Contacts of the strand formed by residues 264 - 273 (chain A) in PDB entry 4DKT
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 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A TRP* 3.8 19.3 - - + +
207A GLU* 3.9 14.9 - - - +
261A PHE* 3.6 13.5 - - - -
262A PRO* 3.7 7.6 - - + +
263A GLY* 1.3 78.9 - - - +
265A ILE* 1.3 63.0 + - - +
266A THR* 4.3 1.8 - - - +
290A VAL* 4.1 13.9 - - + -
291A PHE 3.4 12.6 - - - +
292A ARG* 3.4 50.7 - - + +
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Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 4.2 11.7 - - + -
203A VAL* 4.3 13.2 - - + -
207A GLU* 3.9 14.4 - - + +
210A LYS* 3.9 27.4 - - + +
211A VAL* 4.0 23.8 - - + -
261A PHE* 3.5 27.6 - - + -
264A LEU* 1.3 76.1 - - - +
266A THR* 1.3 64.0 + - - +
267A LEU* 4.4 8.3 - - + -
290A VAL* 3.6 1.1 - - - -
291A PHE* 2.8 50.5 + - + +
293A VAL* 4.0 17.7 - - + -
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A HIS 4.0 0.3 - - - +
203A VAL* 3.7 23.2 - - - +
204A ALA 4.5 1.0 + - - -
207A GLU* 3.1 18.5 + - - +
264A LEU* 5.4 1.7 - - - +
265A ILE* 1.3 74.7 - - - +
267A LEU* 1.3 64.2 + - - +
268A THR* 4.1 9.4 + - - +
288A SER* 3.8 22.0 - - - +
289A VAL 3.4 13.9 - - - +
290A VAL* 4.1 19.0 - - + +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 4.0 3.2 - - - +
183A MET* 3.6 29.4 - - + -
201A LEU* 5.0 5.6 - - + -
202A HIS 3.6 2.0 - - - +
203A VAL* 3.3 36.1 - - + -
211A VAL* 4.8 2.2 - - + -
213A VAL* 3.8 22.7 - - + -
229A LEU* 4.2 6.5 - - + -
251A VAL* 4.0 8.1 - - + -
265A ILE* 4.0 10.3 + - + -
266A THR* 1.3 77.2 - - - +
268A THR* 1.3 61.2 + - - +
288A SER* 3.2 3.5 - - - -
289A VAL* 3.1 40.4 + - + +
291A PHE* 3.9 22.0 - - + -
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Residues in contact with THR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 4.6 0.2 - - - -
201A LEU* 3.2 8.6 - - - +
202A HIS* 2.9 67.4 + - + +
266A THR* 4.1 8.8 + - - +
267A LEU* 1.3 75.4 - - - +
269A ILE* 1.3 68.8 + - - +
286A GLN* 4.3 14.8 - - + +
287A ASP 3.2 16.2 - - - +
288A SER* 3.1 17.4 + - - +
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Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE* 4.8 7.6 - - + -
117A LEU* 3.9 24.8 - - + +
185A LEU* 4.1 16.8 - - + -
199A LEU* 4.3 15.7 - - + -
200A VAL 3.3 15.9 - - - +
201A LEU* 3.8 12.1 - - + -
238A LEU* 3.5 31.6 - - + -
268A THR* 1.3 74.5 - - - +
270A SER* 1.3 64.0 + - - +
285A PHE* 3.8 9.3 - - + +
286A GLN* 3.2 4.7 - - - -
287A ASP* 2.7 51.9 + - + +
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Residues in contact with SER 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A LEU* 3.3 10.3 - - - +
200A VAL* 2.9 51.2 + - - +
202A HIS* 2.8 22.9 + - - -
269A ILE* 1.3 71.0 - - - +
271A LEU* 1.3 59.8 + - - +
272A LEU* 3.9 6.3 - - - -
283A VAL* 4.4 8.7 - - - -
285A PHE* 3.3 4.5 - - - -
286A GLN* 3.2 27.7 + - - +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 4.7 5.4 - - + -
20A VAL* 4.5 11.7 - - + -
113A VAL* 4.9 0.9 - - + -
115A ILE* 4.9 10.8 - - + -
193A PHE* 4.2 22.7 - - + -
194A PHE* 5.0 1.3 - - + -
197A HIS* 4.1 23.1 - - + -
198A THR 4.6 2.2 - - - +
199A LEU* 3.5 25.8 - - + -
270A SER* 1.3 72.0 - - - +
272A LEU* 1.3 64.1 + - - +
283A VAL* 3.5 3.5 - - - -
284A VAL* 2.9 54.7 + - + -
285A PHE* 2.8 32.3 + - + +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A HIS* 3.2 10.7 - - - +
198A THR* 2.9 53.1 + - + +
200A VAL* 3.4 34.1 - - + -
237A TYR* 4.3 7.0 - - + +
270A SER* 4.6 2.5 - - - -
271A LEU* 1.3 75.6 - - - +
273A ASP* 1.3 60.1 + - - +
274A THR 3.6 0.4 + - - -
281A GLU* 3.6 45.1 - - + +
282A ALA 3.9 1.6 - - - -
283A VAL* 3.4 33.4 - - + +
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Residues in contact with ASP 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ASN 3.2 6.4 - - - +
197A HIS* 3.8 17.3 + - + -
271A LEU 4.1 0.2 + - - -
272A LEU* 1.3 70.7 - - - +
274A THR* 1.3 60.0 + - - +
275A SER* 2.9 34.2 + - - -
276A ASN* 5.2 0.7 + - - -
280A PRO 4.2 2.6 - - - +
281A GLU* 3.5 5.2 - - - -
282A ALA* 2.9 47.6 + - + +
284A VAL* 4.0 14.4 - - + +
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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