Contacts of the strand formed by residues 356 - 362 (chain A) in PDB entry 3NBN
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 MET 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A LEU* 3.2 19.8 - - - +
349A ASN* 3.0 31.4 + - + +
354A VAL* 3.3 11.3 + - - +
355A ALA* 1.3 79.2 - - - +
357A LEU* 1.3 63.5 + - - +
380A MET* 3.7 30.5 - - + -
388A LEU* 3.6 35.4 - - + -
389A CYS 3.4 15.5 - - - +
390A VAL* 4.1 13.9 - - + -
391A VAL* 3.8 3.7 - - - +
26C ARG* 4.9 15.5 - - - -
27C ILE* 4.9 15.7 - - - -
30C CYS* 6.0 1.6 - - - -
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Residues in contact with LEU 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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346A LEU* 3.9 23.8 - - + -
347A GLN 3.1 16.2 - - - +
348A LEU* 4.4 8.5 - - + -
349A ASN* 4.4 1.5 - - - +
356A MET* 1.3 81.8 - - - +
358A GLU* 1.3 62.3 + - - +
359A LEU* 3.7 23.8 - - + -
372A PHE* 3.5 26.2 - - + -
388A LEU* 3.3 6.7 - - - +
389A CYS* 3.0 39.8 + - - +
391A VAL* 4.3 3.6 - - + -
412A VAL* 4.9 4.9 - - + -
428A PHE* 3.5 33.7 - - + -
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Residues in contact with GLU 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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345A SER 3.7 1.2 - - - +
346A LEU* 3.6 1.2 - - - -
347A GLN* 2.7 47.9 + - + +
349A ASN* 3.9 18.0 + - - +
357A LEU* 1.3 73.8 - - - +
359A LEU* 1.3 65.3 + - - +
360A THR* 4.1 6.9 + - + +
382A ARG* 5.8 1.2 - - - +
386A SER* 3.8 15.1 - - - -
387A MET 3.2 14.4 - - - +
388A LEU* 3.4 19.7 - - + -
1963B ARG* 5.8 0.5 + - - -
1971B SER* 5.2 0.7 + - - -
2002B LEU* 4.8 1.7 - - - +
2005B ARG* 2.9 50.7 + - - +
2006B LEU* 3.6 18.6 - - - +
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Residues in contact with LEU 359 (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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343A VAL* 4.6 13.5 - - + -
345A SER 3.6 4.5 - - - +
346A LEU* 3.6 29.2 - - + -
357A LEU* 3.7 20.0 - - + +
358A GLU* 1.3 82.6 - - - +
360A THR* 1.3 63.0 + - - +
364A PHE* 3.5 13.6 - - + -
370A VAL* 4.1 24.0 - - + -
386A SER* 3.0 5.4 - - - -
387A MET* 2.5 47.4 + - + +
389A CYS* 4.8 1.8 - - - -
412A VAL* 4.7 6.7 - - + -
414A LEU* 3.9 27.6 - - + -
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Residues in contact with THR 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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343A VAL* 3.7 2.4 - - - +
344A GLU* 3.1 7.2 + - - +
345A SER* 2.9 50.6 + - - +
347A GLN* 4.5 9.0 + - - +
358A GLU* 4.3 11.2 - - - +
359A LEU* 1.3 79.1 - - - +
361A GLY* 1.3 59.3 + - - +
364A PHE* 4.1 1.8 - - - -
385A GLU 3.1 12.1 - - - +
386A SER* 4.8 1.8 - - - -
1995B ASP* 5.4 6.0 + - - +
2005B ARG* 4.0 29.6 - - - +
2035B TRP* 5.1 2.7 - - + -
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Residues in contact with GLY 361 (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 VAL 3.0 15.0 - - - -
344A GLU* 3.6 18.7 - - - +
360A THR* 1.3 75.6 - - - +
362A GLN* 1.3 66.3 + - - +
364A PHE* 3.6 9.8 - - - -
385A GLU* 3.0 27.4 + - - +
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Residues in contact with GLN 362 (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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145A LYS* 5.7 8.5 - - - +
342A VAL* 2.9 33.6 + - + +
344A GLU* 2.6 29.0 + - - +
361A GLY* 1.3 78.4 - - - +
363A ASN* 1.3 82.8 + - - +
364A PHE* 3.3 11.5 - - - -
384A GLY 3.8 6.3 - - - -
385A GLU* 4.3 8.5 - - + +
2061B ARG* 4.1 22.6 + - - +
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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