Contacts of the strand formed by residues 200 - 205 (chain D) 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 ARG 200 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115D PHE 3.9 2.0 - - - -
117D PRO* 3.5 20.1 - - + +
123D VAL* 3.3 28.5 - - - +
124D CYS* 3.4 32.1 - - - +
127D GLU* 2.9 31.7 + - - -
199D LEU* 1.3 79.7 - - - +
201D GLY* 1.3 56.1 + - - +
215D THR 3.5 2.9 - - - +
216D LEU* 3.4 1.7 - - - -
217D ASN* 2.8 40.3 + - + +
218D ASP 4.2 1.8 - - - +
219D LEU* 2.8 30.2 + - - +
221D VAL 3.2 23.7 + - - -
223D ARG* 3.3 24.4 + - - +
462D SO4 4.4 9.7 + - - -
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Residues in contact with GLY 201 (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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114D PHE* 3.4 1.0 - - - -
115D PHE* 2.8 37.6 + - - +
190D VAL* 4.1 11.4 - - - -
199D LEU* 3.3 7.9 + - - -
200D ARG* 1.3 73.1 - - - +
202D LEU* 1.3 57.4 + - - -
203D PHE* 3.8 5.6 - - - -
215D THR 3.4 5.4 - - - -
216D LEU* 3.7 17.3 - - - -
223D ARG* 3.1 6.6 + - - +
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Residues in contact with LEU 202 (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* 3.9 13.0 - - + -
113D PHE 3.8 2.7 - - - -
114D PHE* 3.9 17.0 - - + -
131D PHE* 3.8 20.0 - - + -
201D GLY* 1.3 73.5 - - - +
203D PHE* 1.3 70.0 + - - +
204D ILE* 3.8 26.5 - - + -
213D GLN* 4.1 9.6 - - - +
214D ILE* 3.4 4.7 - - - -
215D THR* 2.8 46.8 + - - +
223D ARG* 4.0 22.2 - - + +
228D THR* 3.7 27.6 - - + +
231D LEU* 6.1 0.4 - - + -
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Residues in contact with PHE 203 (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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79D ALA* 4.0 8.1 - - + -
111D LEU 3.5 2.9 - - - +
112D VAL* 3.6 2.8 - - - -
113D PHE* 2.9 48.3 + + + +
115D PHE* 3.5 29.2 - + - -
188D TYR* 3.4 54.7 - + + -
190D VAL* 3.6 13.9 - - + -
201D GLY 3.8 8.7 - - - -
202D LEU* 1.3 77.3 - - - +
204D ILE* 1.3 63.4 + - - +
205D ILE* 3.9 3.1 + - + -
211D LEU* 3.7 17.0 - - + -
213D GLN 3.3 4.3 - - - -
214D ILE* 3.8 34.1 - - + -
216D LEU* 4.2 8.5 - - + -
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Residues in contact with ILE 204 (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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110D TYR* 4.0 27.4 - - + -
111D LEU 3.6 5.8 - - - +
112D VAL* 4.7 8.1 - - + -
202D LEU* 3.8 18.2 - - + -
203D PHE* 1.3 74.0 - - - +
205D ILE* 1.3 57.6 + - - +
211D LEU* 3.5 2.3 - - - +
212D ARG* 2.8 34.2 + - + +
213D GLN* 2.9 35.5 + - + +
228D THR* 4.1 12.6 - - + +
231D LEU* 3.6 34.3 - - + -
232D VAL* 4.2 13.5 - - + -
235D PHE* 4.7 9.4 - - + -
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Residues in contact with ILE 205 (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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85D ALA* 3.5 26.0 - - + -
103D LEU* 3.9 25.6 - - + -
110D TYR* 3.4 6.6 - - - -
111D LEU* 2.8 48.0 + - + +
113D PHE* 4.2 24.7 - - + -
188D TYR* 3.9 11.7 - - + +
203D PHE* 4.5 3.6 - - + +
204D ILE* 1.3 78.9 - - - +
206D ASP* 1.3 72.0 + - - +
209D GLY* 3.7 26.2 - - - +
210D ILE 3.4 4.5 - - - +
211D LEU* 4.0 10.8 - - + -
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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