Contacts of the strand formed by residues 4796 - 4799 (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 MET4796 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4755E LEU* 5.9 0.4 - - - +
4758E LYS* 3.6 37.9 - - + +
4761E GLN* 3.6 27.4 + - + +
4762E TYR* 3.5 32.5 - - + -
4765E MET* 3.4 27.1 - - + +
4772E ASN* 4.1 5.0 + - - -
4794E HIS 4.3 0.8 + - - -
4795E THR* 1.3 81.1 - - - +
4797E VAL* 1.3 61.1 + - - +
4860E VAL* 5.1 6.7 - - + -
4862E PHE* 5.6 0.4 - - + -
4869E ILE* 3.7 27.6 - - + -
4870E ILE 4.0 1.1 - - - -
4871E SER* 3.6 17.7 - - - +
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Residues in contact with VAL4797 (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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4765E MET* 3.6 3.1 - - - +
4769E TRP* 3.6 10.2 - - - +
4772E ASN* 3.0 32.7 + - + +
4773E VAL* 3.7 26.5 - - + -
4791E ILE* 4.1 29.2 - - + -
4795E THR* 3.5 14.4 - - - +
4796E MET* 1.3 72.8 - - - +
4798E ILE* 1.3 65.1 + - + +
4855E CYS* 4.7 8.1 - - - -
4870E ILE* 2.8 21.0 + - + +
4871E SER 4.4 0.7 - - - -
4872E SER* 4.0 12.6 - - - +
4882E LEU* 3.9 14.4 - - + -
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Residues in contact with ILE4798 (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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4765E MET* 3.7 13.1 - - - -
4769E TRP* 3.7 38.1 - - + -
4773E VAL* 4.3 5.2 - - + -
4785E LEU* 4.0 15.9 - - + -
4796E MET 3.8 0.4 - - - -
4797E VAL* 1.3 89.3 - - + +
4799E GLU* 1.3 69.1 + - - +
4843E PRO* 4.1 5.4 - - + -
4844E ALA* 3.7 38.1 - - + +
4847E ILE* 4.1 10.1 - - + -
4869E ILE* 3.9 1.2 - - - +
4870E ILE* 2.9 40.4 + - + +
4882E LEU* 5.4 0.2 - - + -
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Residues in contact with GLU4799 (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* 2.6 28.5 + - - -
4765E MET* 3.9 10.4 - - + -
4766E LYS* 2.6 26.2 + - + +
4769E TRP* 5.7 0.4 - - - -
4798E ILE* 1.3 81.2 - - - +
4800E TYR* 1.3 65.6 + - - +
4801E ILE* 3.3 26.3 + - + +
4842E GLY* 5.8 0.9 - - - -
4844E ALA* 3.5 12.9 + - - +
4867E LYS* 3.3 24.7 + - - +
4868E ILE 3.4 14.8 - - - +
4869E ILE* 3.9 13.5 - - + -
341F GLU* 5.0 0.7 - - - -
342F ASN* 3.4 19.7 + - - -
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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