Contacts of the helix formed by residues 4784 - 4799 (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 ASP4784 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4667F VAL* 5.8 8.5 - - + -
4780F VAL* 2.9 19.1 + - + +
4781F ILE* 3.4 15.5 + - + +
4782F PHE 4.5 0.2 - - - +
4783F THR* 1.3 78.4 - - - +
4785F ASN* 1.3 61.6 + - - +
4786F SER* 4.2 14.1 - - - +
4787F PHE* 4.1 6.0 - - + +
4788F LEU* 3.0 30.5 + - - +
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Residues in contact with ASN4785 (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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4783F THR 3.6 3.9 + - - +
4784F ASP* 1.3 74.0 - - - +
4786F SER* 1.3 71.6 + - - +
4788F LEU* 4.0 4.7 - - - +
4789F TYR* 3.1 23.4 + - - +
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Residues in contact with SER4786 (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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4659F TYR* 3.4 23.8 + - - -
4667F VAL* 4.7 11.6 - - - +
4784F ASP* 4.2 9.0 - - - +
4785F ASN* 1.3 84.3 + - - +
4787F PHE* 1.3 64.6 + - - +
4789F TYR* 3.4 13.3 + - - +
4790F LEU* 3.5 19.1 + - - +
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Residues in contact with PHE4787 (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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4656F ILE* 4.4 28.9 - - + -
4659F TYR* 4.0 31.8 + + + -
4660F ASN* 5.9 5.2 - - + -
4664F VAL* 4.9 3.4 - - + -
4781F ILE* 3.2 47.6 - - + +
4782F PHE* 4.0 28.9 - + - -
4784F ASP* 3.6 7.0 + - + +
4786F SER* 1.3 80.4 + - - +
4788F LEU* 1.3 62.0 + - - +
4790F LEU* 3.4 6.0 + - + +
4791F GLY* 2.9 28.7 + - - -
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Residues in contact with LEU4788 (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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4782F PHE 4.8 9.9 - - - +
4783F THR 5.6 0.4 - - - -
4784F ASP 3.0 20.2 + - - +
4785F ASN* 4.1 5.4 - - - +
4786F SER 3.3 0.2 - - - -
4787F PHE* 1.3 77.7 - - - +
4789F TYR* 1.3 59.9 + - - +
4791F GLY* 4.4 2.0 - - - +
4792F TRP* 2.9 30.8 + - - +
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Residues in contact with TYR4789 (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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4561F ARG* 4.7 6.7 - - - -
4785F ASN 3.1 18.8 + - - +
4786F SER* 3.7 6.5 - - - +
4787F PHE 3.2 0.4 - - - -
4788F LEU* 1.3 79.6 - - - +
4790F LEU* 1.3 78.2 + - + +
4792F TRP* 3.5 18.3 + + + +
4793F TYR* 3.6 11.1 + - - +
4813F ASP* 2.7 39.6 + - + +
4816F MET* 3.9 18.2 - - + +
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Residues in contact with LEU4790 (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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4561F ARG* 3.5 32.8 - - - +
4655F CYS* 3.8 27.1 - - + +
4656F ILE* 5.3 8.9 - - + +
4659F TYR* 4.9 23.1 - - + -
4786F SER 3.5 12.0 + - - +
4787F PHE* 3.4 9.5 + - + +
4788F LEU 3.4 0.2 - - - -
4789F TYR* 1.3 98.5 - - + +
4791F GLY* 1.3 61.2 + - - +
4793F TYR* 3.4 15.9 + - + +
4794F MET* 3.7 10.0 + - - +
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Residues in contact with GLY4791 (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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4656F ILE* 5.9 6.1 - - - -
4787F PHE* 2.9 22.7 + - - -
4788F LEU* 3.8 2.9 - - - -
4789F TYR 3.3 0.2 - - - -
4790F LEU* 1.3 76.1 - - - +
4792F TRP* 1.3 62.3 + - - +
4794F MET* 3.2 16.7 + - - +
4795F VAL* 3.3 14.2 + - - +
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Residues in contact with TRP4792 (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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4788F LEU 2.9 18.7 + - - +
4789F TYR* 3.9 14.4 - + + +
4790F LEU 3.3 0.2 - - - -
4791F GLY* 1.3 76.7 - - - +
4793F TYR* 1.3 73.2 + + + +
4795F VAL* 3.2 25.9 - - + +
4796F MET* 3.6 16.7 + - + +
4809F ALA* 4.1 35.0 - - + -
4810F HIS* 5.8 0.7 - + - -
4812F LEU* 6.0 3.1 - - + -
4813F ASP* 5.9 4.3 - - + -
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Residues in contact with TYR4793 (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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4561F ARG* 4.6 10.8 - - - +
4564F ALA* 3.8 30.1 + - + +
4568F ALA* 5.1 1.2 - - - +
4648F HIS* 2.4 45.2 + + - -
4652F ALA* 4.3 18.8 - - + -
4789F TYR 3.6 8.7 + - - +
4790F LEU* 3.4 13.4 + - + +
4791F GLY 3.2 0.6 - - - -
4792F TRP* 1.3 90.4 - + + +
4794F MET* 1.3 50.0 + - - +
4796F MET* 4.1 2.0 + - - -
4797F SER* 2.6 30.0 + - - -
4810F HIS* 3.4 38.1 + + + +
4813F ASP* 3.2 37.9 - - + +
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Residues in contact with MET4794 (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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4652F ALA* 4.9 11.4 - - + +
4653F PHE* 5.7 1.1 - - + +
4656F ILE* 3.9 27.6 - - + -
4790F LEU 3.7 7.4 + - - +
4791F GLY* 3.2 10.5 + - - +
4793F TYR* 1.3 76.8 - - - +
4795F VAL* 1.3 64.0 + - - +
4796F MET 3.3 1.8 - - - -
4797F SER* 3.2 20.7 + - - -
4798F LEU* 3.7 9.5 + - - +
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Residues in contact with VAL4795 (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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4791F GLY 3.3 10.8 + - - +
4792F TRP* 3.2 34.1 - - + +
4794F MET* 1.3 78.4 - - - +
4796F MET* 1.3 61.1 + - + +
4797F SER 3.5 0.3 + - - -
4798F LEU* 3.6 11.8 + - - +
4799F LEU* 3.4 22.6 - - + +
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Residues in contact with MET4796 (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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4792F TRP* 3.6 25.7 + - + +
4793F TYR* 4.4 1.1 - - - +
4794F MET 3.3 0.6 - - - -
4795F VAL* 1.3 81.0 - - + +
4797F SER* 1.3 63.4 - - - +
4798F LEU 3.3 0.2 - - - -
4799F LEU* 3.3 21.5 + - + +
4800F GLY* 3.6 7.3 + - - -
4806F PHE* 4.7 12.2 - - + +
4809F ALA* 5.3 6.5 - - + -
4810F HIS* 3.8 25.5 + - + +
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Residues in contact with SER4797 (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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4648F HIS* 4.3 10.5 - - - -
4649F THR* 3.6 36.0 - - - +
4652F ALA* 4.1 10.3 - - - +
4793F TYR 2.6 26.4 + - - -
4794F MET* 3.2 13.3 + - - -
4796F MET* 1.3 78.7 - - - +
4798F LEU* 1.3 61.7 + - - +
4800F GLY* 3.3 10.9 + - - -
4801F HIS* 3.8 5.5 - - - -
4807F PHE* 5.6 0.5 - - - -
4810F HIS* 4.1 12.5 + - - -
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Residues in contact with LEU4798 (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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4649F THR* 5.3 5.6 - - + -
4794F MET 3.7 7.4 + - - +
4795F VAL* 3.6 10.0 + - - +
4796F MET 3.3 0.8 - - - -
4797F SER* 1.3 80.4 - - - +
4799F LEU* 1.3 65.2 + - + +
4800F GLY 3.3 0.7 + - - -
4801F HIS* 3.6 27.6 + - + +
4802F TYR* 4.4 1.9 + - - +
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Residues in contact with LEU4799 (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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4795F VAL* 3.4 24.7 - - + +
4796F MET* 3.3 12.9 + - + +
4797F SER 3.2 0.8 - - - -
4798F LEU* 1.3 79.4 - - + +
4800F GLY* 1.3 63.2 + - - +
4801F HIS 3.3 0.2 - - - -
4802F TYR* 3.2 25.7 + - + +
4804F ASN 3.6 8.1 - - - +
4806F PHE* 4.1 46.7 - - + -
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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