Contacts of the strand formed by residues 832 - 837 (chain E) in PDB entry 3BWE
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 LYS 832 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603D SER* 3.4 41.9 + - - +
630D GLY 5.8 1.1 - - - -
632D LYS* 6.1 0.7 - - - +
803E SER* 3.5 22.8 + - - +
804E LYS 2.9 14.4 + - - +
805E ARG* 3.4 15.8 + - + +
806E ALA 2.7 29.6 + - - +
827E ARG* 5.6 0.2 - - - -
830E GLY* 3.8 8.3 - - - +
831E ILE* 1.3 77.5 - - - +
833E VAL* 1.3 58.6 + - - +
834E THR* 5.3 0.5 + - - -
867E TYR* 5.5 0.7 - - - -
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Residues in contact with VAL 833 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806E ALA* 3.2 7.9 - - + +
808E VAL* 3.4 32.5 - - + -
823E VAL* 4.1 19.5 - - + +
826E MSE 3.7 18.6 - - + -
827E ARG* 3.1 43.8 + - + +
831E ILE* 3.1 24.4 + - + -
832E LYS* 1.3 74.3 - - - +
834E THR* 1.3 69.5 + - - +
835E VAL 4.4 0.7 - - - +
855E ASP* 3.7 1.2 - - - +
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Residues in contact with THR 834 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805E ARG* 5.2 3.8 + - - -
806E ALA 2.9 13.8 + - - -
807E LEU* 3.7 7.0 - - + +
808E VAL 2.9 26.3 + - - -
832E LYS 5.3 0.5 + - - -
833E VAL* 1.3 75.9 + - - +
835E VAL* 1.3 69.3 + - - +
836E ALA* 3.2 3.8 + - + -
855E ASP* 3.4 13.2 - - + +
856E ALA* 4.8 7.4 - - + -
861E ALA* 3.9 27.8 - - + -
864E GLU* 5.9 2.9 - - + +
867E TYR* 4.4 13.8 + - - +
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Residues in contact with VAL 835 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808E VAL* 3.6 13.5 - - + -
810E LEU* 4.2 31.6 - - + -
819E THR* 4.8 4.7 - - - +
823E VAL* 4.0 26.2 - - + -
827E ARG* 3.7 14.4 - - - +
833E VAL* 4.5 0.7 - - + -
834E THR* 1.3 71.4 - - - +
836E ALA* 1.3 58.9 + - - +
852E ILE* 4.7 8.5 - - + -
853E CYS 5.2 1.1 - - - +
854E PRO* 3.4 8.6 - - + +
855E ASP* 2.6 55.6 + - - +
856E ALA 3.4 4.0 + - - -
1050F VAL* 5.7 6.5 - - + -
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Residues in contact with ALA 836 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807E LEU* 3.8 10.5 - - + -
808E VAL 2.6 16.3 + - - +
809E ILE* 3.5 4.0 - - - +
810E LEU* 2.8 27.2 + - - -
834E THR* 3.2 1.5 + - + +
835E VAL* 1.3 72.9 - - - +
837E GLY* 1.3 63.6 + - - +
838E LEU 3.2 0.9 + - - -
854E PRO* 4.3 0.4 - - - -
856E ALA 3.0 11.0 - - - +
857E SER 3.8 12.1 - - - +
858E LEU* 3.8 15.0 - - + +
861E ALA* 3.8 15.5 - - + -
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Residues in contact with GLY 837 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810E LEU* 3.3 9.9 - - - -
836E ALA* 1.3 69.9 - - - +
838E LEU* 1.3 64.9 + - - +
839E ALA 3.3 2.7 - - - -
840E GLY 2.9 24.9 + - - +
844E VAL* 4.3 4.5 - - - -
854E PRO* 3.5 21.1 - - - +
856E ALA 2.9 11.3 + - - -
858E LEU 3.0 16.4 + - - -
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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