Contacts of the strand formed by residues 138 - 143 (chain C) in PDB entry 2F8X
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 ASP 138 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LYS* 3.3 20.1 + - - -
131C MET 3.6 2.9 - - - +
132C PHE* 4.0 3.0 - - - +
133C TYR* 4.9 4.3 - - - -
136C SER 3.5 4.1 + - - +
137C ASP* 1.3 74.7 - - - +
139C ILE* 1.3 79.6 + - - +
140C GLY* 3.4 5.9 + - - -
328C GLU* 5.7 1.0 - - - +
333C VAL* 5.3 2.4 - - - +
334C LEU 5.5 4.3 - - - +
335C ALA 4.3 13.1 - - - +
336C PRO* 4.0 27.4 - - + +
337C VAL* 5.2 0.7 + - - +
49M LEU* 6.1 1.0 - - + +
52M GLU* 4.0 9.0 - - - +
53M ARG* 5.1 7.3 + - + +
56M THR* 2.9 28.0 + - + +
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Residues in contact with ILE 139 (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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66C TRP* 3.7 18.4 - - + -
85C PRO* 4.6 2.5 - - + -
131C MET* 2.7 30.6 + - + +
132C PHE* 3.9 12.7 - - - +
133C TYR* 3.4 54.7 - - + +
138C ASP* 1.3 79.5 + - - +
140C GLY* 1.3 57.5 + - - +
142C PHE* 3.7 26.7 - - + -
326C PHE* 4.4 11.0 - - + -
336C PRO* 4.1 0.9 - - - -
337C VAL* 2.8 38.5 + - - +
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Residues in contact with GLY 140 (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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130C LYS* 3.9 3.3 + - - -
131C MET* 3.0 27.1 + - - +
138C ASP* 3.4 4.2 + - - -
139C ILE* 1.3 85.4 - - - +
141C VAL* 1.3 68.0 + - - +
142C PHE* 3.8 6.7 - - - -
336C PRO* 3.8 10.8 - - - -
338C THR* 3.6 15.0 - - - -
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Residues in contact with VAL 141 (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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128C SER* 3.6 23.6 - - - +
129C VAL 3.6 13.0 - - - +
130C LYS* 4.2 22.9 - - + +
140C GLY* 1.3 77.4 - - - +
142C PHE* 1.3 63.0 + - - +
143C LEU* 4.1 11.8 + - + +
336C PRO* 6.2 0.7 - - + -
338C THR* 2.9 34.8 + - + +
339C PRO* 5.6 0.2 - - - +
52M GLU* 4.2 20.2 - - + +
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Residues in contact with PHE 142 (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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34C VAL* 3.3 44.0 - - + -
36C ILE* 3.9 6.3 - - + +
128C SER* 4.0 0.2 - - - -
129C VAL* 2.8 41.9 + - + +
131C MET* 4.4 7.4 - - - -
139C ILE* 3.7 25.6 - - + -
140C GLY* 3.8 11.4 - - - -
141C VAL* 1.3 75.7 - - - +
143C LEU* 1.3 63.9 + - - +
324C TYR* 3.7 40.6 - + + -
326C PHE* 3.7 22.4 - + - -
337C VAL* 4.5 2.9 - - + -
338C THR* 3.8 15.3 - - - -
340C VAL* 4.0 12.8 - - + -
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Residues in contact with LEU 143 (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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36C ILE* 4.1 4.7 - - - -
126C MET* 4.4 25.7 - - + +
127C LEU 3.1 13.7 - - - +
128C SER* 4.7 8.5 - - - +
141C VAL* 4.3 10.3 - - + +
142C PHE* 1.3 81.3 - - - +
144C SER* 1.3 70.6 + - - +
322C ALA* 3.4 6.4 - - - +
324C TYR* 2.3 44.3 + - + +
363C ASN* 5.9 4.3 - - - +
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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