Contacts of the helix formed by residues 4046 - 4067 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3985B VAL* 4.3 16.6 - - - -
3988B LEU* 5.5 6.3 - - - -
4042B MET 2.5 24.8 + - - -
4043B LEU* 3.3 12.3 - - - +
4044B VAL 3.3 0.2 - - - -
4045B GLU* 1.3 76.2 - - - +
4047B SER* 1.3 55.9 + - - +
4048B SER 3.3 2.2 - - - -
4049B ASN* 3.0 17.4 + - - +
4050B VAL* 2.7 50.6 + - - +
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Residues in contact with SER4047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4043B LEU 2.6 23.2 + - - -
4044B VAL* 2.7 21.0 + - - +
4045B GLU 3.3 1.8 - - - -
4046B SER* 1.3 77.2 - - - +
4048B SER* 1.3 61.4 + - - +
4050B VAL* 3.4 20.2 - - - +
4051B GLU* 3.5 12.8 + - - +
4154B ARG* 6.1 0.2 - - - +
4161B LEU* 6.0 0.5 - - - +
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Residues in contact with SER4048 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4045B GLU 4.6 2.7 + - - -
4046B SER 3.3 0.2 - - - -
4047B SER* 1.3 78.6 - - - +
4049B ASN* 1.3 66.2 + - - +
4051B GLU* 4.1 7.7 + - - +
4052B MET* 3.4 23.9 + - - +
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Residues in contact with ASN4049 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3985B VAL* 4.8 8.5 - - - +
3988B LEU* 4.7 21.5 - - + +
3989B HIS* 3.2 38.4 + - - +
3992B ALA* 4.5 5.5 - - + +
4045B GLU 3.4 10.1 + - - -
4046B SER* 3.0 31.4 + - - +
4048B SER* 1.3 82.6 - - - +
4050B VAL* 1.3 64.3 + - - +
4051B GLU 3.2 1.8 - - - -
4052B MET* 3.3 19.3 + - - +
4053B ILE* 3.7 9.4 + - - +
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Residues in contact with VAL4050 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3988B LEU* 4.9 13.9 - - + -
4043B LEU* 5.0 14.4 - - + +
4046B SER* 2.7 41.8 + - - +
4047B SER* 3.4 15.7 - - - +
4049B ASN* 1.3 72.0 - - - +
4051B GLU* 1.3 60.1 + - - +
4052B MET 3.2 0.2 - - - -
4053B ILE* 3.4 11.9 - - + +
4054B LEU* 3.0 32.7 + - + +
4158B PHE* 5.5 11.9 - - + -
4161B LEU* 6.0 5.4 - - + -
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Residues in contact with GLU4051 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4047B SER 3.5 14.5 + - - +
4048B SER* 4.2 7.0 - - - +
4049B ASN 3.2 0.8 - - - -
4050B VAL* 1.3 81.9 - - - +
4052B MET* 1.3 65.4 + - + +
4053B ILE 3.4 0.2 - - - -
4054B LEU* 4.1 5.2 - - - -
4055B LYS* 3.5 24.4 + - - +
4161B LEU* 4.9 18.4 - - + -
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Residues in contact with MET4052 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3992B ALA* 3.8 25.1 - - + +
3993B HIS* 5.7 9.4 - - + +
3996B MET* 4.6 31.2 - - + +
4048B SER 3.4 20.2 - - - +
4049B ASN* 3.3 9.4 + - - +
4050B VAL 3.2 0.8 - - - -
4051B GLU* 1.3 84.8 - - - +
4053B ILE* 1.3 57.3 + - - +
4055B LYS* 5.0 0.6 - - - +
4056B PHE* 3.2 21.3 + - - +
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Residues in contact with ILE4053 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3988B LEU* 5.6 11.9 - - + -
3991B PHE 5.7 3.8 - - - +
3992B ALA* 5.2 10.8 - - + +
3995B MET* 5.6 5.6 - - + -
4012B LEU* 6.5 0.2 - - + -
4049B ASN 3.8 10.5 - - - +
4050B VAL* 3.4 18.8 - - + +
4052B MET* 1.3 76.5 - - - +
4054B LEU* 1.3 69.0 + - - +
4055B LYS 3.4 0.4 - - - -
4056B PHE* 3.2 26.9 + - + +
4057B PHE* 3.1 43.9 + - + +
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Residues in contact with LEU4054 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4050B VAL* 3.0 20.4 + - + +
4051B GLU* 4.5 4.3 - - - +
4053B ILE* 1.3 79.1 - - + +
4055B LYS* 1.3 58.3 + - - +
4057B PHE* 3.3 3.4 + - - +
4058B ASP* 2.8 37.7 + - - +
4161B LEU* 4.6 23.1 - - + +
4162B ALA* 5.1 9.2 - - + -
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Residues in contact with LYS4055 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4051B GLU 3.5 18.0 + - - +
4052B MET* 5.0 1.3 - - - +
4053B ILE 3.4 0.2 - - - -
4054B LEU* 1.3 76.0 - - - +
4056B PHE* 1.3 63.0 + - - +
4058B ASP* 3.9 7.9 - - - -
4059B MET* 3.2 26.0 + - - +
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Residues in contact with PHE4056 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3995B MET* 3.7 42.4 - - + -
3996B MET* 3.9 31.6 - - + -
3999B ALA* 4.6 6.5 - - + -
4052B MET 3.2 20.5 + - - +
4053B ILE* 3.2 20.3 + - + +
4054B LEU 3.2 0.8 - - - -
4055B LYS* 1.3 78.4 - - - +
4057B PHE* 1.3 83.2 + + - +
4059B MET* 4.5 1.5 - - - +
4060B PHE* 3.2 58.6 + + - -
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Residues in contact with PHE4057 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4012B LEU* 4.3 16.2 - - + -
4053B ILE* 3.1 29.9 + - + +
4054B LEU* 4.0 3.4 - - - +
4056B PHE* 1.3 107.1 - + - +
4058B ASP* 1.3 58.9 + - - +
4059B MET 3.2 1.8 - - - -
4060B PHE* 3.3 7.8 + + + +
4061B LEU* 2.7 37.9 + - - +
4131B ALA* 4.9 15.7 - - + -
4134B ILE* 3.6 46.7 - - + -
4135B GLY* 5.0 9.9 - - - -
4138B VAL* 5.0 9.2 - - + -
4165B ILE* 6.0 3.4 - - + -
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Residues in contact with ASP4058 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4054B LEU* 2.8 22.2 + - - +
4055B LYS* 4.3 6.4 - - - -
4057B PHE* 1.3 80.5 - - - +
4059B MET* 1.3 61.0 + - - +
4061B LEU* 4.0 6.2 - - - +
4062B LYS* 3.2 23.6 + - - +
4161B LEU 3.0 26.0 - - - +
4162B ALA* 4.1 3.4 - - - -
4164B SER* 3.9 24.8 - - - -
4165B ILE* 3.9 24.5 + - - +
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Residues in contact with MET4059 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4055B LYS 3.2 20.4 + - - +
4056B PHE* 4.5 3.4 - - - +
4058B ASP* 1.3 79.2 - - - +
4060B PHE* 1.3 69.0 + - + +
4062B LYS* 3.4 6.2 + - - +
4063B LEU* 3.3 26.4 + - + +
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Residues in contact with PHE4060 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3999B ALA* 5.1 9.9 - - + -
4056B PHE* 3.2 58.3 - + - +
4057B PHE* 3.3 10.9 + + + +
4059B MET* 1.3 80.3 - - + +
4061B LEU* 1.3 65.5 + - - +
4063B LEU* 3.3 37.3 + - + +
4064B LYS* 3.9 4.3 + - - +
4127B PHE* 3.5 41.9 - + + -
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Residues in contact with LEU4061 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4057B PHE* 2.7 23.2 + - + +
4058B ASP* 4.0 6.3 - - - +
4060B PHE* 1.3 74.4 - - - +
4062B LYS* 1.3 59.7 + - - +
4064B LYS* 3.5 19.1 + - + +
4065B ASP* 4.4 1.7 + - - +
4164B SER* 3.3 36.3 - - - +
4165B ILE* 4.0 9.4 - - + -
4168B TYR* 3.6 49.6 - - + -
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Residues in contact with LYS4062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4058B ASP 3.2 17.9 + - - +
4059B MET* 3.8 6.5 - - - +
4060B PHE 3.2 0.2 - - - -
4061B LEU* 1.3 73.2 - - - +
4063B LEU* 1.3 59.2 + - + +
4064B LYS 3.1 3.1 - - - -
4065B ASP* 2.8 25.3 + - - +
4066B ILE* 3.1 26.4 + - + +
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Residues in contact with LEU4063 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4059B MET 3.3 12.6 - - - +
4060B PHE* 3.3 38.9 + - + +
4062B LYS* 1.3 77.0 - - + +
4064B LYS* 1.3 59.9 + - - +
4065B ASP 3.2 0.7 + - - -
4066B ILE* 3.9 17.8 - - + +
4067B VAL* 3.5 24.4 + - - +
4124B ALA* 4.8 19.3 - - + +
4125B ASN* 5.0 3.3 + - - +
4127B PHE* 5.4 4.5 - - + -
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Residues in contact with LYS4064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4060B PHE 3.9 4.0 + - - +
4061B LEU* 3.5 17.6 + - + +
4062B LYS 3.1 1.0 - - - -
4063B LEU* 1.3 78.4 - - - +
4065B ASP* 1.3 58.2 + - - +
4067B VAL* 3.6 15.9 - - + +
4068B GLY* 4.3 3.1 + - - -
4125B ASN* 3.4 35.6 - - - +
4128B GLN* 6.1 4.5 - - + +
4168B TYR* 4.9 18.4 + - + +
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Residues in contact with ASP4065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4061B LEU 4.4 0.9 + - - +
4062B LYS* 2.8 12.2 + - - +
4064B LYS* 1.3 78.8 - - - +
4066B ILE* 1.3 64.0 + - + +
4067B VAL 3.3 1.6 - - - -
4068B GLY* 3.3 2.7 + - - +
4069B SER* 3.0 31.2 + - - -
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Residues in contact with ILE4066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4062B LYS* 3.1 30.7 + - + +
4063B LEU* 3.6 18.1 + - + +
4065B ASP* 1.3 82.8 - - + +
4067B VAL* 1.3 62.2 + - - +
4069B SER* 2.8 21.4 + - - +
4071B ALA* 5.3 5.4 - - + -
4072B PHE* 3.3 26.0 + - + +
4090B LYS* 5.9 4.3 - - + -
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Residues in contact with VAL4067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4063B LEU 3.5 17.7 + - - +
4064B LYS* 3.6 15.0 - - + +
4066B ILE* 1.3 79.1 - - - +
4068B GLY* 1.3 60.8 + - - +
4069B SER 3.5 2.8 + - - +
4072B PHE* 4.5 9.8 - - + +
4073B GLN* 5.5 2.1 + - - +
4124B ALA* 4.2 22.2 - - + -
4125B ASN* 4.5 14.1 - - - +
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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
------------------------------------------------------------
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