Contacts of the strand formed by residues 140 - 149 (chain B) in PDB entry 1SMN


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.
For CSU analysis of other PDB entry

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 SER 140 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  THR*     4.1    13.7    -      -       -      +
     48B  LYS*     4.2    13.3    +      -       -      +
    134B  ILE*     3.6    11.4    -      -       -      +
    138B  ASP      3.7     3.3    +      -       -      -
    139B  ILE*     1.3    72.8    -      -       -      +
    141B  SER*     1.3    66.8    +      -       -      +
    177B  ASN*     2.9    16.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 141 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  HIS*     2.7    29.4    +      -       -      -
     46B  ILE      3.4     7.0    -      -       -      -
     47B  THR*     4.5     0.5    -      -       -      +
    134B  ILE*     3.6     1.3    -      -       -      +
    139B  ILE*     3.6     3.0    -      -       -      +
    140B  SER*     1.3    83.1    +      -       -      +
    142B  VAL*     1.3    67.8    +      -       -      +
    143B  TYR*     3.6    19.1    +      -       -      -
    176B  ILE*     3.4     7.1    -      -       -      +
    177B  ASN*     3.0    33.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 142 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  TYR*     3.8     1.0    -      -       -      +
     45B  HIS*     3.3     5.2    -      -       -      -
     46B  ILE*     2.8    47.2    +      -       +      +
    130B  GLU*     4.0    19.5    -      -       +      +
    133B  LEU*     3.9    31.2    -      -       +      -
    134B  ILE*     4.2    15.3    -      -       +      +
    139B  ILE*     4.3     3.8    -      -       +      -
    141B  SER*     1.3    79.5    -      -       -      +
    143B  TYR*     1.3    59.9    +      -       -      +
    144B  THR*     3.7     9.1    +      -       -      +
    174B  ILE*     3.5    32.1    -      -       +      -
    175B  PHE      3.6     3.6    -      -       -      +
    176B  ILE*     4.3     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 143 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  ASP      4.3     4.9    +      -       -      -
      8B  ASN      3.7    22.0    -      -       -      +
      9B  CYS*     4.0     3.1    -      -       -      +
     10B  ALA*     3.6    32.5    -      -       +      +
     44B  TYR      3.5     1.1    -      -       -      -
     45B  HIS*     3.3    43.1    +      +       +      -
    141B  SER*     3.6    14.3    +      -       -      -
    142B  VAL*     1.3    74.1    -      -       -      +
    144B  THR*     1.3    60.3    +      -       -      +
    145B  VAL*     5.8     1.1    -      -       -      +
    173B  VAL      3.9     0.5    -      -       -      +
    174B  ILE*     3.5     2.4    -      -       -      -
    175B  PHE*     2.9    73.2    +      +       +      -
    177B  ASN      3.5    22.4    -      -       -      -
    219B  TRP*     5.5     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 144 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  ASN      4.8     1.0    -      -       -      +
     42B  VAL      4.5     0.4    -      -       -      -
     43B  ALA*     3.3     3.6    -      -       -      +
     44B  TYR*     2.9    69.0    +      -       +      +
    130B  GLU*     2.7    21.7    +      -       -      +
    142B  VAL*     3.7     5.6    -      -       -      +
    143B  TYR*     1.3    78.4    +      -       -      +
    145B  VAL*     1.3    69.5    +      -       -      +
    172B  LYS*     3.4    25.8    -      -       +      -
    173B  VAL      3.3     7.4    -      -       -      +
    174B  ILE*     3.6    14.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 145 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  CYS*     5.6     4.3    -      -       +      -
     14B  PRO*     3.7    30.3    -      -       +      -
     41B  TRP*     4.2     7.4    -      -       +      -
     42B  VAL      3.3     9.9    -      -       -      +
     43B  ALA*     4.3    11.2    -      -       +      -
    143B  TYR      5.8     0.4    -      -       -      -
    144B  THR*     1.3    79.7    -      -       -      +
    146B  THR*     1.3    63.0    +      -       -      +
    171B  TRP*     3.4    24.2    -      -       +      -
    172B  LYS*     3.5     1.0    -      -       -      -
    173B  VAL*     2.9    35.2    +      -       +      +
    175B  PHE*     6.4     0.7    -      -       +      -
    218B  ILE*     4.4    20.9    -      -       +      -
    219B  TRP*     4.9    10.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 146 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41B  TRP*     3.2     4.0    -      -       -      +
     42B  VAL*     2.9    45.5    +      -       +      +
     44B  TYR*     4.0    11.0    -      -       +      -
     90B  GLN*     3.7    37.1    +      -       +      +
    123B  TRP*     3.5    21.1    -      -       -      -
    144B  THR*     4.6     0.9    -      -       -      -
    145B  VAL*     1.3    75.0    -      -       -      +
    147B  GLY*     1.3    58.2    +      -       -      +
    170B  TYR*     6.1     0.2    -      -       -      -
    171B  TRP*     2.7    26.3    +      -       -      -
    172B  LYS*     4.0    12.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  ASN      3.8     2.9    -      -       -      -
     41B  TRP*     4.4     0.2    -      -       -      -
     90B  GLN*     3.3    10.8    -      -       -      -
    146B  THR*     1.3    80.2    +      -       -      +
    148B  PRO*     1.3    70.9    -      -       -      +
    170B  TYR*     3.4     7.2    -      -       -      +
    171B  TRP*     2.9    46.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 148 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  PHE*     5.1     1.6    -      -       +      -
     39B  ALA      3.2    24.0    -      -       -      +
     40B  ASN*     3.6     9.6    -      -       -      +
     90B  GLN*     3.9     7.4    -      -       -      +
    112B  THR*     5.3     0.9    -      -       +      -
    147B  GLY*     1.3    85.8    -      -       -      +
    149B  LEU*     1.3    62.9    +      -       -      +
    150B  TYR*     3.4    30.1    -      -       +      +
    167B  PRO*     3.5    29.4    -      -       +      -
    169B  ALA      3.2     7.6    -      -       -      +
    170B  TYR*     4.1     8.3    -      -       +      -
    171B  TRP*     3.1    15.1    +      -       -      -
    214B  THR*     4.1     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 149 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148B  PRO*     1.3    72.0    -      -       -      +
    150B  TYR*     1.3    67.0    +      -       -      +
    151B  GLU*     3.5    26.5    -      -       +      +
    167B  PRO*     3.4     4.2    -      -       -      +
    168B  SER*     2.9    25.5    +      -       -      +
    169B  ALA*     2.9    26.4    +      -       +      -
    171B  TRP*     3.9    13.7    -      -       +      -
    189B  LEU*     4.0    16.2    -      -       +      -
    210B  ILE*     6.0     0.4    -      -       -      -
    213B  ARG*     3.3    44.6    -      -       +      +
    214B  THR*     3.2    31.6    -      -       +      -
----------------------------------------------------------
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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
------------------------------------------------------------
  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) +   -    +    +   +   +    +    -
------------------------------------------------------------
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