Contacts of the strand formed by residues 119 - 130 (chain A) in PDB entry 4LL1


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 GLY 119 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  LYS      3.5     6.3    -      -       -      -
     54A  VAL*     4.5     4.0    -      -       -      -
    114A  PHE*     3.0    29.5    +      -       -      +
    115A  LYS*     3.6     6.1    -      -       -      -
    116A  GLY*     2.8    29.3    +      -       -      +
    118A  TYR*     1.3    80.9    -      -       -      +
    120A  SER*     1.3    64.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 120 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  VAL      4.0     0.6    -      -       -      +
     52A  ALA*     3.2     6.8    -      -       -      +
     53A  LYS*     2.9    60.3    +      -       -      +
    111A  GLY      5.4     0.2    -      -       -      -
    114A  PHE      3.9     3.6    +      -       -      +
    115A  LYS*     5.0     3.4    -      -       -      +
    118A  TYR      5.2     0.3    +      -       -      -
    119A  GLY*     1.3    75.9    -      -       -      -
    121A  VAL*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 121 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  VAL      3.6     7.6    -      -       -      +
     52A  ALA*     4.5     3.1    -      -       +      -
    110A  LEU      4.0     6.3    -      -       -      +
    111A  GLY      3.9    22.7    -      -       -      +
    112A  THR*     4.5    13.5    -      -       -      +
    114A  PHE      6.0     0.2    -      -       -      +
    115A  LYS*     5.8     7.3    -      -       +      +
    120A  SER*     1.3    76.5    -      -       -      +
    122A  ASP*     1.3    69.5    +      -       -      +
    123A  TYR*     3.7    27.1    -      -       +      +
    145A  VAL*     4.6    10.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 122 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  CYS      3.5     1.7    -      -       -      +
     50A  GLY*     3.1     5.7    -      -       -      -
     51A  VAL*     2.9    42.5    +      -       +      +
    121A  VAL*     1.3    81.0    -      -       -      +
    123A  TYR*     1.3    61.1    +      -       -      +
    124A  TRP*     3.7    18.2    +      -       -      +
    140A  LYS*     5.4     1.8    +      -       -      -
    142A  ASN*     3.4    22.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 123 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49A  CYS      3.2     2.2    -      -       -      -
     50A  GLY*     3.6    23.8    -      -       -      -
     51A  VAL      4.4     0.2    -      -       -      -
     69A  TYR*     3.4    19.1    -      -       -      +
     70A  LEU*     4.0     9.0    -      -       +      -
    105A  LEU*     3.7    20.2    -      -       +      -
    106A  PRO*     5.3     0.4    -      -       +      +
    110A  LEU*     2.7    38.7    +      -       +      +
    121A  VAL*     3.7    20.2    -      -       +      +
    122A  ASP*     1.3    88.3    +      -       -      +
    124A  TRP*     1.3    60.4    +      -       -      +
    142A  ASN*     3.2     9.6    +      -       -      +
    143A  PHE*     2.8    75.7    +      +       +      +
    145A  VAL*     3.9    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 124 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  LEU*     3.7    24.0    -      -       +      -
     48A  ALA*     3.2     4.0    -      -       -      +
     49A  CYS*     2.8    65.7    +      -       +      +
     51A  VAL*     5.9     4.7    -      -       +      +
    122A  ASP*     3.7    31.3    +      -       -      +
    123A  TYR*     1.3    76.1    -      -       -      +
    125A  VAL*     1.3    62.8    +      -       -      +
    126A  LYS*     3.1    53.4    -      -       +      -
    140A  LYS*     3.5    34.1    -      -       +      +
    141A  LYS      3.5    14.4    -      -       -      +
    142A  ASN*     3.8    10.1    -      -       -      +
    143A  PHE*     3.8     5.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 125 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  VAL*     4.2    21.8    -      -       +      +
     14A  PHE*     3.8    29.6    -      -       +      -
     46A  ILE*     4.1    24.9    -      -       +      -
     47A  LEU      3.4     7.0    -      -       -      +
     48A  ALA*     4.3     1.6    -      -       +      -
    101A  PHE*     4.5     4.0    -      -       +      -
    103A  PHE*     4.1    21.5    -      -       +      -
    124A  TRP*     1.3    81.9    -      -       -      +
    126A  LYS*     1.3    74.2    +      -       -      +
    139A  THR      3.9     0.5    -      -       -      +
    140A  LYS*     3.3     1.9    -      -       -      -
    141A  LYS      2.9    32.4    +      -       -      +
    143A  PHE*     4.1     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 126 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  ILE*     3.2     5.4    -      -       -      +
     47A  LEU*     2.8    39.9    +      -       -      +
    124A  TRP*     3.1    43.3    -      -       +      -
    125A  VAL*     1.3    76.0    -      -       -      +
    127A  ALA*     1.3    58.7    +      -       -      +
    128A  PHE*     3.7    23.7    -      -       +      -
    138A  GLU*     2.8    29.8    -      -       +      +
    139A  THR      3.1     7.4    -      -       -      +
    140A  LYS*     3.9    31.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 127 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  PHE*     3.6    18.7    -      -       +      -
     12A  VAL*     4.1     8.8    -      -       +      +
     31A  VAL*     3.9    23.6    -      -       +      -
     44A  VAL*     5.1     0.4    -      -       +      -
     45A  ARG      3.1    10.5    -      -       -      +
     46A  ILE*     4.1     1.6    -      -       +      -
    125A  VAL      4.1     0.6    +      -       -      -
    126A  LYS*     1.3    73.2    -      -       -      +
    128A  PHE*     1.3    61.4    +      -       -      +
    138A  GLU*     3.3     7.3    -      -       -      +
    139A  THR*     2.9    43.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 128 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  PHE*     3.6     3.6    -      -       -      -
     43A  ALA      3.8     0.7    -      -       -      +
     44A  VAL*     3.2     8.5    -      -       -      +
     45A  ARG*     2.9    84.5    +      -       +      +
     46A  ILE      4.3     0.9    -      -       -      -
     47A  LEU*     3.6    37.0    -      -       +      -
    126A  LYS*     3.7    26.2    -      -       +      -
    127A  ALA*     1.3    75.4    -      -       -      +
    129A  LEU*     1.3    60.1    +      -       -      +
    130A  ASP*     4.1     2.0    +      -       -      +
    136A  THR*     4.8     8.7    -      -       -      +
    137A  GLN      3.4     6.3    -      -       -      +
    138A  GLU*     3.7    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 129 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ILE*     3.9    42.0    -      -       +      -
     10A  PHE*     3.5    20.5    -      -       +      -
     33A  VAL*     4.5    13.5    -      -       +      -
     41A  VAL*     3.7    29.2    -      -       +      -
     43A  ALA      3.7     0.7    -      -       -      -
     44A  VAL*     3.7    22.9    -      -       +      -
     91A  MET*     5.1     0.2    -      -       +      -
    128A  PHE*     1.3    71.4    -      -       -      +
    130A  ASP*     1.3    61.4    +      -       -      +
    131A  ARG*     4.0    16.0    +      -       +      +
    135A  PRO      4.6     0.7    -      -       -      +
    136A  THR*     3.4     4.9    -      -       -      -
    137A  GLN*     2.7    44.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 130 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  VAL*     3.8     2.9    -      -       -      +
     42A  LYS*     2.9    36.6    +      -       +      -
     43A  ALA*     2.9    29.8    +      -       +      +
     45A  ARG*     2.6    48.1    +      -       -      -
    128A  PHE*     4.4     1.3    -      -       -      +
    129A  LEU*     1.3    74.6    -      -       -      +
    131A  ARG*     1.3    64.7    +      -       -      +
    136A  THR*     3.0    26.7    -      -       +      +
----------------------------------------------------------
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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
------------------------------------------------------------
  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