Contacts of the helix formed by residues 4046 - 4067 (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 SER4046 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3985F VAL* 4.3 16.8 - - - -
3988F LEU* 5.5 6.5 - - - -
4042F MET 2.5 23.9 + - - -
4043F LEU* 3.3 12.7 - - - +
4045F GLU* 1.3 75.7 - - - +
4047F SER* 1.3 56.3 + - - +
4048F SER 3.3 2.7 - - - -
4049F ASN* 3.0 17.2 + - - +
4050F VAL* 2.7 49.8 + - - +
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Residues in contact with SER4047 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4043F LEU 2.6 23.5 + - - -
4044F VAL* 2.7 21.3 + - - +
4045F GLU 3.3 2.8 - - - -
4046F SER* 1.3 77.2 - - - +
4048F SER* 1.3 61.0 + - - +
4050F VAL* 3.4 20.1 - - - +
4051F GLU* 3.5 12.3 + - - +
4154F ARG* 6.1 0.2 - - - +
4161F LEU* 6.0 0.5 - - - +
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Residues in contact with SER4048 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4045F GLU 4.6 2.1 + - - -
4046F SER 3.3 0.4 - - - -
4047F SER* 1.3 78.7 - - - +
4049F ASN* 1.3 66.2 + - - +
4051F GLU* 4.1 8.0 + - - +
4052F MET* 3.4 23.2 + - - +
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Residues in contact with ASN4049 (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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3985F VAL* 4.8 8.6 - - - +
3988F LEU* 4.7 21.5 - - + +
3989F HIS* 3.2 38.0 + - - +
3992F ALA* 4.5 6.1 - - + +
4045F GLU 3.4 9.7 + - - -
4046F SER* 3.0 30.3 + - - +
4048F SER* 1.3 83.6 - - - +
4050F VAL* 1.3 65.1 + - + +
4051F GLU 3.2 1.6 - - - -
4052F MET* 3.3 18.8 + - - +
4053F ILE* 3.7 9.4 + - - +
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Residues in contact with VAL4050 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3988F LEU* 4.9 13.7 - - + -
4043F LEU* 5.0 14.1 - - + +
4046F SER* 2.7 42.7 + - - +
4047F SER* 3.4 15.5 - - - +
4049F ASN* 1.3 73.0 - - - +
4051F GLU* 1.3 61.1 + - + +
4053F ILE* 3.4 10.6 - - + +
4054F LEU* 3.0 32.7 + - + +
4158F PHE* 5.5 12.3 - - + -
4161F LEU* 6.0 4.7 - - + -
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Residues in contact with GLU4051 (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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4047F SER 3.5 14.2 + - - +
4048F SER* 4.2 7.4 - - - +
4049F ASN 3.2 1.0 - - - -
4050F VAL* 1.3 81.3 - - - +
4052F MET* 1.3 64.9 + - + +
4054F LEU* 4.1 4.9 - - - -
4055F LYS* 3.5 24.3 + - - +
4161F LEU* 4.9 17.9 - - + -
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Residues in contact with MET4052 (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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3992F ALA* 3.8 25.3 - - + +
3993F HIS* 5.7 9.9 - - + +
3996F MET* 4.6 31.8 - - + +
4048F SER 3.4 20.2 - - - +
4049F ASN* 3.3 9.4 + - - +
4050F VAL 3.2 0.8 - - - -
4051F GLU* 1.3 84.0 - - - +
4053F ILE* 1.3 57.3 + - - +
4055F LYS* 4.6 1.4 - - - +
4056F PHE* 3.2 20.6 + - - +
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Residues in contact with ILE4053 (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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3988F LEU* 5.6 11.9 - - + -
3991F PHE 5.7 3.1 - - - +
3992F ALA* 5.2 9.9 - - + -
3995F MET* 5.6 6.3 - - + -
4049F ASN 3.7 10.1 + - - +
4050F VAL* 3.4 19.7 - - + +
4052F MET* 1.3 77.8 - - - +
4054F LEU* 1.3 70.9 + - - +
4055F LYS 3.4 0.2 - - - -
4056F PHE* 3.4 25.8 - - + +
4057F PHE* 3.1 43.3 + - + +
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Residues in contact with LEU4054 (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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4050F VAL* 3.0 21.1 + - + +
4051F GLU* 4.5 4.7 - - - +
4053F ILE* 1.3 80.6 - - + +
4055F LYS* 1.3 57.5 + - - +
4057F PHE* 3.3 4.0 + - - +
4058F ASP* 2.8 38.3 + - - +
4161F LEU* 4.6 22.7 - - + +
4162F ALA* 5.1 9.0 - - + -
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Residues in contact with LYS4055 (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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4051F GLU 3.5 17.1 + - - +
4052F MET* 5.0 1.1 - - - +
4053F ILE 3.4 0.2 - - - -
4054F LEU* 1.3 76.6 - - - +
4056F PHE* 1.3 64.8 + - - +
4058F ASP* 3.9 8.1 - - - -
4059F MET* 3.2 27.0 + - - +
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Residues in contact with PHE4056 (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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3995F MET* 3.7 42.4 - - + -
3996F MET* 3.9 31.6 - - + -
3999F ALA* 4.6 6.1 - - + -
4052F MET 3.2 20.7 + - - +
4053F ILE* 3.2 18.5 + - + +
4054F LEU 3.2 1.0 - - - -
4055F LYS* 1.3 79.3 - - - +
4057F PHE* 1.3 82.4 + + - +
4059F MET* 4.5 1.3 - - - +
4060F PHE* 3.2 59.9 + + - -
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Residues in contact with PHE4057 (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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4012F LEU* 4.3 16.4 - - + -
4053F ILE* 3.1 30.4 + - + +
4054F LEU* 4.0 3.6 - - - +
4056F PHE* 1.3 105.1 - + - +
4058F ASP* 1.3 59.0 + - - +
4059F MET 3.2 2.0 - - - -
4060F PHE* 3.3 7.8 + + + +
4061F LEU* 2.7 38.5 + - + +
4131F ALA* 4.9 15.0 - - + -
4134F ILE* 3.6 47.3 - - + -
4135F GLY* 4.8 10.3 - - - -
4138F VAL* 5.0 8.3 - - + -
4165F ILE* 6.0 3.8 - - + -
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Residues in contact with ASP4058 (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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4054F LEU* 2.8 22.7 + - - +
4055F LYS* 4.3 5.8 - - - -
4057F PHE* 1.3 78.2 - - - +
4059F MET* 1.3 61.6 + - - +
4061F LEU* 4.0 6.9 - - - +
4062F LYS* 3.2 23.6 + - - +
4161F LEU 3.0 25.6 - - - +
4162F ALA* 4.1 4.0 - - - -
4164F SER* 3.9 24.9 + - - -
4165F ILE* 3.9 23.6 + - - +
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Residues in contact with MET4059 (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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4055F LYS 3.2 20.4 + - - +
4056F PHE* 4.5 2.9 - - - +
4058F ASP* 1.3 78.3 - - - +
4060F PHE* 1.3 70.9 + - + +
4062F LYS* 3.4 6.0 + - - +
4063F LEU* 3.3 26.1 + - + +
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Residues in contact with PHE4060 (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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3999F ALA* 5.1 9.4 - - + -
4056F PHE* 3.2 57.9 + + - +
4057F PHE* 3.3 10.7 + + + +
4059F MET* 1.3 80.2 - - + +
4061F LEU* 1.3 64.8 + - - +
4063F LEU* 3.3 37.7 + - + +
4064F LYS* 3.9 4.7 + - - +
4127F PHE* 3.5 41.9 - + + -
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Residues in contact with LEU4061 (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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4057F PHE 2.7 22.5 + - - +
4058F ASP* 4.0 6.3 - - - +
4060F PHE* 1.3 75.2 - - - +
4062F LYS* 1.3 59.4 + - - +
4064F LYS* 3.5 19.3 + - + +
4065F ASP* 4.4 2.1 + - - +
4164F SER* 3.3 37.0 - - - +
4165F ILE* 4.0 9.0 - - + -
4168F TYR* 3.6 50.7 - - + -
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Residues in contact with LYS4062 (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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4058F ASP 3.2 18.4 + - - +
4059F MET* 3.8 6.3 - - - +
4060F PHE 3.2 0.4 - - - -
4061F LEU* 1.3 73.5 - - - +
4063F LEU* 1.3 60.3 + - + +
4064F LYS 3.1 2.0 - - - -
4065F ASP* 2.8 25.9 + - - +
4066F ILE* 3.1 26.9 + - + +
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Residues in contact with LEU4063 (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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4059F MET* 3.3 12.3 - - + +
4060F PHE* 3.3 38.7 + - + +
4062F LYS* 1.3 77.0 - - + +
4064F LYS* 1.3 61.2 + - - +
4065F ASP 3.2 0.6 + - - -
4066F ILE* 3.9 17.2 - - + +
4067F VAL* 3.5 24.6 + - - +
4124F ALA* 4.8 18.9 - - + +
4125F ASN* 5.0 3.9 + - - +
4127F PHE* 5.4 3.6 - - + -
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Residues in contact with LYS4064 (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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4060F PHE 3.9 4.4 + - - +
4061F LEU* 3.5 18.7 + - + +
4062F LYS 3.1 0.6 - - - -
4063F LEU* 1.3 77.3 - - - +
4065F ASP* 1.3 56.6 + - - +
4067F VAL* 3.6 16.6 - - + +
4068F GLY* 4.3 2.8 + - - -
4125F ASN* 3.4 35.1 - - - +
4128F GLN* 6.1 4.3 - - + +
4168F TYR* 4.9 18.6 + - + +
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Residues in contact with ASP4065 (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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4061F LEU 4.4 1.3 + - - +
4062F LYS* 2.8 12.0 + - - +
4064F LYS* 1.3 79.1 - - + +
4066F ILE* 1.3 64.0 + - + +
4067F VAL 3.3 1.6 - - - -
4068F GLY* 3.3 2.6 + - - +
4069F SER* 3.0 31.5 + - - -
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Residues in contact with ILE4066 (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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4062F LYS* 3.1 30.0 + - + +
4063F LEU* 3.6 19.0 + - + +
4065F ASP* 1.3 81.0 - - + +
4067F VAL* 1.3 62.0 + - - +
4069F SER* 2.8 21.6 + - - +
4071F ALA* 5.3 6.1 - - + -
4072F PHE* 3.3 26.0 - - + +
4090F LYS* 5.9 4.0 - - + -
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Residues in contact with VAL4067 (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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4063F LEU 3.5 17.5 + - - +
4064F LYS* 3.6 15.0 - - + +
4066F ILE* 1.3 78.9 - - - +
4068F GLY* 1.3 61.2 + - - +
4069F SER 3.5 3.0 - - - +
4072F PHE* 4.5 10.0 - - + +
4073F GLN* 5.5 2.3 + - - +
4124F ALA* 4.2 22.4 - - + -
4125F ASN* 4.5 13.7 - - - +
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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
------------------------------------------------------------
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