Contacts of the strand formed by residues 215 - 225 (chain B) in PDB entry 5FLM


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 TYR 215 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210B  LYS      4.2     7.4    +      -       -      +
    211B  LYS      5.5     0.2    -      -       -      +
    213B  SER*     3.0    31.3    +      -       -      +
    214B  LYS*     1.3    82.8    -      -       +      +
    216B  ALA*     1.3    62.4    +      -       -      +
    217B  TYR      4.0     3.1    -      -       -      +
    218B  THR*     3.4    27.4    -      -       +      -
    236B  TRP*     6.1     1.3    -      -       +      -
    238B  SER*     3.4    28.3    -      -       -      -
    239B  MET      3.3     5.6    -      -       -      +
    240B  LEU*     3.4    36.3    -      -       +      -
    241B  ALA*     4.5     1.8    -      -       -      -
    257B  VAL*     3.6    17.7    +      -       +      +
    259B  THR*     3.9    12.0    +      -       -      -
    266B  GLU*     2.3    37.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 216 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209B  ALA*     3.5    18.4    -      -       -      +
    210B  LYS      4.9     1.3    +      -       -      +
    215B  TYR*     1.3    74.0    -      -       -      +
    217B  TYR*     1.3    89.4    +      -       +      +
    218B  THR*     5.6     0.4    -      -       -      -
    239B  MET*     2.9    11.3    +      -       +      +
    241B  ALA*     4.0    19.7    -      -       +      +
    242B  ARG*     5.7     2.5    -      -       -      +
    254B  GLN*     4.6    12.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 217 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207B  VAL*     4.6     3.1    -      -       +      -
    208B  PHE      3.7     3.1    -      -       -      +
    209B  ALA*     4.1     6.3    -      -       +      -
    215B  TYR*     3.4     0.5    -      -       -      +
    216B  ALA*     1.3   107.6    -      -       +      +
    218B  THR*     1.3    61.7    -      -       -      +
    238B  SER*     3.3     4.3    -      -       -      -
    239B  MET*     2.9    37.3    +      -       +      -
    242B  ARG*     6.0     0.9    -      -       -      -
    254B  GLN*     5.5     3.6    -      -       -      -
    372B  LEU*     3.6    20.8    -      -       +      +
    375B  ALA*     3.4    22.1    +      -       +      -
    376B  ALA*     3.4    28.3    -      -       +      -
    382B  LEU*     3.8    36.6    -      -       +      -
    103I  ARG*     2.3    42.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 218 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206B  TYR      4.0     0.5    -      -       -      +
    207B  VAL*     3.5     1.9    -      -       -      -
    208B  PHE*     2.9    47.9    +      -       -      +
    209B  ALA*     5.0     0.5    -      -       -      -
    210B  LYS*     5.2    17.3    +      -       +      +
    213B  SER*     4.8     4.7    -      -       -      +
    215B  TYR*     3.4    28.5    -      -       +      +
    216B  ALA      5.6     0.4    -      -       -      -
    217B  TYR*     1.3    74.5    -      -       -      +
    219B  GLY*     1.3    60.6    +      -       -      +
    220B  GLU*     4.2     2.7    +      -       -      +
    236B  TRP*     5.1     9.9    -      -       +      -
    238B  SER*     3.3    22.0    -      -       -      +
    372B  LEU*     4.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205B  VAL*     5.3     3.1    -      -       -      -
    206B  TYR      2.8    14.8    -      -       -      -
    207B  VAL*     4.1     8.7    -      -       -      -
    218B  THR*     1.3    74.4    -      -       -      +
    220B  GLU*     1.3    63.3    +      -       -      +
    236B  TRP*     3.6     3.1    -      -       -      +
    237B  VAL*     2.8    43.5    +      -       -      +
    368B  MET*     6.2     2.2    -      -       -      -
    372B  LEU*     3.9     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 220 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200B  MET*     4.7     9.5    -      -       -      +
    204B  THR      3.9     1.6    -      -       -      +
    205B  VAL*     3.5     7.4    -      -       -      +
    206B  TYR*     2.9    45.2    +      -       +      +
    208B  PHE*     4.1    21.6    -      -       +      -
    218B  THR*     5.2     2.0    -      -       -      +
    219B  GLY*     1.3    76.3    -      -       -      +
    221B  CYS*     1.3    63.5    +      -       -      +
    222B  ARG*     4.8    16.0    -      -       +      +
    234B  THR*     5.5     1.3    -      -       -      -
    235B  ILE      3.4     9.9    -      -       -      +
    236B  TRP*     2.5    48.1    +      -       +      -
    237B  VAL      4.7     0.2    -      -       -      +
    368B  MET*     5.4     3.8    -      -       -      -
    385B  ARG*     5.3     2.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 221 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203B  ASN*     3.8    27.8    -      -       -      -
    204B  THR      4.1     6.5    -      -       -      +
    205B  VAL*     4.5     4.0    -      -       +      -
    220B  GLU*     1.3    76.0    -      -       -      +
    222B  ARG*     1.3    64.6    +      -       -      +
    223B  SER*     3.6    14.8    +      -       -      -
    233B  SER      3.6     3.3    -      -       -      +
    235B  ILE*     3.2    32.8    +      -       +      +
    348B  LEU*     5.9     0.2    -      -       -      -
    350B  HIS*     4.0     1.1    -      -       -      -
    364B  PHE*     3.7    29.6    -      -       +      -
    368B  MET*     3.5    24.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 222 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199B  LYS*     5.5     5.5    -      -       -      +
    200B  MET*     3.0    58.7    +      -       -      +
    201B  ALA      4.1     5.8    +      -       -      +
    202B  THR*     3.1    19.7    -      -       +      +
    203B  ASN      2.8    24.5    +      -       -      -
    204B  THR      4.6     3.4    +      -       -      -
    206B  TYR*     5.8     3.6    -      -       +      -
    220B  GLU*     4.2    17.2    -      -       +      +
    221B  CYS*     1.3    70.7    -      -       -      +
    223B  SER*     1.3    57.5    +      -       -      +
    232B  THR*     3.7    26.3    +      -       +      +
    233B  SER      4.0     3.8    -      -       -      -
    234B  THR*     3.9    25.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 223 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203B  ASN*     3.6     5.2    -      -       -      -
    221B  CYS*     3.9     9.1    +      -       -      -
    222B  ARG*     1.3    75.5    -      -       -      +
    224B  CYS*     1.3    66.3    +      -       -      +
    232B  THR*     3.7     0.7    -      -       -      -
    233B  SER*     2.8    60.2    +      -       -      +
    235B  ILE*     5.1     3.5    -      -       -      +
    348B  LEU*     4.4     3.4    -      -       -      -
    349B  PRO*     3.2    10.7    -      -       -      +
    350B  HIS*     3.3    33.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 224 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202B  THR*     4.3    21.1    -      -       -      +
    203B  ASN*     3.3    12.3    +      -       -      +
    222B  ARG      4.4     0.2    +      -       -      -
    223B  SER*     1.3    79.5    -      -       -      +
    225B  LEU*     1.3    64.0    +      -       -      +
    226B  GLU      3.8     2.4    +      -       -      -
    227B  ASN*     5.0     8.3    -      -       -      +
    229B  SER      5.2     0.7    -      -       -      +
    230B  ARG      4.7     5.8    -      -       -      +
    231B  PRO      3.1    28.9    -      -       -      -
    232B  THR*     3.5    15.5    -      -       -      +
    349B  PRO*     4.4     7.0    -      -       -      -
    350B  HIS*     3.2    22.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 225 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224B  CYS*     1.3    72.3    -      -       -      +
    226B  GLU*     1.3    81.6    +      -       +      +
    227B  ASN*     2.6    18.2    +      -       -      -
    228B  SER*     2.7    22.3    +      -       -      -
    229B  SER*     3.8    18.1    +      -       -      +
    349B  PRO*     3.5    30.6    -      -       +      +
    350B  HIS*     4.2    10.5    -      -       -      +
    352B  GLY*     6.2     0.7    -      -       -      -
    353B  VAL*     3.8    24.0    -      -       +      -
----------------------------------------------------------
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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
------------------------------------------------------------
  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