + - - +
231C LEU* 3.5 23.9 + - + +
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Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 5.3 4.9 - - + +
54C SER* 4.4 8.7 - - - +
55C THR* 4.7 9.9 - - - +
79C VAL* 3.6 27.6 - - + -
80C THR 4.0 0.9 - - - +
81C ARG* 4.2 10.5 - - + -
123C ARG 4.1 0.5 - - - +
124C ALA* 3.5 3.6 - - - -
125C GLU* 3.1 42.1 + - + +
127C ARG* 3.6 38.1 - - + +
228C PHE* 3.7 27.8 + - + -
229C LEU* 1.3 71.3 - - - +
231C LEU* 1.3 60.6 + - - +
232C MET* 3.7 24.4 - - + +
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Residues in contact with LEU 231 (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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78C GLU 4.6 0.4 - - - -
79C VAL* 3.2 10.0 - - - +
80C THR* 2.8 49.5 + - - +
81C ARG 5.5 0.2 - - - -
82C VAL* 4.4 8.5 - - + -
111C LEU* 4.3 22.0 - - + +
114C ALA* 4.5 9.9 - - + -
115C VAL* 4.3 20.0 - - + -
121C LEU* 4.5 9.4 - - + -
123C ARG 3.8 1.8 - - - -
124C ALA* 3.7 25.6 - - + -
175C VAL* 4.2 9.6 - - + -
179C LEU* 6.5 0.2 - - + -
229C LEU* 3.7 30.7 - - + +
230C LEU* 1.3 72.3 - - - +
232C MET* 1.3 63.4 + - - +
233C ALA 4.1 0.7 - - - +
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Residues in contact with MET 232 (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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55C THR* 4.6 12.6 - - + -
77C LYS* 4.3 11.4 - - + -
78C GLU 3.8 4.9 - - - -
79C VAL* 3.6 23.1 - - + +
121C LEU* 4.7 1.5 - - - +
122C SER* 2.2 35.0 + - - +
123C ARG* 2.8 49.3 + - + +
125C GLU* 3.3 24.9 - - + +
127C ARG* 4.7 2.2 - - - +
230C LEU* 3.7 20.6 - - + +
231C LEU* 1.3 80.7 - - - +
233C ALA* 1.3 56.0 + - - +
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Residues in contact with ALA 233 (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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77C LYS* 3.3 4.4 - - - -
78C GLU* 2.6 46.4 + - - +
114C ALA 5.5 1.1 - - - +
115C VAL* 3.7 33.2 - - + -
120C LEU* 3.3 20.6 - - + +
121C LEU* 4.0 3.6 - - + -
122C SER* 3.9 0.9 - - - -
231C LEU* 4.1 0.6 - - + -
232C MET* 1.3 75.4 - - - +
234C THR* 1.3 62.7 + - - +
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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