Contacts of the strand formed by residues 4865 - 4872 (chain E) in PDB entry 5F6K
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 GLY4865 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4804E ILE* 5.9 3.1 - - - -
4862E PHE* 3.0 31.9 + - - +
4863E GLU 3.1 3.2 + - - -
4864E ARG* 1.3 81.5 - - - +
4866E HIS* 1.3 69.7 - - - -
4867E LYS* 3.8 10.9 + - - +
344F GLU* 6.0 1.3 - - - -
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Residues in contact with HIS4866 (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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4804E ILE* 4.2 10.7 - - - +
4829E MET* 3.7 32.7 - - + +
4830E ASP* 3.6 24.6 + - - -
4833E HIS* 5.5 4.6 + + - -
4859E VAL* 3.9 18.2 - - + -
4860E VAL 3.8 5.4 - - - -
4861E THR* 4.0 30.4 + - + -
4862E PHE 4.7 3.0 + - - -
4865E GLY* 1.3 77.2 - - - -
4867E LYS* 1.3 70.1 + - - +
342F ASN* 3.6 10.7 + - - -
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Residues in contact with LYS4867 (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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4762E TYR* 3.9 25.6 + - + +
4799E GLU* 3.3 18.5 + - - +
4829E MET* 5.3 0.2 - - - -
4858E GLU 3.4 2.4 - - - +
4859E VAL* 3.5 3.9 - - - +
4860E VAL* 3.1 47.1 + - + +
4862E PHE* 4.8 10.5 - - + -
4864E ARG* 4.6 16.4 + - - +
4865E GLY* 4.0 13.6 - - - +
4866E HIS* 1.3 83.8 + - - +
4868E ILE* 1.3 64.2 + - - +
4869E ILE* 3.8 13.2 - - + -
341F GLU* 4.8 8.7 + - - +
342F ASN* 3.7 26.7 + - - +
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Residues in contact with ILE4868 (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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4799E GLU* 3.4 7.3 + - - +
4800E TYR* 2.8 55.9 + - + +
4827E PHE* 3.6 40.2 - - + -
4829E MET* 3.7 17.5 - - + -
4835E ILE* 3.6 24.7 - - + +
4857E ALA* 4.5 3.8 - - + -
4858E GLU 3.8 2.0 - - - +
4859E VAL* 3.6 32.3 - - + +
4867E LYS* 1.3 73.9 - - - +
4869E ILE* 1.3 61.7 + - - +
4870E ILE* 4.5 11.4 - - + -
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Residues in contact with ILE4869 (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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4762E TYR* 3.5 37.5 - - + -
4765E MET* 3.9 9.6 - - + -
4796E MET* 3.7 41.1 - - + -
4798E ILE 3.9 4.0 - - - +
4799E GLU* 3.9 7.2 - - + -
4856E VAL 3.5 2.6 - - - +
4857E ALA* 3.6 0.9 - - - -
4858E GLU* 3.0 37.1 + - + +
4860E VAL* 3.7 29.8 - - + -
4867E LYS* 4.0 4.5 - - + -
4868E ILE* 1.3 80.6 - - - +
4870E ILE* 1.3 66.7 + - - +
4871E SER* 3.7 9.8 + - - +
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Residues in contact with ILE4870 (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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4796E MET* 3.8 0.5 - - - -
4797E VAL* 2.8 30.4 + - + +
4798E ILE* 2.9 28.2 + - + +
4800E TYR* 4.9 11.7 - - + +
4827E PHE* 5.4 0.2 - - + -
4844E ALA* 4.9 2.9 - - + -
4847E ILE* 4.0 25.4 - - + -
4855E CYS* 3.7 31.4 - - + -
4856E VAL 3.4 4.0 - - - +
4857E ALA* 3.6 27.8 - - + -
4868E ILE* 4.5 10.1 - - + -
4869E ILE* 1.3 73.5 - - - +
4871E SER* 1.3 60.3 - - - +
4882E LEU* 5.9 0.9 - - + -
4884E TYR* 4.2 22.0 - - + -
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Residues in contact with SER4871 (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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4794E HIS* 4.9 3.1 - - - -
4795E THR 3.2 13.2 - - - -
4796E MET* 3.6 26.0 + - - +
4855E CYS* 3.2 7.3 - - - -
4856E VAL* 2.8 43.3 + - - +
4858E GLU* 6.1 2.3 - - - +
4869E ILE* 3.7 7.1 + - - +
4870E ILE* 1.3 75.0 - - - +
4872E SER* 1.3 65.4 + - - +
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Residues in contact with SER4872 (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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4791E ILE* 4.1 10.5 - - - -
4792E GLU 2.7 26.0 + - - -
4794E HIS* 2.8 32.1 + - - -
4795E THR* 3.0 17.4 + - - -
4797E VAL* 4.0 3.4 - - - +
4854E ASN 3.5 5.6 - - - -
4855E CYS* 4.2 2.9 - - - -
4856E VAL* 5.1 1.4 - - - +
4871E SER* 1.3 73.5 - - - +
4873E SER* 1.3 58.8 + - - +
4874E ARG 3.3 16.6 - - - -
4876E ILE* 3.8 15.9 - - - -
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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