Contacts of the strand formed by residues 110 - 115 (chain D) in PDB entry 3TJK
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D LYS* 1.3 79.7 - - - +
111D LEU* 1.3 59.5 + - - +
142D ASN* 3.0 10.2 + - - +
143D THR* 3.3 25.9 - - + +
144D GLU* 2.9 22.3 + - - +
204D ILE* 3.9 22.0 - - + -
205D ILE 3.3 13.5 - - - -
206D ASP* 3.3 19.7 - - + -
207D ASP* 3.7 17.3 - - + -
212D ARG* 3.3 18.5 + - + -
232D VAL* 4.4 9.4 - - + -
235D PHE* 3.3 26.2 - - + +
236D GLN* 3.6 28.0 - - + -
239D ASP* 2.6 29.5 + - - -
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D TRP* 4.1 11.0 - - + -
103D LEU* 3.7 29.6 - - + -
106D TYR* 3.9 37.5 - - + -
109D LYS 3.7 0.9 + - - +
110D TYR* 1.3 76.0 - - - +
112D VAL* 1.3 75.1 + - - +
113D PHE* 3.8 10.9 + - + -
143D THR* 4.5 0.4 - - - -
144D GLU 3.5 20.4 - - - +
146D VAL* 3.7 23.3 - - + -
203D PHE 3.5 3.3 - - - +
204D ILE* 3.5 3.1 - - - +
205D ILE* 2.8 49.4 + - + +
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D LEU* 1.3 73.7 - - - +
113D PHE* 1.3 58.5 + - - +
114D PHE* 4.5 7.6 - - + -
131D PHE* 4.2 9.2 - - + -
138D PHE* 3.8 28.3 - - + -
143D THR* 3.8 14.8 - - + -
144D GLU 2.9 10.5 + - - +
145D VAL* 3.4 8.7 - - + +
146D VAL 2.9 26.7 + - - +
202D LEU* 3.7 36.1 - - + -
203D PHE 3.5 3.6 - - - -
204D ILE* 4.7 2.5 - - + -
228D THR* 3.9 15.3 - - + -
232D VAL* 4.0 9.4 - - + -
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Residues in contact with PHE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D TRP* 3.4 50.3 - + - -
111D LEU* 4.2 7.4 - - + -
112D VAL* 1.3 71.9 - - - +
114D PHE* 1.3 59.8 + - - +
115D PHE* 3.5 37.2 - + - -
146D VAL* 3.5 28.9 - - + -
148D CYS* 4.1 14.6 - - + -
177D LEU* 4.1 5.8 - - + -
184D ILE* 4.0 8.7 - - + -
188D TYR* 3.8 24.0 - + - -
203D PHE* 2.8 41.5 + + - +
205D ILE* 4.1 15.9 - - + -
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Residues in contact with PHE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D VAL* 4.5 6.3 - - + -
113D PHE* 1.3 77.2 - - - +
115D PHE* 1.3 57.7 + - - +
116D TYR* 4.4 5.6 - + + -
127D GLU* 4.7 8.1 - - + -
128D ILE* 4.2 28.3 - - + -
131D PHE* 3.8 27.8 - + + -
145D VAL* 3.6 27.8 - - + -
146D VAL 2.9 15.1 + - - -
147D ALA* 3.2 33.5 - - + -
148D CYS* 2.8 32.0 + - - +
174D ILE* 4.9 2.2 - - + -
201D GLY 3.4 9.6 - - - +
202D LEU* 3.9 16.4 - - + -
223D ARG* 3.7 30.5 - - - +
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Residues in contact with PHE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D PHE* 3.5 33.7 - + - -
114D PHE* 1.3 76.1 - - - +
116D TYR* 1.3 59.7 + - - +
148D CYS* 3.0 37.7 - - + -
184D ILE* 3.8 11.2 - - + -
185D SER* 3.8 17.3 - - - -
188D TYR* 3.6 29.4 - - + -
190D VAL* 3.6 17.7 - - + -
198D THR* 3.6 26.2 - - + +
199D LEU 3.8 4.4 - - - +
201D GLY 2.8 14.2 + - - +
203D PHE* 3.7 20.0 - + - -
223D ARG* 2.9 25.2 + - - -
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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