Contacts of the strand formed by residues 110 - 115 (chain C) in PDB entry 3TJF
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 110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106C TYR* 5.4 0.2 - - - -
109C LYS* 1.3 80.5 - - - +
111C LEU* 1.3 59.2 + - - +
142C ASN* 3.2 7.1 + - - +
143C THR* 3.4 27.0 - - + +
144C GLU* 2.9 23.7 + - - +
204C ILE* 4.0 21.8 - - + -
205C ILE 3.4 12.8 - - - -
206C ASP* 3.3 20.1 - - + +
207C ASP* 3.7 17.5 - - + +
212C ARG* 3.3 18.7 + - + -
232C VAL* 4.2 10.5 - - + -
235C PHE* 3.3 23.2 - - + +
236C GLN* 3.4 32.5 - - + +
239C ASP* 2.6 29.9 + - - -
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Residues in contact with LEU 111 (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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88C TRP* 4.2 7.4 - - + -
103C LEU* 3.6 31.0 - - + -
106C TYR* 4.1 32.3 - - + -
109C LYS 4.7 1.6 - - - +
110C TYR* 1.3 76.6 - - - +
112C VAL* 1.3 79.1 + - - +
113C PHE* 3.7 14.3 + - + -
143C THR* 4.6 0.4 - - - -
144C GLU 3.4 19.1 - - - +
146C VAL* 3.8 24.2 - - + -
203C PHE 3.5 3.6 - - - +
204C ILE* 3.6 3.0 - - - +
205C ILE* 2.7 49.8 + - + +
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Residues in contact with VAL 112 (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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111C LEU* 1.3 74.1 - - - +
113C PHE* 1.3 59.6 + - - +
114C PHE* 4.5 3.6 - - + -
131C PHE* 4.1 11.0 - - + -
138C PHE* 4.1 7.0 - - + -
143C THR* 4.0 10.3 - - + -
144C GLU 2.8 13.6 + - - +
145C VAL* 3.3 13.7 - - + +
146C VAL 3.0 27.2 + - - +
202C LEU* 3.9 21.8 - - + -
203C PHE 3.6 3.1 - - - -
204C ILE* 4.5 4.9 - - + -
228C THR* 3.8 33.4 - - + -
232C VAL* 3.8 22.9 - - + -
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Residues in contact with PHE 113 (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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88C TRP* 3.4 51.4 - + - -
111C LEU* 4.2 6.7 - - + -
112C VAL* 1.3 71.8 - - - +
114C PHE* 1.3 63.1 + - - +
115C PHE* 3.6 34.3 - + - -
146C VAL* 3.5 21.1 - - + -
148C CYS* 4.1 10.1 - - + -
177C LEU* 3.9 17.0 - - + -
184C ILE* 4.1 8.7 - - + -
188C TYR* 3.7 24.2 - + - -
203C PHE* 2.9 43.5 + - + +
205C ILE* 4.0 14.8 - - + -
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Residues in contact with PHE 114 (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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112C VAL* 4.5 8.3 - - + -
113C PHE* 1.3 77.5 - - - +
115C PHE* 1.3 64.2 + - - +
116C TYR* 4.4 5.4 - + + -
127C GLU* 4.5 9.9 - - + -
128C ILE* 4.2 26.2 - - + -
131C PHE* 4.1 26.9 - + + -
145C VAL* 3.7 27.6 - - + -
146C VAL 2.9 15.3 + - - -
147C ALA* 3.2 32.5 - - + -
148C CYS* 2.8 26.7 + - - +
174C ILE* 5.1 2.5 - - + -
201C GLY 3.4 8.7 - - - +
202C LEU* 3.9 16.8 - - + -
223C ARG* 3.7 30.7 - - - +
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Residues in contact with PHE 115 (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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113C PHE* 3.6 30.7 - + - -
114C PHE* 1.3 77.4 - - - +
116C TYR* 1.3 60.2 + - - +
148C CYS* 3.1 37.0 - - + +
184C ILE* 3.9 7.6 - - + -
185C SER* 3.8 20.0 - - - -
188C TYR* 3.6 32.5 - + + -
190C VAL* 3.8 11.0 - - + -
198C THR* 3.6 32.1 - - + +
199C LEU 4.1 3.1 - - - +
200C ARG* 3.7 0.7 - - - -
201C GLY 2.7 21.7 + - - +
203C PHE* 3.8 14.1 - + - -
223C ARG* 2.8 26.6 + - - -
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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