Contacts of the helix formed by residues 4046 - 4067 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3985D VAL* 4.3 16.6 - - - -
3988D LEU* 5.5 6.1 - - - -
4042D MET 2.5 24.7 + - - -
4043D LEU* 3.3 12.8 - - - +
4044D VAL 3.3 0.4 - - - -
4045D GLU* 1.3 76.5 - - - +
4047D SER* 1.3 54.8 + - - +
4048D SER 3.3 2.7 - - - -
4049D ASN* 3.0 18.2 + - - +
4050D VAL* 2.7 50.2 + - - +
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Residues in contact with SER4047 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4043D LEU 2.6 22.4 + - - -
4044D VAL* 2.7 19.7 + - - +
4045D GLU 3.3 2.4 - - - -
4046D SER* 1.3 77.4 - - - +
4048D SER* 1.3 62.1 + - - +
4050D VAL* 3.4 20.6 - - - +
4051D GLU* 3.5 12.1 + - - +
4154D ARG* 6.1 0.3 - - - +
4161D LEU* 6.0 0.7 - - - +
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Residues in contact with SER4048 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4045D GLU 4.6 2.1 + - - -
4046D SER 3.3 0.4 - - - -
4047D SER* 1.3 78.5 - - - +
4049D ASN* 1.3 64.5 + - - +
4051D GLU* 4.1 6.9 + - - +
4052D MET* 3.4 23.4 - - - +
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Residues in contact with ASN4049 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3985D VAL* 4.8 9.0 - - - +
3988D LEU* 4.7 21.5 - - + +
3989D HIS* 3.2 37.3 + - - +
3992D ALA* 4.5 6.1 - - + +
4045D GLU 3.4 9.5 + - - -
4046D SER* 3.0 31.3 + - - +
4048D SER* 1.3 83.3 - - - +
4050D VAL* 1.3 64.2 + - + +
4051D GLU 3.2 2.2 - - - -
4052D MET* 3.3 19.2 + - - +
4053D ILE* 3.7 9.2 + - - +
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Residues in contact with VAL4050 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3988D LEU* 4.9 13.5 - - + -
4043D LEU* 5.0 14.8 - - + +
4046D SER* 2.7 41.7 + - - +
4047D SER* 3.4 16.2 - - - +
4049D ASN* 1.3 73.1 - - - +
4051D GLU* 1.3 60.0 + - + +
4053D ILE* 3.4 11.2 - - + +
4054D LEU* 3.0 33.8 + - + +
4158D PHE* 5.5 12.3 - - + -
4161D LEU* 6.0 4.3 - - + -
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Residues in contact with GLU4051 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4047D SER 3.5 13.8 + - - +
4048D SER* 4.2 7.2 - - - +
4049D ASN 3.2 1.0 - - - -
4050D VAL* 1.3 81.8 - - + +
4052D MET* 1.3 66.6 + - + +
4054D LEU* 4.1 5.2 - - - -
4055D LYS* 3.5 24.3 + - - +
4161D LEU* 4.9 17.5 - - + -
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Residues in contact with MET4052 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3992D ALA* 3.8 25.3 - - + +
3993D HIS* 5.7 9.6 - - + +
3996D MET* 4.6 31.3 - - + +
4048D SER 3.4 20.6 - - - +
4049D ASN* 3.3 10.1 + - - +
4050D VAL 3.2 0.8 - - - -
4051D GLU* 1.3 84.3 - - - +
4053D ILE* 1.3 56.4 + - - +
4055D LYS* 5.0 1.2 - - - +
4056D PHE* 3.2 20.9 + - - +
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Residues in contact with ILE4053 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3988D LEU* 5.6 12.1 - - + -
3991D PHE 5.7 3.6 - - - +
3992D ALA* 5.2 10.1 - - + -
3995D MET* 5.6 6.1 - - + -
4012D LEU* 6.5 0.2 - - + -
4049D ASN 3.7 10.3 + - - +
4050D VAL* 3.4 18.8 - - + +
4052D MET* 1.3 75.6 - - - +
4054D LEU* 1.3 69.8 + - + +
4055D LYS 3.4 0.2 - - - -
4056D PHE* 3.4 26.5 - - + +
4057D PHE* 3.1 44.0 + - + +
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Residues in contact with LEU4054 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4050D VAL* 3.0 19.6 + - + +
4051D GLU* 4.5 4.5 - - - +
4053D ILE* 1.3 80.1 - - + +
4055D LYS* 1.3 56.7 + - - +
4057D PHE* 3.3 3.7 + - - +
4058D ASP* 2.8 37.9 + - - +
4161D LEU* 4.6 22.7 - - + +
4162D ALA* 5.1 9.2 - - + -
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Residues in contact with LYS4055 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4051D GLU 3.5 17.7 + - - +
4052D MET 5.0 1.1 - - - +
4054D LEU* 1.3 75.8 - - - +
4056D PHE* 1.3 64.2 + - - +
4057D PHE 3.3 0.2 - - - -
4058D ASP* 3.9 8.3 - - - -
4059D MET* 3.2 26.7 + - - +
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Residues in contact with PHE4056 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3995D MET* 3.7 42.2 - - + -
3996D MET* 3.9 32.8 - - + -
3999D ALA* 4.6 6.5 - - + -
4052D MET 3.2 19.5 + - - +
4053D ILE* 3.2 20.9 + - + +
4054D LEU 3.2 0.6 - - - -
4055D LYS* 1.3 80.4 - - - +
4057D PHE* 1.3 84.2 + + - +
4059D MET* 4.3 1.4 - - - +
4060D PHE* 3.2 58.5 + + - -
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Residues in contact with PHE4057 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4012D LEU* 4.3 16.4 - - + -
4053D ILE* 3.1 30.7 + - + +
4054D LEU* 4.0 3.6 - - - +
4056D PHE* 1.3 107.5 - + - +
4058D ASP* 1.3 59.5 + - - +
4059D MET 3.2 1.8 - - - -
4060D PHE* 3.3 8.0 + + + +
4061D LEU* 2.7 37.7 + - + +
4131D ALA* 4.9 14.6 - - + -
4134D ILE* 3.6 46.4 - - + -
4135D GLY* 5.0 9.6 - - - -
4138D VAL* 5.0 8.5 - - + -
4165D ILE* 6.0 4.0 - - + -
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Residues in contact with ASP4058 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4054D LEU* 2.8 23.3 + - - +
4055D LYS* 4.3 6.2 - - - -
4057D PHE* 1.3 79.3 - - - +
4059D MET* 1.3 60.4 + - - +
4061D LEU* 4.0 5.5 - - - +
4062D LYS* 3.2 23.9 + - - +
4161D LEU 3.0 26.2 - - - +
4162D ALA* 4.1 3.6 - - - +
4164D SER* 3.9 25.1 - - - -
4165D ILE* 3.9 24.9 + - - +
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Residues in contact with MET4059 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4055D LYS 3.2 19.1 + - - +
4056D PHE* 4.5 2.9 - - - +
4058D ASP* 1.3 78.9 - - - +
4060D PHE* 1.3 70.4 + - + +
4062D LYS* 3.4 6.4 + - - +
4063D LEU* 3.3 25.6 + - - +
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Residues in contact with PHE4060 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3999D ALA* 5.1 9.6 - - + -
4056D PHE* 3.2 59.0 + + - +
4057D PHE* 3.3 10.7 + + + +
4059D MET* 1.3 80.8 - - + +
4061D LEU* 1.3 66.5 + - - +
4063D LEU* 3.3 37.2 + - + +
4064D LYS* 3.9 4.5 + - - +
4127D PHE* 3.5 41.8 - + + -
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Residues in contact with LEU4061 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4057D PHE 2.7 23.6 + - - +
4058D ASP* 4.0 6.3 - - - +
4059D MET 3.3 0.2 - - - -
4060D PHE* 1.3 74.6 - - - +
4062D LYS* 1.3 60.9 + - - +
4064D LYS* 3.5 18.4 + - + +
4065D ASP* 4.4 1.6 + - - +
4164D SER* 3.3 37.0 - - - +
4165D ILE* 4.0 9.0 - - + -
4168D TYR* 3.6 50.3 - - + -
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Residues in contact with LYS4062 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4058D ASP 3.2 17.7 + - - +
4059D MET* 3.8 6.3 - - - +
4060D PHE 3.2 0.4 - - - -
4061D LEU* 1.3 72.5 - - - +
4063D LEU* 1.3 60.6 + - + +
4064D LYS 3.1 2.5 - - - -
4065D ASP* 2.8 25.1 + - - +
4066D ILE* 3.1 26.2 + - + +
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Residues in contact with LEU4063 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4059D MET* 3.3 13.5 - - + +
4060D PHE* 3.3 38.7 + - + +
4062D LYS* 1.3 77.5 - - + +
4064D LYS* 1.3 62.2 + - - +
4065D ASP 3.4 0.3 + - - -
4066D ILE* 3.9 17.9 - - + +
4067D VAL* 3.5 23.9 + - - +
4124D ALA* 4.8 20.1 - - + +
4125D ASN* 5.0 3.2 + - - +
4127D PHE* 5.4 4.0 - - + -
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Residues in contact with LYS4064 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4060D PHE 3.9 4.0 + - - +
4061D LEU* 3.5 18.3 + - + +
4062D LYS 3.1 1.2 - - - -
4063D LEU* 1.3 78.3 - - - +
4065D ASP* 1.3 57.1 + - - +
4067D VAL* 3.6 16.0 - - + +
4068D GLY* 4.3 2.6 + - - -
4125D ASN* 3.4 36.0 - - - +
4128D GLN* 6.1 4.7 - - + +
4168D TYR* 4.9 17.6 + - + -
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Residues in contact with ASP4065 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4061D LEU 5.3 1.1 - - - +
4062D LYS* 2.8 12.0 + - - +
4064D LYS* 1.3 78.6 - - - +
4066D ILE* 1.3 63.7 + - + +
4067D VAL 3.3 2.2 - - - -
4068D GLY* 3.3 2.7 + - - +
4069D SER* 3.0 31.3 + - - -
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Residues in contact with ILE4066 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4062D LYS* 3.1 30.7 + - + +
4063D LEU* 3.6 19.9 + - + +
4065D ASP* 1.3 81.0 - - + +
4067D VAL* 1.3 61.6 + - - +
4069D SER* 2.8 21.1 + - - +
4071D ALA* 5.3 5.6 - - + -
4072D PHE* 3.3 26.2 - - + +
4090D LYS* 5.9 3.8 - - + -
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Residues in contact with VAL4067 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4063D LEU 3.5 18.4 + - - +
4064D LYS* 3.6 14.8 - - + +
4066D ILE* 1.3 78.5 - - - +
4068D GLY* 1.3 62.2 + - - +
4069D SER 4.4 3.4 - - - +
4072D PHE* 4.5 9.8 - - + +
4073D GLN* 5.5 1.9 + - - +
4124D ALA* 4.2 21.8 - - + -
4125D ASN* 4.5 13.9 - - - +
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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
------------------------------------------------------------
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