Contacts of the strand formed by residues 201 - 211 (chain B) in PDB entry 3A4T
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 LEU 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B PHE* 4.1 9.7 - - - -
157B PHE 3.8 9.4 - - - +
159B LYS 4.2 0.7 - - - -
160B ILE* 3.5 27.8 - - + +
197B GLY 3.4 3.5 + - - +
198B ILE* 3.3 30.9 + - + +
199B ASP 3.4 0.2 - - - -
200B LEU* 1.3 80.1 - - - +
202B LYS* 1.3 65.7 + - - +
203B LYS 3.7 0.3 + - - -
205B GLY* 3.7 25.6 - - - +
206B GLU* 3.1 27.6 - - - +
207B LEU* 3.6 22.7 - - + +
271B LEU 4.8 0.9 - - - +
273B LYS* 3.1 31.5 + - + +
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Residues in contact with LYS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 5.2 4.9 - - - +
156B PHE* 3.6 33.8 - - + +
157B PHE 2.9 21.6 + - - +
158B ASP* 2.8 39.3 + - - +
201B LEU* 1.3 75.4 - - - +
203B LYS* 1.3 74.9 + - - +
204B ASP 3.3 0.3 + - - -
205B GLY* 2.8 17.2 + - - +
273B LYS* 3.7 6.2 - - - +
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Residues in contact with LYS 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B LEU 3.7 1.2 + - - -
202B LYS* 1.3 80.3 - - - +
204B ASP* 1.3 83.8 + - - +
205B GLY 3.2 2.3 + - - -
273B LYS* 3.9 11.5 - - + +
274B ILE* 3.5 37.0 + - - +
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Residues in contact with ASP 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B LYS 3.3 0.2 + - - -
203B LYS* 1.3 87.4 - - - +
205B GLY* 1.3 62.9 + - - +
206B GLU* 4.0 6.9 + - - +
272B ARG* 4.1 21.4 + - + +
273B LYS 2.8 25.6 + - - +
274B ILE* 4.3 7.1 - - - +
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Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B PHE 4.6 0.7 - - - -
158B ASP* 3.1 19.5 - - - -
159B LYS* 5.3 0.2 - - - -
201B LEU* 3.7 10.5 - - - +
202B LYS* 2.8 24.2 + - - -
203B LYS 3.1 2.6 + - - -
204B ASP* 1.3 75.0 - - - +
206B GLU* 1.3 60.0 + - - -
272B ARG* 3.3 3.3 - - - -
273B LYS 3.0 24.4 + - - -
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 3.6 4.3 - - + +
80B ASN* 5.5 0.2 - - - +
158B ASP 3.3 6.1 + - - -
159B LYS* 2.8 42.1 + - - +
160B ILE 2.9 23.2 + - - -
201B LEU* 3.1 6.4 - - - +
204B ASP 4.2 7.1 - - - +
205B GLY* 1.3 78.9 - - - +
207B LEU* 1.3 61.1 + - - +
236B ILE* 4.0 17.3 - - + +
270B LYS* 3.2 35.1 + - - -
271B LEU 3.2 7.9 - - - +
272B ARG* 3.7 17.4 + - - +
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 4.2 0.2 - - - -
160B ILE* 3.3 25.1 - - + +
162B LEU* 4.6 10.5 - - + -
194B ILE* 4.3 9.9 - - + +
197B GLY* 3.6 39.0 - - - +
198B ILE* 3.9 8.5 - - + +
201B LEU* 3.6 14.4 - - + -
206B GLU* 1.3 76.2 - - - +
208B VAL* 1.3 78.0 + - - +
209B TYR* 3.8 10.8 - - + +
270B LYS* 3.3 3.1 - - - +
271B LEU* 2.8 59.7 + - + +
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PRO* 4.0 21.3 - - + +
78B VAL* 3.9 13.2 - - + -
79B LEU* 3.6 44.4 - - + +
160B ILE 3.0 7.0 + - - +
161B LEU* 3.8 6.8 - - + +
162B LEU* 2.8 33.8 + - - +
207B LEU* 1.3 76.1 - - - +
209B TYR* 1.3 63.6 + - - +
210B SER 4.5 0.4 - - - +
268B ILE* 3.6 24.2 - - + -
269B ALA 3.3 9.2 - - - +
270B LYS* 3.9 10.3 - - + -
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Residues in contact with TYR 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LEU* 3.5 26.2 - - + -
164B ALA* 3.8 20.2 - - + -
190B GLN* 2.9 30.8 + - + +
194B ILE* 4.3 6.7 - - + -
207B LEU* 3.8 12.5 - - + +
208B VAL* 1.3 73.6 - - - +
210B SER* 1.3 71.8 + - - +
211B THR* 4.1 7.8 - - + +
218B GLU 2.8 28.8 + - - -
219B ASN 4.4 0.9 - - - -
222B VAL* 3.8 20.1 - - + +
223B ILE* 3.9 28.5 - - + -
267B PHE* 4.2 20.0 - + - -
268B ILE* 3.4 2.8 - - - -
269B ALA 2.8 36.3 + - - +
271B LEU* 5.6 0.4 - - + -
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PRO* 3.4 34.1 - - - +
161B LEU* 4.0 1.4 - - - +
162B LEU 2.9 7.3 + - - +
163B ASP* 2.7 34.1 + - - +
164B ALA* 2.9 29.5 + - - +
208B VAL* 4.0 0.6 - - - -
209B TYR* 1.3 81.9 - - - +
211B THR* 1.3 65.2 + - - +
266B PHE* 3.9 4.3 - - - -
267B PHE 3.2 11.7 - - - -
268B ILE* 4.4 3.4 - - - -
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Residues in contact with THR 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ASP* 4.2 2.7 - - - -
164B ALA* 3.0 20.5 + - - -
165B PRO 3.4 6.8 + - - -
166B CYS* 3.2 14.2 - - - +
190B GLN* 4.0 0.5 + - - -
209B TYR* 4.1 13.2 - - + +
210B SER* 1.3 77.6 - - - +
212B CYS* 1.3 58.4 + - - +
213B SER* 3.1 13.2 + - - +
218B GLU* 3.8 13.5 - - + +
219B ASN* 3.3 29.8 - - - +
266B PHE* 3.4 10.2 - - - -
267B PHE* 2.9 29.9 + - + -
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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