Contacts of the strand formed by residues 851 - 855 (chain E) in PDB entry 2BT4
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 VAL 851 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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808E PRO* 4.0 5.9 - - - +
809E ILE* 3.3 12.6 - - + +
811E ILE* 3.8 23.3 - - + -
837E GLU* 4.9 1.6 - - + +
840E CYS* 3.6 13.9 - - + +
841E VAL* 3.7 31.9 - - + +
844E ALA* 3.5 23.3 - - + -
850E THR* 1.3 81.4 - - - +
852E ASP* 1.3 60.7 + - - +
853E PHE* 4.3 17.9 + - + -
942E VAL* 5.0 1.6 - - + -
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Residues in contact with ASP 852 (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 PRO* 4.3 7.9 - - + +
809E ILE 2.9 7.4 + - - +
810E MET* 3.5 5.7 - - - +
811E ILE 2.9 23.4 + - - +
851E VAL* 1.3 72.1 - - - +
853E PHE* 1.3 59.1 + - - +
854E ARG* 2.9 41.7 + - - +
868E GLU* 4.7 0.2 - - - +
873E HIS* 2.9 37.9 + - + +
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Residues in contact with PHE 853 (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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811E ILE* 3.4 36.3 - - + -
813E ASN* 3.4 20.2 - - - -
833E LEU* 3.8 42.4 - - + -
836E VAL* 3.9 13.7 - - + -
837E GLU* 3.7 62.1 + - + +
840E CYS* 4.0 8.5 - - + -
851E VAL* 3.9 8.8 - - + +
852E ASP* 1.3 72.6 + - - +
854E ARG* 1.3 70.4 + - - +
855E GLN* 5.5 0.2 - - + -
938E TYR* 4.7 0.2 - + - -
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Residues in contact with ARG 854 (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 MET* 3.7 14.7 - - - +
811E ILE 2.8 7.6 + - - +
812E LEU* 3.6 4.2 - - + -
813E ASN* 2.9 31.7 + - - -
852E ASP* 2.9 41.5 + - - +
853E PHE* 1.3 84.8 - - - +
855E GLN* 1.3 61.2 + - - +
865E TRP* 3.1 60.2 - - + +
868E GLU* 2.8 42.6 + - - -
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Residues in contact with GLN 855 (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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813E ASN* 3.2 17.0 - - + +
814E GLY 2.9 22.2 + - - +
816E ASN 3.7 1.0 - - - +
817E LEU* 4.4 0.2 - - + -
818E ASN* 3.5 31.3 + - - +
833E LEU* 3.7 31.9 - - + -
853E PHE* 5.5 0.4 - - + -
854E ARG* 1.3 76.3 - - - +
856E SER* 1.3 79.5 + - - +
857E ASN* 3.0 27.3 + - - +
861E GLU* 4.9 0.2 - - - +
865E TRP* 3.5 10.7 - - - -
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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
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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