Contacts of the helix formed by residues 4842 - 4847 (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 GLY4842 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4799E GLU 5.8 1.1 - - - -
4801E ILE* 3.4 26.8 + - - +
4841E GLY* 1.3 74.4 - - - -
4843E PRO* 1.3 68.3 - - - +
4844E ALA* 3.1 7.2 - - - +
4845E ARG* 2.9 37.6 + - - +
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Residues in contact with PRO4843 (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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4769E TRP* 3.6 35.7 - - + -
4773E VAL* 4.9 2.2 - - + -
4775E LEU* 4.6 13.0 - - + -
4785E LEU* 3.8 29.0 - - + +
4798E ILE* 4.1 8.5 - - + -
4842E GLY* 1.3 83.3 - - - +
4844E ALA* 1.3 61.3 + - - +
4845E ARG 3.0 1.1 - - - -
4846E TYR* 3.1 32.1 + - + +
340F ASP* 5.8 1.1 - - - +
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Residues in contact with ALA4844 (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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4785E LEU* 4.2 0.2 - - - -
4798E ILE* 3.7 24.7 - - + +
4799E GLU 3.5 25.4 - - - +
4800E TYR* 3.7 28.8 - - + +
4801E ILE 5.1 0.2 - - - +
4842E GLY 3.0 2.7 + - - +
4843E PRO* 1.3 77.7 - - - +
4845E ARG* 1.3 61.1 + - - +
4846E TYR 3.1 1.3 + - - -
4847E ILE* 3.3 31.9 + - + +
4870E ILE* 4.9 1.1 - - + -
4884E TYR* 5.2 1.0 + - - -
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Residues in contact with ARG4845 (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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4800E TYR* 3.7 17.1 + - + +
4825E TYR* 3.5 40.8 - - + -
4837E ALA* 3.8 35.3 + - + -
4838E THR 3.9 12.5 + - - -
4839E LEU 5.6 2.2 + - - -
4841E GLY* 3.1 26.8 + - - +
4842E GLY* 2.9 19.7 + - - +
4844E ALA* 1.3 78.4 - - - +
4846E TYR* 1.3 91.0 + - + +
4847E ILE 3.3 3.0 + - - +
5002E SAH 3.6 21.8 - - - +
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Residues in contact with TYR4846 (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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4775E LEU* 3.6 41.7 - - + -
4783E LEU* 3.4 39.3 - - + +
4784E GLY* 3.3 20.0 - - - -
4785E LEU 4.4 1.1 - - - -
4825E TYR* 3.6 21.4 + + - -
4843E PRO* 3.1 17.0 + - + +
4844E ALA 3.1 1.4 - - - -
4845E ARG* 1.3 115.5 + - + +
4847E ILE* 1.3 62.8 + - - +
4848E ASN 3.3 3.1 + - - -
5002E SAH 3.6 21.4 - - + +
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Residues in contact with ILE4847 (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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4785E LEU* 3.6 36.8 - - + +
4798E ILE* 4.1 5.2 - - + -
4844E ALA* 3.3 25.5 + - + +
4845E ARG 3.3 1.8 - - - +
4846E TYR* 1.3 76.4 - - - +
4848E ASN* 1.3 56.4 + - - +
4870E ILE* 4.0 31.4 - - + -
4882E LEU* 3.3 32.8 - - + +
4883E CYS* 3.9 0.9 - - - -
4884E TYR* 3.5 30.6 + - + -
4886E TYR* 2.6 27.8 + - - -
5002E SAH 3.9 2.1 - - - +
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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