Contacts of the strand formed by residues 407 - 411 (chain B) in PDB entry 1NDM
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 THR 407 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B GLU* 3.6 34.0 + - + -
307B SER* 4.6 2.7 - - - +
308B GLY 4.8 7.4 + - - +
310B SER* 5.9 0.7 - - - -
320B LEU* 4.0 28.5 - - + -
391B ALA 3.9 0.2 - - - +
392B THR* 3.9 3.9 - - - +
393B TYR* 2.8 41.1 + - - +
406B GLY* 1.3 75.1 - - - -
408B SER* 1.3 65.6 + - - +
409B VAL* 4.0 2.6 + - + -
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B SER* 3.5 20.6 - - - -
391B ALA 3.5 7.2 - - - -
392B THR* 3.6 17.7 + - - +
407B THR* 1.3 75.6 + - - +
409B VAL* 1.3 71.0 + - - +
410B THR* 5.7 1.8 - - - -
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Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLY 5.5 0.2 - - - +
309B PRO 3.7 22.9 - - - +
310B SER 3.3 7.0 - - - +
312B VAL* 3.9 16.8 - - + -
318B LEU* 3.7 22.4 - - + -
320B LEU* 4.2 19.3 - - + -
389B ASP 4.2 0.6 - - - +
390B THR* 3.4 4.9 - - - +
391B ALA 2.9 31.5 + - - +
393B TYR* 4.0 26.7 - - + -
407B THR* 4.2 5.2 - - + +
408B SER* 1.3 81.8 - - - +
410B THR* 1.3 68.3 + - - +
411B VAL* 5.3 1.1 - - + -
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Residues in contact with THR 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B SER 2.8 11.4 + - - -
311B LEU* 3.5 8.8 - - + +
312B VAL* 2.9 26.7 + - - +
390B THR* 3.9 19.0 - - + +
408B SER* 5.5 2.1 - - - -
409B VAL* 1.3 78.2 + - - +
411B VAL* 1.3 73.5 + - - +
412B SER* 3.9 10.3 - - - -
446B PHE* 4.9 6.7 - - + -
447B PRO* 6.4 1.8 - - - -
448B GLU* 5.4 2.9 + - - +
476B LEU* 6.3 0.4 - - + -
483B TYR* 3.6 24.5 + - + +
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B VAL* 3.0 15.7 - - + +
314B PRO* 3.8 15.0 - - + -
318B LEU* 5.0 6.1 - - + -
385B VAL* 3.8 27.6 - - + -
386B THR* 3.0 42.8 - - - +
387B THR* 3.0 26.2 - - - +
389B ASP* 4.0 21.3 - - + +
390B THR* 3.1 8.6 + - - -
409B VAL* 5.3 0.2 - - + -
410B THR* 1.3 75.6 - - - +
412B SER* 1.3 64.0 + - - +
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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
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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