Contacts of the strand formed by residues 93 - 97 (chain F) in PDB entry 2JG8
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 93 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D TYR* 3.9 18.8 - - + -
184D VAL* 3.6 34.3 - - + -
219D ILE* 4.0 6.1 - - + -
220D PHE* 4.2 15.9 - - + -
92F SER* 1.3 76.7 + - - +
94F PHE* 1.3 69.4 + - - +
117F THR* 4.9 1.1 - - + -
118F ASN* 3.8 3.1 - - - +
119F PRO* 3.2 38.6 - - + +
120F GLN* 3.1 7.5 + - - +
122F ASP* 4.7 1.5 + - - +
211F GLY 3.3 6.1 - - - -
212F PHE* 3.7 18.4 - - + -
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Residues in contact with PHE 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D VAL* 4.0 4.1 - - - +
92F SER* 5.6 0.2 - - - -
93F VAL* 1.3 78.3 - - - +
95F THR* 1.3 67.2 + - - +
96F VAL* 4.0 7.4 - - + -
117F THR* 3.2 14.1 - - - +
118F ASN* 3.4 20.6 - - - +
122F ASP* 5.1 1.3 - - + -
123F TYR* 3.9 25.1 - + + -
130F PHE* 3.3 38.6 - + + -
140F PHE* 4.2 4.9 - + - -
209F PHE* 3.5 53.2 - + - -
210F SER* 3.3 4.1 - - - -
211F GLY* 2.9 57.8 + - - +
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Residues in contact with THR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D MET* 4.0 6.5 - - + -
184D VAL* 3.0 27.3 + - - +
94F PHE* 1.3 72.5 + - - +
96F VAL* 1.3 64.4 + - - +
116F LEU* 2.9 49.0 + - + -
117F THR* 2.8 16.1 + - - +
208F VAL* 3.3 28.7 - - + -
209F PHE 3.4 4.3 - - - -
210F SER* 2.6 20.5 + - - +
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Residues in contact with VAL 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F PHE* 4.0 14.4 - - + -
95F THR* 1.3 78.8 - - - +
97F THR* 1.3 62.3 + - - +
112F PHE* 3.4 24.9 - - + +
114F ALA 3.3 12.8 - - - +
115F VAL* 4.1 20.2 - - + +
116F LEU* 4.5 0.7 - - - +
117F THR 4.8 0.2 - - - +
118F ASN* 5.0 1.1 - - + -
123F TYR* 3.6 37.7 - - + -
208F VAL* 3.2 7.2 - - - +
209F PHE* 2.8 52.7 + - + +
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Residues in contact with THR 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C GLN* 2.6 41.8 + - - +
165D LEU* 3.8 18.0 - - - +
96F VAL* 1.3 75.6 - - - +
98F ARG* 1.3 63.3 + - - +
112F PHE* 3.6 5.8 - - - -
113F ASN 3.3 5.9 + - - -
114F ALA* 2.8 51.7 + - + +
116F LEU* 4.6 13.5 - - + -
207F SER 2.8 21.6 + - - -
208F VAL* 4.6 0.2 - - - -
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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