Contacts of the strand formed by residues 354 - 360 (chain B) in PDB entry 6T8B
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 VAL 354 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B GLU* 4.2 19.5 - - + +
347B LEU* 3.7 30.7 - - + -
348B LYS* 5.8 2.0 + - - +
352B VAL* 3.7 21.8 - - + +
353B GLU* 1.3 86.4 - - - +
355B SER* 1.3 65.2 + - - +
370B ILE* 3.5 29.2 - - + -
371B GLN 3.4 8.7 - - - +
372B PRO* 4.0 17.5 - - + -
373B ALA* 5.4 0.2 - - - -
381B ILE* 4.8 4.7 - - + -
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Residues in contact with SER 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLU* 3.3 10.2 + - - -
354B VAL* 1.3 81.1 - - - +
356B VAL* 1.3 68.8 + - - +
357B ASP* 3.2 13.2 + - - +
370B ILE* 3.8 2.9 - - - -
371B GLN* 3.0 28.7 + - - +
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B SER* 3.7 34.5 - - - +
341B ARG* 4.4 6.6 + - - +
343B LEU* 4.1 10.8 - - + -
344B GLU* 2.5 39.4 + - + +
355B SER* 1.3 72.7 + - - +
357B ASP* 1.3 67.0 + - - +
358B SER 3.9 19.5 - - - +
359B VAL* 4.0 9.0 - - + -
368B PHE* 4.8 4.3 - - + -
369B GLU 4.0 4.5 - - - +
370B ILE* 3.6 23.3 - - + -
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Residues in contact with ASP 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B SER* 3.2 15.3 + - - +
356B VAL* 1.3 76.9 - - - +
358B SER* 1.3 65.5 + - - +
369B GLU* 3.0 13.6 + - + +
371B GLN* 2.8 29.2 - - - +
408B THR* 3.2 25.2 - - + +
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Residues in contact with SER 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B VAL* 3.9 2.8 - - - +
357B ASP* 1.3 79.9 - - - +
359B VAL* 1.3 70.8 + - - +
360B HIS* 3.4 10.6 + - - -
369B GLU* 2.5 60.8 + - - +
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Residues in contact with VAL 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU* 4.0 36.8 - - + +
337B GLU* 6.1 0.2 - - - -
340B SER* 4.4 6.1 - - - -
356B VAL* 4.0 11.0 - - + -
358B SER* 1.3 81.5 - - - +
360B HIS* 1.3 69.1 + - - +
361B PRO* 3.2 11.6 - - - +
366B THR* 5.0 3.8 - - - -
367B ARG 3.9 4.5 - - - +
368B PHE* 3.5 43.5 - - + -
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Residues in contact with HIS 360 (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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358B SER* 3.4 12.1 + - - -
359B VAL* 1.3 74.8 + - - +
361B PRO* 1.3 68.8 - - - +
365B ILE 4.4 0.5 - - - +
366B THR* 3.4 1.1 - - - -
367B ARG* 2.8 60.4 + - + +
369B GLU* 2.5 34.9 + - + -
406B LYS* 5.2 5.0 + - - -
447B ILE* 6.0 0.5 - - - +
448B GLY* 5.1 12.5 - - - +
450B ARG* 5.7 8.0 + - - -
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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
------------------------------------------------------------
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