Contacts of the strand formed by residues 354 - 360 (chain A) in PDB entry 6T8G
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A LEU* 4.5 10.3 - - + -
344A GLU* 3.7 22.3 + - + +
347A LEU* 3.7 36.1 - - + +
348A LYS* 6.2 0.4 - - - +
352A VAL* 5.7 1.6 - - + -
353A GLU* 1.3 81.2 - - - +
355A SER* 1.3 64.2 + - - +
370A ILE* 3.7 30.3 - - + -
371A GLN 3.6 5.8 - - - +
372A PRO* 3.6 29.4 - - + -
373A ALA* 5.0 1.1 - - - +
376A VAL* 6.3 0.2 - - + -
381A ILE* 6.0 3.1 - - + -
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Residues in contact with SER 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLU* 3.3 7.0 - - - -
354A VAL* 1.3 78.7 - - - +
356A VAL* 1.3 65.1 + - - +
357A ASP* 3.3 2.8 + - - +
370A ILE* 3.4 3.3 - - - -
371A GLN* 3.0 39.9 + - - +
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A SER* 3.7 46.4 - - - +
341A ARG* 4.2 8.3 + - - +
343A LEU* 4.1 7.9 - - + -
344A GLU* 2.5 26.9 + - + +
355A SER* 1.3 72.7 - - - +
357A ASP* 1.3 60.8 + - - +
358A SER* 4.2 13.9 - - - +
359A VAL* 4.3 9.0 - - + -
368A PHE* 4.8 5.2 - - + -
369A GLU 3.8 9.0 - - - +
370A ILE* 3.8 18.4 - - + -
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Residues in contact with ASP 357 (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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355A SER* 3.3 7.2 + - - +
356A VAL* 1.3 74.1 - - - +
358A SER* 1.3 60.2 + - - +
369A GLU* 2.6 26.8 + - + +
371A GLN* 4.7 12.4 - - + +
406A LYS* 4.1 18.4 + - - -
408A THR* 4.2 7.6 - - + +
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Residues in contact with SER 358 (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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356A VAL* 3.8 3.7 - - - +
357A ASP* 1.3 80.3 - - - +
359A VAL* 1.3 80.8 + - - +
360A HIS* 3.8 13.3 + - - -
368A PHE* 3.6 1.7 - - - -
369A GLU* 2.7 61.7 + - - +
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Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LEU* 3.7 45.8 - - + -
340A SER* 3.8 22.7 - - - +
356A VAL* 4.3 6.7 - - + -
358A SER* 1.3 89.5 + - - +
360A HIS* 1.3 73.5 + - - +
361A PRO* 3.9 5.5 - - + +
366A THR* 4.8 0.9 - - + -
367A ARG 4.1 13.2 - - - +
368A PHE* 4.2 8.5 - - + -
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Residues in contact with HIS 360 (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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358A SER* 3.8 11.4 + - - -
359A VAL* 1.3 78.0 + - - +
361A PRO* 1.3 70.9 - - - +
366A THR* 3.3 4.7 - - - +
367A ARG* 3.2 52.9 + - + +
369A GLU* 2.4 46.5 + - + -
447A ILE* 5.9 1.3 - - + +
448A GLY* 5.5 8.7 - - - -
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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