Contacts of the strand formed by residues 110 - 115 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106E TYR* 5.2 0.2 - - - -
109E LYS* 1.3 79.3 - - - +
111E LEU* 1.3 58.1 + - - +
142E ASN* 3.2 8.4 + - - +
143E THR* 3.3 26.4 - - + +
144E GLU* 3.0 23.7 + - - +
204E ILE* 4.0 21.3 - - + -
205E ILE 3.3 12.8 - - - -
206E ASP* 3.3 15.5 - - + -
207E ASP* 3.5 23.3 - - + +
212E ARG* 3.3 12.7 + - + -
232E VAL* 4.2 11.4 - - + -
235E PHE* 3.3 31.1 + - + +
236E GLN* 3.6 30.7 - - + +
239E ASP* 2.6 29.5 + - - -
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Residues in contact with LEU 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E TRP* 4.0 12.6 - - + -
103E LEU* 3.6 29.8 - - + -
106E TYR* 3.9 34.5 - - + -
109E LYS 4.9 0.9 - - - +
110E TYR* 1.3 75.6 - - - +
112E VAL* 1.3 82.1 + - - +
113E PHE* 4.1 11.7 - - + -
144E GLU 3.5 14.4 - - - +
146E VAL* 3.8 24.0 - - + +
203E PHE 3.4 3.6 - - - +
204E ILE* 3.5 2.3 - - - +
205E ILE* 2.7 50.4 + - + +
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Residues in contact with VAL 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E LEU* 1.3 77.0 - - - +
113E PHE* 1.3 58.0 + - - +
114E PHE* 4.0 3.8 + - + -
131E PHE* 4.2 10.5 - - + -
138E PHE* 4.2 6.1 - - + -
143E THR* 3.8 20.9 - - + -
144E GLU 2.8 12.9 + - - +
145E VAL* 3.3 13.4 - - + +
146E VAL 2.9 26.3 + - - +
202E LEU* 3.9 22.7 - - + -
203E PHE 3.6 3.1 - - - -
204E ILE* 4.5 4.0 - - + -
228E THR* 3.7 33.9 - - + -
232E VAL* 3.9 12.8 - - + -
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Residues in contact with PHE 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E TRP* 3.4 49.4 - + - -
111E LEU* 3.8 7.4 + - + -
112E VAL* 1.3 71.2 - - - +
114E PHE* 1.3 63.4 + - - +
115E PHE* 3.5 35.2 - + - -
146E VAL* 3.5 22.9 - - + -
148E CYS* 4.1 9.9 - - + -
177E LEU* 3.8 17.3 - - + -
184E ILE* 4.0 9.4 - - + -
188E TYR* 3.8 25.6 - + - -
203E PHE* 2.9 39.4 + + + +
205E ILE* 4.1 14.4 - - + -
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Residues in contact with PHE 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E VAL* 4.5 7.9 - - + -
113E PHE* 1.3 76.7 - - - +
115E PHE* 1.3 63.7 + - - +
116E TYR* 4.5 5.4 - + + -
127E GLU* 4.6 9.2 - - + -
128E ILE* 4.2 25.1 - - + -
131E PHE* 4.0 25.8 - + + -
145E VAL* 3.6 28.7 - - + -
146E VAL 2.9 16.1 + - - +
147E ALA* 3.2 32.9 - - + -
148E CYS* 2.9 25.6 + - - +
174E ILE* 5.1 2.2 - - + -
201E GLY 3.3 11.0 - - - +
202E LEU* 3.8 15.7 - - + -
223E ARG* 3.7 30.7 - - - +
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Residues in contact with PHE 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E PHE* 3.5 30.1 - + - -
114E PHE* 1.3 78.0 - - - +
116E TYR* 1.3 61.5 + - - +
148E CYS* 3.1 35.9 - - + +
149E SER* 5.4 0.2 - - - -
184E ILE* 3.9 8.7 - - + -
185E SER* 3.9 17.3 - - - -
188E TYR* 3.6 22.9 - + + -
190E VAL* 3.7 17.3 - - + -
198E THR* 3.6 25.4 - - + +
199E LEU 4.2 4.0 - - - +
200E ARG* 3.8 0.7 - - - -
201E GLY 2.8 22.1 + - - +
203E PHE* 3.6 24.2 - + - -
223E 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