Contacts of the helix formed by residues 4807 - 4818 (chain C) 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 ASN4807 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4806C ARG* 1.3 74.1 - - - +
4808C GLU* 1.3 66.2 + - + +
4810C ALA* 3.0 10.9 + - - +
4811C ASN* 2.9 33.2 + - - +
4828C ARG* 2.8 35.0 + - - +
4831C ASN 2.8 23.4 + - - -
4832C ASP* 3.5 19.3 + - - +
4834C VAL* 3.9 2.8 - - - +
2M ARG* 5.5 1.7 + - - +
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Residues in contact with GLU4808 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4806C ARG* 3.4 2.7 - - + +
4807C ASN* 1.3 79.5 - - + +
4809C VAL* 1.3 64.8 + - - +
4811C ASN* 3.2 27.1 + - - +
4812C ARG* 3.1 27.2 + - - +
352D PHE* 3.7 24.4 - - + -
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Residues in contact with VAL4809 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4805C ILE* 3.9 20.9 - - + -
4806C ARG* 3.4 20.2 - - + +
4807C ASN 3.2 0.8 - - - -
4808C GLU* 1.3 78.2 - - - +
4810C ALA* 1.3 52.5 + - - +
4812C ARG* 3.1 6.3 + - - +
4813C LYS* 2.8 53.9 + - + +
345D TYR* 4.1 15.3 - - + -
347D GLU* 3.6 33.7 - - + +
351D GLU* 4.3 10.3 - - + +
352D PHE* 3.8 17.9 - - + -
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Residues in contact with ALA4810 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4805C ILE* 3.6 23.1 - - + +
4806C ARG 2.9 12.7 + - - +
4807C ASN* 3.0 10.7 + - - +
4809C VAL* 1.3 77.6 - - - +
4811C ASN* 1.3 58.5 + - - +
4814C GLU* 2.9 31.8 + - - +
4826C MET* 3.7 18.0 - - - +
4828C ARG* 5.6 1.3 - - - +
4834C VAL* 4.2 16.4 - - + -
2M ARG* 5.6 4.7 - - - +
3M THR* 5.5 2.2 - - + -
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Residues in contact with ASN4811 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4807C ASN* 2.9 16.5 + - - +
4808C GLU* 3.2 39.7 + - - +
4809C VAL 3.2 0.2 - - - -
4810C ALA* 1.3 78.9 - - - +
4812C ARG* 1.3 66.4 + - + +
4814C GLU* 3.6 7.5 + - - +
4815C LYS* 3.2 28.1 + - - +
2M ARG* 3.2 41.6 + - - +
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Residues in contact with ARG4812 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4808C GLU 3.1 16.5 + - - +
4809C VAL* 3.1 9.8 + - + +
4811C ASN* 1.3 79.7 + - + +
4813C LYS* 1.3 65.8 + - + +
4815C LYS* 3.4 10.9 + - - +
4816C LEU* 3.1 21.6 + - - +
351D GLU* 4.3 17.5 - - + +
352D PHE* 3.1 39.7 + - + +
353D ASP 4.8 2.7 + - - -
354D ILE* 3.8 30.8 - - - +
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Residues in contact with LYS4813 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4805C ILE* 4.5 8.5 - - + -
4809C VAL* 2.8 34.7 + - + +
4812C ARG* 1.3 73.1 - - + +
4814C GLU* 1.3 52.2 + - - +
4816C LEU* 3.0 17.4 + - + +
4817C TYR* 2.5 69.2 + - + +
4826C MET* 3.6 18.8 - - + -
4836C ASP* 4.9 2.9 - - - -
4839C LEU* 5.0 8.9 - - - +
345D TYR* 2.9 43.8 + - - -
348D ARG* 5.3 2.8 - - - +
351D GLU* 3.7 10.0 + - - -
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Residues in contact with GLU4814 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4810C ALA 2.9 18.5 + - - +
4811C ASN* 3.8 9.1 - - - +
4812C ARG 3.2 0.2 - - - -
4813C LYS* 1.3 76.6 - - - +
4815C LYS* 1.3 57.6 + - + +
4817C TYR* 3.6 7.5 - - + +
4818C GLU* 2.6 59.6 + - + +
4824C VAL* 6.2 0.4 - - + +
4826C MET* 4.0 11.0 - - + +
2M ARG* 3.3 50.2 + - - +
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Residues in contact with LYS4815 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4811C ASN 3.2 17.7 - - - +
4812C ARG* 3.9 11.0 - - - +
4813C LYS 3.3 0.6 - - - -
4814C GLU* 1.3 80.7 - - + +
4816C LEU* 1.3 57.1 + - - +
4818C GLU* 2.9 37.8 + - - +
4819C SER* 3.2 9.2 + - - -
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Residues in contact with LEU4816 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4812C ARG 3.1 13.2 + - - +
4813C LYS* 3.0 25.7 + - + +
4815C LYS* 1.3 74.2 - - - +
4817C TYR* 1.3 62.3 + - + +
4818C GLU 2.7 17.9 - - - +
4819C SER* 3.8 3.8 + - - +
4820C GLN* 3.1 43.3 - - - +
348D ARG* 6.1 4.0 - - - +
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Residues in contact with TYR4817 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4813C LYS* 2.5 44.4 + - + +
4814C GLU* 3.7 6.1 - - - +
4816C LEU* 1.3 78.7 - - + +
4818C GLU* 1.3 65.3 + - - +
4820C GLN* 3.7 5.4 + - - +
4821C ASN 3.6 2.9 + - - -
4822C ARG* 3.2 45.2 + - + +
4823C GLY 4.7 10.3 - - - +
4826C MET* 3.5 21.1 - - + -
4836C ASP* 2.4 33.0 + - - -
4838C THR* 3.2 38.8 - - + -
4839C LEU* 3.8 31.1 - - + +
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Residues in contact with GLU4818 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4814C GLU* 2.6 46.4 + - + +
4815C LYS* 2.9 30.3 - - - +
4816C LEU 2.7 14.7 - - - +
4817C TYR* 1.3 68.0 - - - +
4819C SER* 1.3 73.7 + - - +
4820C GLN 2.9 7.3 + - - -
4821C ASN* 4.4 4.3 - - - +
4822C ARG 5.0 1.3 - - - +
4823C GLY 6.3 0.9 - - - +
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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