Contacts of the strand formed by residues 341 - 344 (chain A) in PDB entry 1T8U
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 PHE 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A PHE* 3.6 42.4 - + + -
319A PRO* 3.6 35.2 - - + -
320A ALA* 3.6 23.6 - - + -
323A LEU* 4.5 1.1 - - + -
336A ILE* 4.0 21.8 - - + -
337A THR 3.5 21.3 - - - -
338A ASP* 3.1 15.9 + - - +
340A HIS* 1.3 83.8 - - + +
342A TYR* 1.3 62.7 + - - +
350A PRO* 4.8 7.6 - - + -
351A CYS 3.4 11.4 - - - +
352A LEU* 3.7 13.2 - - + -
353A LYS* 3.6 16.2 + - - -
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Residues in contact with TYR 342 (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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341A PHE* 1.3 77.0 - - - +
343A PHE* 1.3 74.6 + - - +
344A ASN 3.4 0.7 + - - -
350A PRO* 4.3 1.8 - - - -
351A CYS* 2.7 38.1 + - + +
352A LEU 5.2 0.2 - - - -
353A LYS* 4.7 15.5 - - - -
361A PRO* 6.3 0.4 - - + -
143B LEU* 4.0 26.5 - - + -
147B GLU* 2.6 42.7 + - - +
207B LEU* 4.0 42.2 - - + +
208B ASP* 4.6 22.3 + - + -
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Residues in contact with PHE 343 (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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316A ILE* 5.7 2.0 - - + -
342A TYR* 1.3 89.5 - - - +
344A ASN* 1.3 57.6 + - - +
345A LYS* 3.6 26.0 + - + -
348A GLY* 3.4 42.2 - - - -
349A PHE* 3.5 15.9 - - - -
350A PRO* 3.7 14.3 - - + +
147B GLU* 4.5 2.3 - - - +
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Residues in contact with ASN 344 (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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342A TYR* 3.4 2.1 + - - -
343A PHE* 1.3 72.2 - - - +
345A LYS* 1.3 53.0 + - - +
346A THR* 3.0 15.1 + - - -
347A LYS* 2.7 34.9 + - + +
348A GLY* 2.7 34.8 + - - -
349A PHE 3.0 20.2 + - - +
351A CYS* 3.4 14.4 - - - -
363A CYS* 3.4 17.8 - - - -
139B GLY* 4.2 6.1 + - - -
143B LEU* 3.1 38.9 - - + +
147B GLU* 5.0 0.2 - - - -
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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