Contacts of the strand formed by residues 259 - 265 (chain A) in PDB entry 1TAD
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 SER 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A THR* 3.3 16.3 + - - +
216A CYS* 3.2 16.3 - - - -
217A ILE 2.8 24.8 + - - -
257A THR 3.8 2.7 + - - -
258A THR* 1.3 74.8 - - - +
260A ILE* 1.3 59.6 - - - +
261A VAL* 5.6 1.3 - - - -
313A LYS* 4.7 2.9 - - - +
338A ILE* 4.9 13.4 - - - +
339A ILE* 5.1 5.9 - - - -
342A GLU 3.5 26.9 + - - -
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Residues in contact with ILE 260 (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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217A ILE* 3.4 31.2 - - + +
219A PHE* 5.1 1.6 - - + -
246A PHE* 4.4 15.5 - - + -
249A ILE* 4.6 2.9 - - + +
250A CYS* 4.2 30.3 - - - +
255A PHE* 4.4 17.7 - - + +
258A THR 3.4 12.4 + - - +
259A SER* 1.3 77.9 - - - +
261A VAL* 1.3 75.9 + - - +
313A LYS* 3.6 22.1 + - - +
314A GLU 4.6 1.4 + - - +
315A ILE* 3.4 39.0 - - + +
316A TYR 3.7 1.7 + - - -
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Residues in contact with VAL 261 (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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216A CYS* 4.5 7.6 - - - -
217A ILE 2.8 9.9 + - - +
218A ILE* 3.4 36.3 - - + -
219A PHE* 2.8 29.7 + - - +
259A SER* 5.3 1.1 - - - -
260A ILE* 1.3 82.4 - - - +
262A LEU* 1.3 59.6 + - - +
263A PHE* 4.2 11.2 - - + -
315A ILE* 4.2 2.5 - - - -
316A TYR* 3.2 35.4 - - + +
335A VAL* 4.4 17.7 - - + -
338A ILE* 4.7 12.3 - - + -
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Residues in contact with LEU 262 (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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219A PHE* 3.3 35.9 - - + +
221A ALA* 4.1 17.9 - - + -
246A PHE* 4.4 8.3 - - + -
261A VAL* 1.3 72.7 - - - +
263A PHE* 1.3 64.5 + - - +
264A LEU* 4.0 23.3 - - + -
300A LYS 4.9 1.1 - - - +
303A PHE* 3.6 36.8 - - + -
304A LEU* 4.3 13.7 - - + -
315A ILE* 4.1 9.8 - - + +
316A TYR* 2.8 10.0 + - - +
317A SER* 3.1 32.6 - - - -
318A HIS 3.1 6.1 + - - +
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Residues in contact with PHE 263 (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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45A ILE* 4.2 32.3 - - + -
218A ILE* 3.6 36.3 - - + -
219A PHE 2.7 12.5 + - - +
220A ILE* 3.5 16.3 - - + +
221A ALA* 2.9 27.0 + - - -
261A VAL* 4.2 6.5 - - + -
262A LEU* 1.3 80.6 - - - +
264A LEU* 1.3 60.6 + - - +
265A ASN* 3.2 2.3 + - - -
316A TYR* 5.2 3.1 - + - -
318A HIS 3.6 5.6 - - - -
320A THR* 3.8 24.0 - - + +
328A VAL* 5.7 4.3 - - + -
331A VAL* 3.6 31.9 - - + -
332A PHE* 5.1 6.5 - + + -
335A VAL* 3.9 22.4 - - + -
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Residues in contact with LEU 264 (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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221A ALA* 3.4 11.4 - - + +
223A LEU* 3.4 31.0 - - + +
239A MET* 5.8 0.2 - - + -
262A LEU* 3.9 26.9 + - + +
263A PHE* 1.3 69.2 - - - +
265A ASN* 1.3 58.0 + - - +
296A GLY 4.3 3.6 - - - +
299A ILE* 4.2 19.3 - - + -
300A LYS* 3.7 39.5 - - + +
303A PHE* 4.2 12.6 - - + -
317A SER* 5.0 3.8 - - - -
318A HIS 2.8 14.6 + - - +
319A MET* 3.2 16.3 - - + -
320A THR 2.8 26.0 + - - -
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Residues in contact with ASN 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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40A SER 2.9 23.3 + - - +
41A GLY* 3.8 3.6 - - - -
45A ILE* 5.9 0.7 - - - -
220A ILE* 3.5 24.3 - - + +
221A ALA 2.8 10.9 + - - +
223A LEU* 2.9 27.6 + - - +
263A PHE* 3.2 0.4 + - - -
264A LEU* 1.3 75.3 - - - +
266A LYS* 1.3 76.2 + - + +
267A LYS 3.3 1.3 - - - -
320A THR* 3.0 16.4 + - - +
322A ALA* 2.8 35.4 + - - +
351A GDP 3.0 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