Contacts of the helix formed by residues 4907 - 4922 (chain F) in PDB entry 6X34
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 TYR4907 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4856F PHE* 4.7 37.3 - + + -
4857F PHE* 4.8 10.5 - + + -
4859F LYS* 5.9 5.4 - - - -
4860F PHE* 4.7 7.2 - + + -
4905F ASP 3.3 2.2 + - - -
4906F GLU* 1.3 79.5 - - + +
4908F GLU* 1.3 63.2 + - - +
4909F LEU 3.6 1.3 - - - -
4910F TYR* 3.9 30.3 - + + +
4911F ARG* 3.2 22.2 + - - +
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Residues in contact with GLU4908 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4860F PHE* 6.3 0.2 - - - -
4902F PRO* 5.3 11.3 - - - +
4904F GLY 3.4 22.4 - - - +
4905F ASP* 3.5 13.6 + - - +
4906F GLU 3.2 1.0 - - - -
4907F TYR* 1.3 78.6 - - - +
4909F LEU* 1.3 64.8 + - - +
4911F ARG* 3.4 3.1 + - - +
4912F VAL* 3.3 26.5 + - - +
4882H LEU* 6.3 0.2 - - - -
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Residues in contact with LEU4909 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4908F GLU* 1.3 77.1 - - - +
4910F TYR* 1.3 64.4 + - - +
4912F VAL* 3.4 8.3 + - - +
4913F VAL* 3.3 25.2 + - - +
4882H LEU* 5.4 10.5 - - + -
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Residues in contact with TYR4910 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4852F VAL* 5.9 2.1 - - - +
4856F PHE* 4.9 23.2 - + - -
4857F PHE* 3.7 29.6 - + - -
4907F TYR* 3.8 30.4 + + + +
4908F GLU 3.2 0.6 - - - -
4909F LEU* 1.3 80.6 - - - +
4911F ARG* 1.3 58.9 + - - +
4913F VAL* 3.3 23.0 - - + +
4914F PHE* 3.3 15.4 + - + +
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Residues in contact with ARG4911 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4857F PHE* 4.1 15.7 - - + -
4860F PHE* 4.1 24.5 - - + -
4902F PRO* 5.3 9.6 - - + -
4907F TYR 3.2 19.1 + - - +
4908F GLU* 3.9 4.0 - - - +
4909F LEU 3.3 0.2 - - - -
4910F TYR* 1.3 75.8 - - - +
4912F VAL* 1.3 63.9 + - - +
4914F PHE* 3.6 5.4 + - + +
4915F ASP* 3.3 22.2 + - - +
4886H TYR* 4.6 2.0 + - - -
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Residues in contact with VAL4912 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4902F PRO* 5.2 13.9 - - + -
4908F GLU 3.3 16.3 + - - +
4909F LEU* 3.7 10.1 - - - +
4910F TYR 3.3 0.8 - - - -
4911F ARG* 1.3 76.5 - - - +
4913F VAL* 1.3 66.9 + - + +
4914F PHE 3.3 0.2 + - - -
4915F ASP 3.4 1.9 + - - -
4916F ILE* 3.2 29.3 + - + +
4882H LEU* 3.8 39.9 - - + -
4886H TYR* 3.5 38.1 - - + -
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Residues in contact with VAL4913 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4909F LEU 3.3 12.4 + - - +
4910F TYR* 3.3 28.3 - - + +
4912F VAL* 1.3 79.7 - - - +
4914F PHE* 1.3 62.1 + - - +
4916F ILE* 3.3 10.3 + - + +
4917F THR* 3.2 28.8 + - + +
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Residues in contact with PHE4914 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4849F TYR* 3.5 47.1 - + + -
4852F VAL* 4.2 13.9 - - + -
4853F ALA* 5.3 0.7 - - + -
4857F PHE* 3.5 37.5 - + + -
4861F TYR* 4.4 15.7 - - - -
4884F HIS* 6.2 0.2 - + - -
4895F ILE* 4.5 14.8 - - + -
4899F ILE* 6.5 0.2 - - + -
4910F TYR* 3.3 18.8 + + + +
4911F ARG* 3.7 9.0 - - + +
4912F VAL 3.2 0.4 - - - -
4913F VAL* 1.3 83.5 - - - +
4915F ASP* 1.3 63.2 + - + +
4917F THR* 3.3 9.7 - - + +
4918F PHE* 3.1 36.1 + + + +
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Residues in contact with ASP4915 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4895F ILE* 4.1 22.2 + - + +
4896F GLY* 5.1 2.9 - - - +
4899F ILE* 5.6 1.1 - - + -
4911F ARG 3.3 8.3 + - - +
4913F VAL 3.4 0.2 - - - -
4914F PHE* 1.3 80.9 - - + +
4916F ILE* 1.3 61.5 + - - +
4918F PHE* 3.7 9.0 - - - +
4919F PHE* 3.0 28.9 + - - +
4886H TYR* 3.6 34.8 - - + +
4890H ARG* 5.5 2.0 - - - +
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Residues in contact with ILE4916 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4912F VAL* 3.2 20.6 + - + +
4913F VAL* 3.6 15.5 - - + +
4914F PHE 3.2 0.6 - - - -
4915F ASP* 1.3 78.3 - - - +
4917F THR* 1.3 61.9 + - - +
4919F PHE* 3.3 6.7 + - + +
4920F PHE* 3.1 51.2 + - + -
4885H MET* 4.1 21.1 - - + +
4886H TYR* 3.7 40.8 - - + +
4889H VAL* 5.5 1.8 - - + -
4890H ARG* 5.0 8.3 - - + +
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Residues in contact with THR4917 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4849F TYR* 3.6 18.1 + - + +
4913F VAL* 3.2 21.0 + - + +
4914F PHE* 3.3 15.9 - - + +
4916F ILE* 1.3 78.1 - - - +
4918F PHE* 1.3 63.0 + - - +
4919F PHE 3.3 0.2 - - - -
4920F PHE* 3.7 9.4 - - - -
4921F PHE* 3.1 47.3 + - - +
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Residues in contact with PHE4918 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4846F VAL* 4.5 13.9 - - + -
4849F TYR* 3.8 41.1 - + + -
4884F HIS* 5.3 13.2 - + + -
4888F GLY* 5.3 8.1 - - - -
4894F GLY* 4.8 4.3 - - - -
4895F ILE* 3.7 52.0 - - + -
4914F PHE* 3.1 30.7 + + + +
4915F ASP* 3.7 7.2 - - - +
4916F ILE 3.2 0.4 - - - -
4917F THR* 1.3 78.9 - - - +
4919F PHE* 1.3 59.5 + - - +
4921F PHE* 5.2 0.2 - - - -
4922F VAL* 3.2 57.7 + - + +
4923F ILE* 3.6 1.6 - - + +
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Residues in contact with PHE4919 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4892F GLY 4.2 8.7 - - - -
4894F GLY* 4.5 10.8 - - - -
4915F ASP 3.0 18.0 + - - +
4916F ILE* 3.3 6.0 + - + +
4918F PHE* 1.3 78.0 - - - +
4920F PHE* 1.3 83.1 + + - +
4923F ILE* 3.4 41.8 - - + +
4924F VAL* 3.4 19.8 - - + +
4889H VAL* 3.2 38.4 - - + -
4890H ARG* 3.5 35.4 - - + -
4892H GLY* 5.7 2.2 - - - -
4927H LEU* 4.7 15.0 - - + -
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Residues in contact with PHE4920 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4916F ILE* 3.1 39.9 + - + +
4917F THR* 4.0 9.2 - - - +
4918F PHE 3.3 0.4 - - - -
4919F PHE* 1.3 104.4 - + - +
4921F PHE* 1.3 65.2 + - + +
4924F VAL* 3.2 27.8 - - + +
4925F ILE* 3.4 11.3 - - - +
4839H VAL* 6.2 5.8 - - + -
4842H LEU* 5.3 9.2 - - + -
4885H MET* 4.2 17.7 - - + -
4889H VAL* 3.7 22.9 - - + -
4927H LEU* 6.0 1.8 - - + -
4930H ILE* 6.1 4.9 - - + -
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Residues in contact with PHE4921 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4849F TYR* 4.3 13.2 - + + +
4917F THR* 3.1 42.3 + - - +
4918F PHE* 4.6 1.3 - - - +
4920F PHE* 1.3 83.9 - - + +
4922F VAL* 1.3 68.5 + - + +
4923F ILE 3.3 0.2 - - - -
4925F ILE* 3.0 24.3 + - + +
4926F LEU* 2.9 24.3 + - - +
4828H VAL* 4.8 22.7 - - + -
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Residues in contact with VAL4922 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4842F LEU* 5.4 3.9 - - + +
4845F VAL* 4.0 29.8 - - + -
4846F VAL* 4.4 10.8 - - + -
4849F TYR* 4.9 4.5 - - + -
4888F GLY 6.4 1.6 - - - -
4889F VAL* 6.3 3.8 - - + -
4918F PHE* 3.2 50.5 + - + +
4921F PHE* 1.3 83.3 - - + +
4923F ILE* 1.3 72.2 + - + +
4926F LEU* 3.3 23.5 - - + +
4927F LEU* 3.4 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